From 3b9963d0060546b02ebc116ae4e93c091c297666 Mon Sep 17 00:00:00 2001 From: Mira Kuntz Date: Tue, 20 Feb 2024 17:19:15 +0100 Subject: [PATCH 1/8] add encode api --- lib/galaxy/managers/configuration.py | 9 +++++++++ lib/galaxy/webapps/galaxy/api/configuration.py | 15 +++++++++++++++ 2 files changed, 24 insertions(+) diff --git a/lib/galaxy/managers/configuration.py b/lib/galaxy/managers/configuration.py index d15b2d941d75..513df907bcf0 100644 --- a/lib/galaxy/managers/configuration.py +++ b/lib/galaxy/managers/configuration.py @@ -18,6 +18,7 @@ from galaxy.managers.markdown_util import weasyprint_available from galaxy.schema import SerializationParams from galaxy.structured_app import StructuredApp +from galaxy.util import unicodify log = logging.getLogger(__name__) @@ -56,6 +57,14 @@ def decode_id( decoded_id = self._app.security.decode_id(encoded_id) return {"decoded_id": decoded_id} + def encode_id( + self, + decoded_id: int, + ) -> Dict[str, str]: + # Handle the special case for library folders + encoded_id = unicodify(self._app.security.encode_id(decoded_id)) + return {"encoded_id": encoded_id} + def tool_lineages(self) -> List[Dict[str, Dict]]: rval = [] for id, tool in self._app.toolbox.tools(): diff --git a/lib/galaxy/webapps/galaxy/api/configuration.py b/lib/galaxy/webapps/galaxy/api/configuration.py index fff240830645..8c6197b74f79 100644 --- a/lib/galaxy/webapps/galaxy/api/configuration.py +++ b/lib/galaxy/webapps/galaxy/api/configuration.py @@ -39,6 +39,11 @@ description="Encoded id to be decoded", ) +DecodedIdPathParam = Path( + ..., + title="Decoded id", + description="Decoded id to be Encoded", +) @router.cbv class FastAPIConfiguration: @@ -103,6 +108,16 @@ def decode_id(self, encoded_id: str = EncodedIdPathParam) -> Dict[str, int]: """Decode a given id.""" return self.configuration_manager.decode_id(encoded_id) + @router.get( + "/api/configuration/encode/{decoded_id}", + require_admin=True, + summary="Encode a given id", + response_description="Encoded id", + ) + def encode_id(self, decoded_id: str = DecodedIdPathParam) -> Dict[str, str]: + """Decode a given id.""" + return self.configuration_manager.encode_id(decoded_id) + @router.get( "/api/configuration/tool_lineages", require_admin=True, From 17651ee875ff9ca30c16ff386b2be52a22063ff4 Mon Sep 17 00:00:00 2001 From: Mira <86979912+mira-miracoli@users.noreply.github.com> Date: Tue, 20 Feb 2024 17:25:12 +0100 Subject: [PATCH 2/8] typo --- lib/galaxy/webapps/galaxy/api/configuration.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/webapps/galaxy/api/configuration.py b/lib/galaxy/webapps/galaxy/api/configuration.py index 8c6197b74f79..2cc338c7dbc3 100644 --- a/lib/galaxy/webapps/galaxy/api/configuration.py +++ b/lib/galaxy/webapps/galaxy/api/configuration.py @@ -42,7 +42,7 @@ DecodedIdPathParam = Path( ..., title="Decoded id", - description="Decoded id to be Encoded", + description="Decoded id to be encoded", ) @router.cbv From 6b2a4836942c48d5a41d9840f5fd7d8ec19724e7 Mon Sep 17 00:00:00 2001 From: Mira Kuntz Date: Wed, 21 Feb 2024 09:19:57 +0100 Subject: [PATCH 3/8] nl --- lib/galaxy/webapps/galaxy/api/configuration.py | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/galaxy/webapps/galaxy/api/configuration.py b/lib/galaxy/webapps/galaxy/api/configuration.py index 2cc338c7dbc3..47e6f43c1fdc 100644 --- a/lib/galaxy/webapps/galaxy/api/configuration.py +++ b/lib/galaxy/webapps/galaxy/api/configuration.py @@ -45,6 +45,7 @@ description="Decoded id to be encoded", ) + @router.cbv class FastAPIConfiguration: configuration_manager: ConfigurationManager = depends(ConfigurationManager) From fa661b72c748fe3a6a5c9cf76c1d97aba8cf959c Mon Sep 17 00:00:00 2001 From: Mira Kuntz Date: Wed, 21 Feb 2024 09:55:09 +0100 Subject: [PATCH 4/8] build-api-schema results --- _schema.yaml | 37009 ++++++++++++++++++++++++++++++++++++++++++++ _shed_schema.yaml | 3010 ++++ 2 files changed, 40019 insertions(+) create mode 100644 _schema.yaml create mode 100644 _shed_schema.yaml diff --git a/_schema.yaml b/_schema.yaml new file mode 100644 index 000000000000..f3f8562ef745 --- /dev/null +++ b/_schema.yaml @@ -0,0 +1,37009 @@ +components: + schemas: + APIKeyModel: + properties: + create_time: + description: The time and date this API key was created. + format: date-time + title: Create Time + type: string + key: + description: API key to interact with the Galaxy API + title: Key + type: string + required: + - key + - create_time + title: APIKeyModel + type: object + APIKeyResponse: + properties: + api_key: + title: Api Key + type: string + required: + - api_key + title: APIKeyResponse + type: object + AccessMethod: + properties: + access_id: + anyOf: + - type: string + - type: 'null' + description: An arbitrary string to be passed to the `/access` method to + get an `AccessURL`. This string must be unique within the scope of a single + object. Note that at least one of `access_url` and `access_id` must be + provided. + title: Access Id + access_url: + anyOf: + - $ref: '#/components/schemas/AccessURL' + - type: 'null' + authorizations: + anyOf: + - $ref: '#/components/schemas/Authorizations' + - type: 'null' + region: + anyOf: + - type: string + - type: 'null' + description: Name of the region in the cloud service provider that the object + belongs to. + examples: + - us-east-1 + title: Region + type: + allOf: + - $ref: '#/components/schemas/AccessMethodType' + description: Type of the access method. + required: + - type + title: AccessMethod + type: object + AccessMethodType: + enum: + - s3 + - gs + - ftp + - gsiftp + - globus + - htsget + - https + - file + title: AccessMethodType + type: string + AccessURL: + properties: + headers: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: An optional list of headers to include in the HTTP request + to `url`. These headers can be used to provide auth tokens required to + fetch the object bytes. + examples: + - 'Authorization: Basic Z2E0Z2g6ZHJz' + title: Headers + url: + description: A fully resolvable URL that can be used to fetch the actual + object bytes. + title: Url + type: string + required: + - url + title: AccessURL + type: object + ActionLink: + description: An action link to be displayed in the notification as a button. + properties: + action_name: + description: The name of the action, will be the button title. + title: Action name + type: string + link: + description: The link to be opened when the button is clicked. + title: Link + type: string + required: + - action_name + - link + title: ActionLink + type: object + AnonUserModel: + properties: + nice_total_disk_usage: + description: Size of all non-purged, unique datasets of the user in a nice + format. + title: Nice total disc usage + type: string + quota_percent: + description: Percentage of the storage quota applicable to the user. + title: Quota percent + total_disk_usage: + description: Size of all non-purged, unique datasets of the user in bytes. + title: Total disk usage + type: number + required: + - total_disk_usage + - nice_total_disk_usage + title: AnonUserModel + type: object + ArchiveHistoryRequestPayload: + properties: + archive_export_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: The encoded ID of the export record to associate with this + history archival.This is used to be able to recover the history from the + export record. + title: Export Record ID + purge_history: + default: false + description: Whether to purge the history after archiving it. It requires + an `archive_export_id` to be set. + title: Purge History + type: boolean + title: ArchiveHistoryRequestPayload + type: object + ArchivedHistoryDetailed: + additionalProperties: true + properties: + annotation: + anyOf: + - type: string + - type: 'null' + description: An annotation to provide details or to help understand the + purpose and usage of this item. + title: Annotation + archived: + description: Whether this item has been archived and is no longer active. + title: Archived + type: boolean + contents_url: + description: The relative URL to access the contents of this History. + title: Contents URL + type: string + count: + description: The number of items in the history. + title: Count + type: integer + create_time: + description: The time and date this item was created. + format: date-time + title: Create Time + type: string + deleted: + description: Whether this item is marked as deleted. + title: Deleted + type: boolean + export_record_data: + anyOf: + - $ref: '#/components/schemas/ExportRecordData' + - type: 'null' + description: The export record data associated with this archived history. + Used to recover the history. + title: Export Record Data + genome_build: + anyOf: + - type: string + - type: 'null' + default: '?' + description: TODO + title: Genome Build + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: History ID + type: string + importable: + description: Whether this History can be imported by other users with a + shared link. + title: Importable + type: boolean + model_class: + const: History + description: The name of the database model class. + title: Model class + type: string + name: + description: The name of the history. + title: Name + type: string + preferred_object_store_id: + anyOf: + - type: string + - type: 'null' + description: The ID of the object store that should be used to store new + datasets in this history. + title: Preferred Object Store ID + published: + description: Whether this resource is currently publicly available to all + users. + title: Published + type: boolean + purged: + description: Whether this item has been permanently removed. + title: Purged + type: boolean + size: + description: The total size of the contents of this history in bytes. + title: Size + type: integer + slug: + anyOf: + - type: string + - type: 'null' + description: Part of the URL to uniquely identify this History by link in + a readable way. + title: Slug + state: + allOf: + - $ref: '#/components/schemas/DatasetState' + description: The current state of the History based on the states of the + datasets it contains. + title: State + state_details: + additionalProperties: + type: integer + description: A dictionary keyed to possible dataset states and valued with + the number of datasets in this history that have those states. + title: State Counts + type: object + state_ids: + additionalProperties: + items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + type: array + description: A dictionary keyed to possible dataset states and valued with + lists containing the ids of each HDA in that state. + title: State IDs + type: object + tags: + $ref: '#/components/schemas/TagCollection' + update_time: + description: The last time and date this item was updated. + format: date-time + title: Update Time + type: string + url: + deprecated: true + description: The relative URL to access this item. + title: URL + type: string + user_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: The encoded ID of the user that owns this History. + title: User ID + username: + anyOf: + - type: string + - type: 'null' + description: Owner of the history + title: Username + username_and_slug: + anyOf: + - type: string + - type: 'null' + description: The relative URL in the form of /u/{username}/h/{slug} + title: Username and slug + required: + - model_class + - id + - name + - deleted + - purged + - archived + - url + - published + - count + - annotation + - tags + - update_time + - contents_url + - size + - create_time + - importable + - state + - state_ids + - state_details + title: ArchivedHistoryDetailed + type: object + ArchivedHistorySummary: + additionalProperties: true + properties: + annotation: + anyOf: + - type: string + - type: 'null' + description: An annotation to provide details or to help understand the + purpose and usage of this item. + title: Annotation + archived: + description: Whether this item has been archived and is no longer active. + title: Archived + type: boolean + count: + description: The number of items in the history. + title: Count + type: integer + deleted: + description: Whether this item is marked as deleted. + title: Deleted + type: boolean + export_record_data: + anyOf: + - $ref: '#/components/schemas/ExportRecordData' + - type: 'null' + description: The export record data associated with this archived history. + Used to recover the history. + title: Export Record Data + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: History ID + type: string + model_class: + const: History + description: The name of the database model class. + title: Model class + type: string + name: + description: The name of the history. + title: Name + type: string + preferred_object_store_id: + anyOf: + - type: string + - type: 'null' + description: The ID of the object store that should be used to store new + datasets in this history. + title: Preferred Object Store ID + published: + description: Whether this resource is currently publicly available to all + users. + title: Published + type: boolean + purged: + description: Whether this item has been permanently removed. + title: Purged + type: boolean + tags: + $ref: '#/components/schemas/TagCollection' + update_time: + description: The last time and date this item was updated. + format: date-time + title: Update Time + type: string + url: + deprecated: true + description: The relative URL to access this item. + title: URL + type: string + required: + - model_class + - id + - name + - deleted + - purged + - archived + - url + - published + - count + - annotation + - tags + - update_time + title: ArchivedHistorySummary + type: object + AsyncFile: + properties: + storage_request_id: + format: uuid + title: Storage Request Id + type: string + task: + $ref: '#/components/schemas/AsyncTaskResultSummary' + required: + - storage_request_id + - task + title: AsyncFile + type: object + AsyncTaskResultSummary: + properties: + id: + description: Celery AsyncResult ID for this task + title: ID + type: string + ignored: + description: Indicated whether the Celery AsyncResult will be available + for retrieval + title: Ignored + type: boolean + name: + anyOf: + - type: string + - type: 'null' + title: Name of task being done derived from Celery AsyncResult + queue: + anyOf: + - type: string + - type: 'null' + title: Queue of task being done derived from Celery AsyncResult + required: + - id + - ignored + title: AsyncTaskResultSummary + type: object + Authorizations: + properties: + bearer_auth_issuers: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: If authorizations contain `BearerAuth` this is an optional + list of issuers that may authorize access to this object. The caller must + provide a token from one of these issuers. If this is empty or missing + it assumed the caller knows which token to send via other means. It is + strongly recommended that the caller validate that it is appropriate to + send the requested token to the DRS server to mitigate attacks by malicious + DRS servers requesting credentials they should not have. + title: Bearer Auth Issuers + passport_auth_issuers: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: If authorizations contain `PassportAuth` this is a required + list of visa issuers (as found in a visa's `iss` claim) that may authorize + access to this object. The caller must only provide passports that contain + visas from this list. It is strongly recommended that the caller validate + that it is appropriate to send the requested passport/visa to the DRS + server to mitigate attacks by malicious DRS servers requesting credentials + they should not have. + title: Passport Auth Issuers + supported_types: + anyOf: + - items: + $ref: '#/components/schemas/SupportedType' + type: array + - type: 'null' + description: An Optional list of support authorization types. More than + one can be supported and tried in sequence. Defaults to `None` if empty + or missing. + title: Supported Types + title: Authorizations + type: object + BadgeDict: + properties: + message: + anyOf: + - type: string + - type: 'null' + title: Message + source: + enum: + - admin + - galaxy + title: Source + type: string + type: + anyOf: + - enum: + - faster + - slower + - short_term + - backed_up + - not_backed_up + - more_secure + - less_secure + - more_stable + - less_stable + type: string + - enum: + - cloud + - quota + - no_quota + - restricted + type: string + title: Type + required: + - type + - message + - source + title: BadgeDict + type: object + BasicRoleModel: + properties: + id: + description: Encoded ID of the role + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + name: + description: Name of the role + title: Name + type: string + type: + description: Type or category of the role + title: Type + type: string + required: + - id + - name + - type + title: BasicRoleModel + type: object + Body_create_api_histories_post: + properties: + all_datasets: + default: true + title: All Datasets + archive_file: + title: Archive File + archive_source: + title: Archive Source + archive_type: + default: url + title: Archive Type + history_id: + title: History Id + name: + title: Name + title: Body_create_api_histories_post + type: object + Body_fetch_form_api_tools_fetch_post: + properties: + files: + anyOf: + - items: + format: binary + type: string + type: array + - type: 'null' + title: Files + history_id: + title: History Id + targets: + title: Targets + required: + - history_id + - targets + title: Body_fetch_form_api_tools_fetch_post + type: object + BroadcastNotificationContent: + properties: + action_links: + anyOf: + - items: + $ref: '#/components/schemas/ActionLink' + type: array + - type: 'null' + description: The optional action links (buttons) to be displayed in the + notification. + title: Action links + category: + const: broadcast + default: broadcast + title: Category + message: + description: The message of the notification (supports Markdown). + title: Message + type: string + subject: + description: The subject of the notification. + title: Subject + type: string + required: + - subject + - message + title: BroadcastNotificationContent + type: object + BroadcastNotificationCreateRequest: + description: A notification create request specific for broadcasting. + properties: + category: + const: broadcast + default: broadcast + title: Category + content: + allOf: + - $ref: '#/components/schemas/BroadcastNotificationContent' + description: The content of the broadcast notification. Broadcast notifications + are displayed prominently to all users and can contain action links to + redirect the user to a specific page. + title: Content + expiration_time: + anyOf: + - format: date-time + type: string + - type: 'null' + description: The time when the notification should expire. By default it + will expire after 6 months. Expired notifications will be permanently + deleted. + title: Expiration time + publication_time: + anyOf: + - format: date-time + type: string + - type: 'null' + description: The time when the notification should be published. Notifications + can be created and then scheduled to be published at a later time. + title: Publication time + source: + description: The source of the notification. Represents the agent that created + the notification. E.g. 'galaxy' or 'admin'. + title: Source + type: string + variant: + allOf: + - $ref: '#/components/schemas/NotificationVariant' + description: The variant of the notification. Represents the intent or relevance + of the notification. E.g. 'info' or 'urgent'. + title: Variant + required: + - source + - variant + - content + title: BroadcastNotificationCreateRequest + type: object + BroadcastNotificationListResponse: + description: A list of broadcast notifications. + items: + $ref: '#/components/schemas/BroadcastNotificationResponse' + title: BroadcastNotificationListResponse + type: array + BroadcastNotificationResponse: + description: A notification response specific for broadcasting. + properties: + category: + const: broadcast + default: broadcast + title: Category + content: + $ref: '#/components/schemas/BroadcastNotificationContent' + create_time: + description: The time when the notification was created. + format: date-time + title: Create time + type: string + expiration_time: + anyOf: + - format: date-time + type: string + - type: 'null' + description: The time when the notification will expire. If not set, the + notification will never expire. Expired notifications will be permanently + deleted. + title: Expiration time + id: + description: The encoded ID of the notification. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + publication_time: + description: The time when the notification was published. Notifications + can be created and then published at a later time. + format: date-time + title: Publication time + type: string + source: + description: The source of the notification. Represents the agent that created + the notification. E.g. 'galaxy' or 'admin'. + title: Source + type: string + update_time: + description: The time when the notification was last updated. + format: date-time + title: Update time + type: string + variant: + allOf: + - $ref: '#/components/schemas/NotificationVariant' + description: The variant of the notification. Represents the intent or relevance + of the notification. E.g. 'info' or 'urgent'. + title: Variant + required: + - id + - source + - variant + - create_time + - update_time + - publication_time + - content + title: BroadcastNotificationResponse + type: object + BrowsableFilesSourcePlugin: + additionalProperties: true + properties: + browsable: + const: true + title: Browsable + doc: + description: Documentation or extended description for this plugin. + examples: + - Galaxy's library import directory + title: Documentation + type: string + id: + description: The `FilesSource` plugin identifier + examples: + - _import + title: ID + type: string + label: + description: The display label for this plugin. + examples: + - Library Import Directory + title: Label + type: string + requires_groups: + anyOf: + - type: string + - type: 'null' + description: Only users belonging to the groups specified here can access + this files source. + title: Requires groups + requires_roles: + anyOf: + - type: string + - type: 'null' + description: Only users with the roles specified here can access this files + source. + title: Requires roles + type: + description: The type of the plugin. + examples: + - gximport + title: Type + type: string + uri_root: + description: The URI root used by this type of plugin. + examples: + - gximport:// + title: URI root + type: string + writable: + description: Whether this files source plugin allows write access. + examples: + - false + title: Writeable + type: boolean + required: + - id + - type + - label + - doc + - browsable + - writable + - uri_root + title: BrowsableFilesSourcePlugin + type: object + BulkOperationItemError: + properties: + error: + title: Error + type: string + item: + $ref: '#/components/schemas/EncodedHistoryContentItem' + required: + - item + - error + title: BulkOperationItemError + type: object + ChangeDatatypeOperationParams: + properties: + datatype: + title: Datatype + type: string + type: + const: change_datatype + title: Type + required: + - type + - datatype + title: ChangeDatatypeOperationParams + type: object + ChangeDbkeyOperationParams: + properties: + dbkey: + title: Dbkey + type: string + type: + const: change_dbkey + title: Type + required: + - type + - dbkey + title: ChangeDbkeyOperationParams + type: object + CheckForUpdatesResponse: + properties: + message: + description: Unstructured description of tool shed updates discovered or + failure + title: Message + type: string + status: + description: '''ok'' or ''error''' + enum: + - ok + - error + title: Status + type: string + required: + - status + - message + title: CheckForUpdatesResponse + type: object + Checksum: + properties: + checksum: + description: The hex-string encoded checksum for the data + title: Checksum + type: string + type: + description: 'The digest method used to create the checksum. + + The value (e.g. `sha-256`) SHOULD be listed as `Hash Name String` in the + https://www.iana.org/assignments/named-information/named-information.xhtml#hash-alg[IANA + Named Information Hash Algorithm Registry]. Other values MAY be used, + as long as implementors are aware of the issues discussed in https://tools.ietf.org/html/rfc6920#section-9.4[RFC6920]. + + GA4GH may provide more explicit guidance for use of non-IANA-registered + algorithms in the future. Until then, if implementers do choose such an + algorithm (e.g. because it''s implemented by their storage provider), + they SHOULD use an existing standard `type` value such as `md5`, `etag`, + `crc32c`, `trunc512`, or `sha1`.' + examples: + - sha-256 + title: Type + type: string + required: + - checksum + - type + title: Checksum + type: object + CleanableItemsSummary: + properties: + total_items: + description: The total number of items that could be purged. + title: Total Items + type: integer + total_size: + description: The total size in bytes that can be recovered by purging all + the items. + title: Total Size + type: integer + required: + - total_size + - total_items + title: CleanableItemsSummary + type: object + CleanupStorageItemsRequest: + properties: + item_ids: + items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + title: Item Ids + type: array + required: + - item_ids + title: CleanupStorageItemsRequest + type: object + CloudDatasets: + properties: + authz_id: + description: The ID of CloudAuthz to be used for authorizing access to the + resource provider. You may get a list of the defined authorizations via + `/api/cloud/authz`. Also, you can use `/api/cloud/authz/create` to define + a new authorization. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Authentication ID + type: string + bucket: + description: The name of a bucket to which data should be sent (e.g., a + bucket name on AWS S3). + title: Bucket + type: string + dataset_ids: + anyOf: + - items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + type: array + - type: 'null' + description: A list of dataset IDs belonging to the specified history that + should be sent to the given bucket. If not provided, Galaxy sends all + the datasets belonging the specified history. + title: Objects + history_id: + description: The ID of history from which the object should be downloaded + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: History ID + type: string + overwrite_existing: + anyOf: + - type: boolean + - type: 'null' + default: false + description: A boolean value. If set to 'True', and an object with same + name of the dataset to be sent already exist in the bucket, Galaxy replaces + the existing object with the dataset to be sent. If set to 'False', Galaxy + appends datetime to the dataset name to prevent overwriting an existing + object. + title: Spaces to tabs + required: + - history_id + - bucket + - authz_id + title: CloudDatasets + type: object + CloudDatasetsResponse: + properties: + bucket_name: + description: The name of bucket to which the listed datasets are queued + to be sent + title: Bucket + type: string + failed_dataset_labels: + description: The datasets for which Galaxy failed to create (and queue) + send job + items: + type: string + title: Failed datasets + type: array + sent_dataset_labels: + description: The datasets for which Galaxy succeeded to create (and queue) + send job + items: + type: string + title: Send datasets + type: array + required: + - sent_dataset_labels + - failed_dataset_labels + - bucket_name + title: CloudDatasetsResponse + type: object + CloudObjects: + properties: + authz_id: + description: The ID of CloudAuthz to be used for authorizing access to the + resource provider. You may get a list of the defined authorizations via + `/api/cloud/authz`. Also, you can use `/api/cloud/authz/create` to define + a new authorization. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Authentication ID + type: string + bucket: + description: The name of a bucket from which data should be fetched from + (e.g., a bucket name on AWS S3). + title: Bucket + type: string + history_id: + description: The ID of history to which the object should be received to. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: History ID + type: string + input_args: + anyOf: + - $ref: '#/components/schemas/InputArguments' + - type: 'null' + description: A summary of the input arguments, which is optional and will + default to {}. + title: Input arguments + objects: + description: A list of the names of objects to be fetched. + items: + type: string + title: Objects + type: array + required: + - history_id + - bucket + - objects + - authz_id + title: CloudObjects + type: object + CollectionElementIdentifier: + properties: + collection_type: + anyOf: + - type: string + - type: 'null' + description: The type of the collection, can be `list`, `paired`, or define + subcollections using `:` as separator like `list:paired` or `list:list`. + title: Collection Type + element_identifiers: + anyOf: + - items: + $ref: '#/components/schemas/CollectionElementIdentifier' + type: array + - type: 'null' + description: List of elements that should be in the new sub-collection. + title: Element Identifiers + id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: The encoded ID of the element. + title: ID + name: + anyOf: + - type: string + - type: 'null' + description: The name of the element. + title: Name + src: + allOf: + - $ref: '#/components/schemas/ColletionSourceType' + description: The source of the element. + title: Source + tags: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: The list of tags associated with the element. + title: Tags + required: + - src + title: CollectionElementIdentifier + type: object + ColletionSourceType: + enum: + - hda + - ldda + - hdca + - new_collection + title: ColletionSourceType + type: string + CompositeDataElement: + additionalProperties: false + properties: + MD5: + anyOf: + - type: string + - type: 'null' + title: Md5 + auto_decompress: + default: false + description: Decompress compressed data before sniffing? + title: Auto Decompress + type: boolean + collection_type: + anyOf: + - type: string + - type: 'null' + title: Collection Type + composite: + $ref: '#/components/schemas/CompositeItems' + created_from_basename: + anyOf: + - type: string + - type: 'null' + title: Created From Basename + dbkey: + default: '?' + title: Dbkey + type: string + deferred: + default: false + title: Deferred + type: boolean + description: + anyOf: + - type: string + - type: 'null' + title: Description + elements_from: + anyOf: + - $ref: '#/components/schemas/ElementsFromType' + - type: 'null' + ext: + default: auto + title: Ext + type: string + extra_files: + anyOf: + - $ref: '#/components/schemas/ExtraFiles' + - type: 'null' + info: + anyOf: + - type: string + - type: 'null' + title: Info + name: + anyOf: + - type: string + - type: integer + - type: number + - type: boolean + - type: 'null' + title: Name + space_to_tab: + default: false + title: Space To Tab + type: boolean + src: + const: composite + title: Src + tags: + anyOf: + - items: + type: string + type: array + - type: 'null' + title: Tags + to_posix_lines: + default: false + title: To Posix Lines + type: boolean + required: + - src + - composite + title: CompositeDataElement + type: object + CompositeFileInfo: + properties: + description: + anyOf: + - type: string + - type: 'null' + description: Summary description of the purpouse of this file + title: Description + is_binary: + description: Whether this file is a binary file + title: Is binary + type: boolean + mimetype: + anyOf: + - type: string + - type: 'null' + description: The MIME type of this file + title: MIME type + name: + description: The name of this composite file + title: Name + type: string + optional: + description: '' + title: Optional + type: boolean + space_to_tab: + description: '' + title: Spaces to tabulation + type: boolean + substitute_name_with_metadata: + anyOf: + - type: string + - type: 'null' + description: '' + title: Substitute name with metadata + to_posix_lines: + description: '' + title: To posix lines + type: boolean + required: + - name + - optional + - mimetype + - description + - substitute_name_with_metadata + - is_binary + - to_posix_lines + - space_to_tab + title: CompositeFileInfo + type: object + CompositeItems: + properties: + elements: + items: + anyOf: + - $ref: '#/components/schemas/FileDataElement' + - $ref: '#/components/schemas/PastedDataElement' + - $ref: '#/components/schemas/UrlDataElement' + - $ref: '#/components/schemas/PathDataElement' + - $ref: '#/components/schemas/ServerDirElement' + - $ref: '#/components/schemas/FtpImportElement' + title: Elements + type: array + required: + - elements + title: CompositeItems + type: object + ComputeDatasetHashPayload: + properties: + extra_files_path: + anyOf: + - type: string + - type: 'null' + description: If set, extra files path to compute a hash for. + title: Extra Files Path + hash_function: + anyOf: + - $ref: '#/components/schemas/HashFunctionNameEnum' + - type: 'null' + default: MD5 + description: Hash function name to use to compute dataset hashes. + title: ComputeDatasetHashPayload + type: object + ConcreteObjectStoreModel: + properties: + badges: + items: + $ref: '#/components/schemas/BadgeDict' + title: Badges + type: array + description: + anyOf: + - type: string + - type: 'null' + title: Description + device: + anyOf: + - type: string + - type: 'null' + title: Device + name: + anyOf: + - type: string + - type: 'null' + title: Name + object_store_id: + anyOf: + - type: string + - type: 'null' + title: Object Store Id + private: + title: Private + type: boolean + quota: + $ref: '#/components/schemas/QuotaModel' + required: + - private + - quota + - badges + title: ConcreteObjectStoreModel + type: object + ConcreteObjectStoreQuotaSourceDetails: + properties: + enabled: + description: Whether the object store tracks quota on the data (independent + of Galaxy's configuration) + title: Enabled + type: boolean + source: + anyOf: + - type: string + - type: 'null' + description: The quota source label corresponding to the object store the + dataset is stored in (or would be stored in) + title: Source + required: + - source + - enabled + title: ConcreteObjectStoreQuotaSourceDetails + type: object + ContentsObject: + properties: + contents: + anyOf: + - items: + $ref: '#/components/schemas/ContentsObject' + type: array + - type: 'null' + description: If this ContentsObject describes a nested bundle and the caller + specified "?expand=true" on the request, then this contents array must + be present and describe the objects within the nested bundle. + title: Contents + drs_uri: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: A list of full DRS identifier URI paths that may be used to + obtain the object. These URIs may be external to this DRS instance. + examples: + - drs://drs.example.org/314159 + title: Drs Uri + id: + anyOf: + - type: string + - type: 'null' + description: A DRS identifier of a `DrsObject` (either a single blob or + a nested bundle). If this ContentsObject is an object within a nested + bundle, then the id is optional. Otherwise, the id is required. + title: Id + name: + description: A name declared by the bundle author that must be used when + materialising this object, overriding any name directly associated with + the object itself. The name must be unique within the containing bundle. + This string is made up of uppercase and lowercase letters, decimal digits, + hyphen, period, and underscore [A-Za-z0-9.-_]. See http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap03.html#tag_03_282[portable + filenames]. + title: Name + type: string + required: + - name + title: ContentsObject + type: object + ConvertedDatasetsMap: + additionalProperties: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + description: Map of `file extension` -> `converted dataset encoded id` + example: + csv: dataset_id + title: ConvertedDatasetsMap + type: object + CreateEntryPayload: + properties: + name: + description: The name of the entry to create. + examples: + - my_new_entry + title: Name + type: string + target: + description: The target file source to create the entry in. + title: Target + type: string + required: + - target + - name + title: CreateEntryPayload + type: object + CreateHistoryContentFromStore: + properties: + model_store_format: + anyOf: + - $ref: '#/components/schemas/ModelStoreFormat' + - type: 'null' + store_content_uri: + anyOf: + - type: string + - type: 'null' + title: Store Content Uri + store_dict: + anyOf: + - type: object + - type: 'null' + title: Store Dict + title: CreateHistoryContentFromStore + type: object + CreateHistoryContentPayload: + additionalProperties: true + properties: + collection_type: + anyOf: + - type: string + - type: 'null' + description: The type of the collection, can be `list`, `paired`, or define + subcollections using `:` as separator like `list:paired` or `list:list`. + title: Collection Type + content: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: 'Depending on the `source` it can be: + + - The encoded id from the library dataset + + - The encoded id from the library folder + + - The encoded id from the HDA + + - The encoded id from the HDCA + + ' + title: Content + copy_elements: + anyOf: + - type: boolean + - type: 'null' + default: true + description: If the source is a collection, whether to copy child HDAs into + the target history as well. Prior to the galaxy release 23.1 this defaulted + to false. + title: Copy Elements + dbkey: + anyOf: + - type: string + - type: 'null' + description: TODO + title: DBKey + element_identifiers: + anyOf: + - items: + $ref: '#/components/schemas/CollectionElementIdentifier' + type: array + - type: 'null' + description: List of elements that should be in the new collection. + title: Element Identifiers + folder_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: The ID of the library folder that will contain the collection. + Required if `instance_type=library`. + title: Folder Id + hide_source_items: + anyOf: + - type: boolean + - type: 'null' + default: false + description: Whether to mark the original HDAs as hidden. + title: Hide Source Items + history_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: The ID of the history that will contain the collection. Required + if `instance_type=history`. + title: History Id + instance_type: + anyOf: + - enum: + - history + - library + type: string + - type: 'null' + default: history + description: The type of the instance, either `history` (default) or `library`. + title: Instance Type + name: + anyOf: + - type: string + - type: 'null' + description: The name of the new collection. + title: Name + source: + anyOf: + - $ref: '#/components/schemas/HistoryContentSource' + - type: 'null' + description: The source of the content. Can be other history element to + be copied or library elements. + title: Source + type: + anyOf: + - $ref: '#/components/schemas/HistoryContentType' + - type: 'null' + default: dataset + description: The type of content to be created in the history. + title: Type + title: CreateHistoryContentPayload + type: object + CreateHistoryFromStore: + properties: + model_store_format: + anyOf: + - $ref: '#/components/schemas/ModelStoreFormat' + - type: 'null' + store_content_uri: + anyOf: + - type: string + - type: 'null' + title: Store Content Uri + store_dict: + anyOf: + - type: object + - type: 'null' + title: Store Dict + title: CreateHistoryFromStore + type: object + CreateInvocationsFromStorePayload: + properties: + history_id: + description: The ID of the history associated with the invocations. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: History ID + type: string + legacy_job_state: + default: false + deprecated: true + description: "Populate the invocation step state with the job state instead\ + \ of the invocation step state.\n This will also produce one step\ + \ per job in mapping jobs to mimic the older behavior with respect to\ + \ collections.\n Partially scheduled steps may provide incomplete\ + \ information and the listed steps outputs\n are not the mapped\ + \ over step outputs but the individual job outputs." + title: Legacy Job State + type: boolean + model_store_format: + anyOf: + - $ref: '#/components/schemas/ModelStoreFormat' + - type: 'null' + step_details: + default: false + description: Include details for individual invocation steps and populate + a steps attribute in the resulting dictionary + title: Include step details + type: boolean + store_content_uri: + anyOf: + - type: string + - type: 'null' + title: Store Content Uri + store_dict: + anyOf: + - type: object + - type: 'null' + title: Store Dict + view: + anyOf: + - $ref: '#/components/schemas/InvocationSerializationView' + - type: 'null' + description: The name of the view used to serialize this item. This will + return a predefined set of attributes of the item. + examples: + - element + title: View + required: + - history_id + title: CreateInvocationsFromStorePayload + type: object + CreateLibrariesFromStore: + properties: + model_store_format: + anyOf: + - $ref: '#/components/schemas/ModelStoreFormat' + - type: 'null' + store_content_uri: + anyOf: + - type: string + - type: 'null' + title: Store Content Uri + store_dict: + anyOf: + - type: object + - type: 'null' + title: Store Dict + title: CreateLibrariesFromStore + type: object + CreateLibraryFilePayload: + properties: + from_hda_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: The ID of an accessible HDA to copy into the library. + title: From HDA ID + from_hdca_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: The ID of an accessible HDCA to copy into the library. Nested + collections are not allowed, you must flatten the collection first. + title: From HDCA ID + ldda_message: + anyOf: + - type: string + - type: 'null' + default: '' + description: The new message attribute of the LDDA created. + title: LDDA Message + title: CreateLibraryFilePayload + type: object + CreateLibraryFolderPayload: + properties: + description: + anyOf: + - type: string + - type: 'null' + default: '' + description: A detailed description of the library folder. + title: Description + name: + description: The name of the library folder. + title: Name + type: string + required: + - name + title: CreateLibraryFolderPayload + type: object + CreateLibraryPayload: + properties: + description: + anyOf: + - type: string + - type: 'null' + default: '' + description: A detailed description of the Library. + title: Description + name: + description: The name of the Library. + title: Name + type: string + synopsis: + anyOf: + - type: string + - type: 'null' + default: '' + description: A short text describing the contents of the Library. + title: Synopsis + required: + - name + title: CreateLibraryPayload + type: object + CreateMetricsPayload: + properties: + metrics: + default: [] + examples: + - args: '{"test":"value"}' + level: 0 + namespace: test-source + time: '2021-01-23T18:25:43.511Z' + items: + $ref: '#/components/schemas/Metric' + title: List of metrics to be recorded. + type: array + title: CreateMetricsPayload + type: object + CreateNewCollectionPayload: + properties: + collection_type: + anyOf: + - type: string + - type: 'null' + description: The type of the collection, can be `list`, `paired`, or define + subcollections using `:` as separator like `list:paired` or `list:list`. + title: Collection Type + copy_elements: + anyOf: + - type: boolean + - type: 'null' + default: true + description: Whether to create a copy of the source HDAs for the new collection. + title: Copy Elements + element_identifiers: + anyOf: + - items: + $ref: '#/components/schemas/CollectionElementIdentifier' + type: array + - type: 'null' + description: List of elements that should be in the new collection. + title: Element Identifiers + folder_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: The ID of the library folder that will contain the collection. + Required if `instance_type=library`. + title: Folder Id + hide_source_items: + anyOf: + - type: boolean + - type: 'null' + default: false + description: Whether to mark the original HDAs as hidden. + title: Hide Source Items + history_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: The ID of the history that will contain the collection. Required + if `instance_type=history`. + title: History Id + instance_type: + anyOf: + - enum: + - history + - library + type: string + - type: 'null' + default: history + description: The type of the instance, either `history` (default) or `library`. + title: Instance Type + name: + anyOf: + - type: string + - type: 'null' + description: The name of the new collection. + title: Name + title: CreateNewCollectionPayload + type: object + CreatePagePayload: + additionalProperties: true + properties: + annotation: + anyOf: + - type: string + - type: 'null' + description: Annotation that will be attached to the page. + title: Annotation + content: + anyOf: + - type: string + - type: 'null' + default: '' + description: Raw text contents of the last page revision (type dependent + on content_format). + title: Content + content_format: + allOf: + - $ref: '#/components/schemas/PageContentFormat' + default: html + description: Either `markdown` or `html`. + title: Content format + invocation_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: Encoded ID used by workflow generated reports. + title: Workflow invocation ID + slug: + description: The title slug for the page URL, must be unique. + pattern: ^[a-z0-9\-]+$ + title: Identifier + type: string + title: + description: The name of the page. + title: Title + type: string + required: + - title + - slug + title: CreatePagePayload + type: object + CreateQuotaParams: + properties: + amount: + description: Quota size (E.g. ``10000MB``, ``99 gb``, ``0.2T``, ``unlimited``) + title: Amount + type: string + default: + allOf: + - $ref: '#/components/schemas/DefaultQuotaValues' + default: 'no' + description: Whether or not this is a default quota. Valid values are ``no``, + ``unregistered``, ``registered``. None is equivalent to ``no``. + title: Default + description: + description: Detailed text description for this Quota. + title: Description + type: string + in_groups: + anyOf: + - items: + type: string + type: array + - type: 'null' + default: [] + description: A list of group IDs or names to associate with this quota. + title: Groups + in_users: + anyOf: + - items: + type: string + type: array + - type: 'null' + default: [] + description: A list of user IDs or user emails to associate with this quota. + title: Users + name: + description: The name of the quota. This must be unique within a Galaxy + instance. + title: Name + type: string + operation: + allOf: + - $ref: '#/components/schemas/QuotaOperation' + default: '=' + description: 'Quotas can have one of three `operations`:- `=` : The quota + is exactly the amount specified- `+` : The amount specified will be added + to the amounts of the user''s other associated quota definitions- `-` + : The amount specified will be subtracted from the amounts of the user''s + other associated quota definitions' + title: Operation + quota_source_label: + anyOf: + - type: string + - type: 'null' + description: If set, quota source label to apply this quota operation to. + Otherwise, the default quota is used. + title: Quota Source Label + required: + - name + - description + - amount + title: CreateQuotaParams + type: object + CreateQuotaResult: + properties: + id: + description: The `encoded identifier` of the quota. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + message: + description: Text message describing the result of the operation. + title: Message + type: string + model_class: + const: Quota + description: The name of the database model class. + title: Model class + type: string + name: + description: The name of the quota. This must be unique within a Galaxy + instance. + title: Name + type: string + quota_source_label: + anyOf: + - type: string + - type: 'null' + description: Quota source label + title: Quota Source Label + url: + deprecated: true + description: The relative URL to get this particular Quota details from + the rest API. + title: URL + type: string + required: + - model_class + - id + - name + - url + - message + title: CreateQuotaResult + type: object + CreatedEntryResponse: + properties: + external_link: + anyOf: + - type: string + - type: 'null' + description: An optional external link to the created entry if available. + title: External link + name: + description: The name of the created entry. + examples: + - my_new_entry + title: Name + type: string + uri: + description: The URI of the created entry. + examples: + - gxfiles://my_new_entry + title: URI + type: string + required: + - name + - uri + title: CreatedEntryResponse + type: object + CreatedUserModel: + properties: + active: + description: User is active + title: Active + type: boolean + deleted: + description: ' User is deleted' + title: Deleted + type: boolean + email: + description: Email of the user + title: Email + type: string + id: + description: Encoded ID of the user + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + last_password_change: + anyOf: + - format: date-time + type: string + - type: 'null' + description: '' + title: Last password change + model_class: + const: User + description: The name of the database model class. + title: Model class + type: string + nice_total_disk_usage: + description: Size of all non-purged, unique datasets of the user in a nice + format. + title: Nice total disc usage + type: string + preferred_object_store_id: + anyOf: + - type: string + - type: 'null' + description: The ID of the object store that should be used to store new + datasets in this history. + title: Preferred Object Store ID + total_disk_usage: + description: Size of all non-purged, unique datasets of the user in bytes. + title: Total disk usage + type: number + username: + description: The name of the user. + title: user_name + type: string + required: + - model_class + - total_disk_usage + - nice_total_disk_usage + - id + - username + - email + - deleted + - active + - last_password_change + title: CreatedUserModel + type: object + CustomBuildCreationPayload: + properties: + len|type: + allOf: + - $ref: '#/components/schemas/CustomBuildLenType' + description: The type of the len file. + title: Length type + len|value: + description: The content of the length file. + title: Length value + type: string + name: + description: The name of the custom build. + title: Name + type: string + required: + - name + - len|type + - len|value + title: CustomBuildCreationPayload + type: object + CustomBuildLenType: + enum: + - file + - fasta + - text + title: CustomBuildLenType + type: string + CustomBuildModel: + properties: + count: + anyOf: + - type: string + - type: 'null' + description: The number of chromosomes/contigs. + title: Count + fasta: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: The primary id of the fasta file from a history. + title: Fasta + id: + description: The ID of the custom build. + title: ID + type: string + len: + description: The primary id of the len file. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Length + type: string + linecount: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: The primary id of a linecount dataset. + title: Line count + name: + description: The name of the custom build. + title: Name + type: string + required: + - name + - len + - id + title: CustomBuildModel + type: object + CustomBuildsCollection: + items: + $ref: '#/components/schemas/CustomBuildModel' + title: CustomBuildsCollection + type: array + CustomBuildsMetadataResponse: + properties: + fasta_hdas: + description: "A list of label/value pairs with all the datasets of type\ + \ `FASTA` contained in the History.\n - `label` is item position followed\ + \ by the name of the dataset.\n - `value` is the encoded database ID of\ + \ the dataset.\n" + items: + $ref: '#/components/schemas/LabelValuePair' + title: Fasta HDAs + type: array + installed_builds: + description: TODO + items: + $ref: '#/components/schemas/LabelValuePair' + title: Installed Builds + type: array + required: + - installed_builds + - fasta_hdas + title: CustomBuildsMetadataResponse + type: object + CustomHistoryItem: + additionalProperties: true + description: 'Can contain any serializable property of the item. + + + Allows arbitrary custom keys to be specified in the serialization + + parameters without a particular view (predefined set of keys).' + properties: {} + title: CustomHistoryItem + type: object + DCESummary: + description: Dataset Collection Element summary information. + properties: + element_identifier: + description: The actual name of this element. + title: Element Identifier + type: string + element_index: + description: The position index of this element inside the collection. + title: Element Index + type: integer + element_type: + allOf: + - $ref: '#/components/schemas/DCEType' + description: The type of the element. Used to interpret the `object` field. + title: Element Type + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Dataset Collection Element ID + type: string + model_class: + const: DatasetCollectionElement + description: The name of the database model class. + title: Model class + type: string + object: + anyOf: + - $ref: '#/components/schemas/HDAObject' + - $ref: '#/components/schemas/HDADetailed' + - $ref: '#/components/schemas/DCObject' + description: The element's specific data depending on the value of `element_type`. + title: Object + required: + - model_class + - id + - element_index + - element_identifier + - element_type + - object + title: DCESummary + type: object + DCEType: + description: Available types of dataset collection elements. + enum: + - hda + - dataset_collection + title: DCEType + type: string + DCObject: + description: Dataset Collection Object + properties: + collection_type: + description: The type of the collection, can be `list`, `paired`, or define + subcollections using `:` as separator like `list:paired` or `list:list`. + title: Collection Type + type: string + contents_url: + anyOf: + - description: The relative URL to access the contents of this History. + title: Contents URL + type: string + - type: 'null' + title: Contents Url + element_count: + anyOf: + - type: integer + - type: 'null' + description: The number of elements contained in the dataset collection. + It may be None or undefined if the collection could not be populated. + title: Element Count + elements: + default: [] + description: The summary information of each of the elements inside the + dataset collection. + items: + $ref: '#/components/schemas/DCESummary' + title: Elements + type: array + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Dataset Collection ID + type: string + model_class: + const: DatasetCollection + description: The name of the database model class. + title: Model class + type: string + populated: + description: Whether the dataset collection elements (and any subcollections + elements) were successfully populated. + title: Populated + type: boolean + required: + - model_class + - id + - collection_type + title: DCObject + type: object + DataElementsFromTarget: + properties: + auto_decompress: + default: false + description: Decompress compressed data before sniffing? + title: Auto Decompress + type: boolean + destination: + discriminator: + mapping: + hdas: '#/components/schemas/HdaDestination' + library: '#/components/schemas/LibraryDestination' + library_folder: '#/components/schemas/LibraryFolderDestination' + propertyName: type + oneOf: + - $ref: '#/components/schemas/HdaDestination' + - $ref: '#/components/schemas/LibraryFolderDestination' + - $ref: '#/components/schemas/LibraryDestination' + title: Destination + elements_from: + $ref: '#/components/schemas/ElementsFromType' + ftp_path: + anyOf: + - type: string + - type: 'null' + title: Ftp Path + path: + anyOf: + - type: string + - type: 'null' + title: Path + server_dir: + anyOf: + - type: string + - type: 'null' + title: Server Dir + src: + $ref: '#/components/schemas/ItemsFromSrc' + url: + anyOf: + - type: string + - type: 'null' + title: Url + required: + - src + - destination + - elements_from + title: DataElementsFromTarget + type: object + DataElementsTarget: + properties: + auto_decompress: + default: false + description: Decompress compressed data before sniffing? + title: Auto Decompress + type: boolean + destination: + discriminator: + mapping: + hdas: '#/components/schemas/HdaDestination' + library: '#/components/schemas/LibraryDestination' + library_folder: '#/components/schemas/LibraryFolderDestination' + propertyName: type + oneOf: + - $ref: '#/components/schemas/HdaDestination' + - $ref: '#/components/schemas/LibraryFolderDestination' + - $ref: '#/components/schemas/LibraryDestination' + title: Destination + elements: + items: + anyOf: + - discriminator: + mapping: + composite: '#/components/schemas/CompositeDataElement' + files: '#/components/schemas/FileDataElement' + ftp_import: '#/components/schemas/FtpImportElement' + pasted: '#/components/schemas/PastedDataElement' + path: '#/components/schemas/PathDataElement' + server_dir: '#/components/schemas/ServerDirElement' + url: '#/components/schemas/UrlDataElement' + propertyName: src + oneOf: + - $ref: '#/components/schemas/FileDataElement' + - $ref: '#/components/schemas/PastedDataElement' + - $ref: '#/components/schemas/UrlDataElement' + - $ref: '#/components/schemas/PathDataElement' + - $ref: '#/components/schemas/ServerDirElement' + - $ref: '#/components/schemas/FtpImportElement' + - $ref: '#/components/schemas/CompositeDataElement' + - $ref: '#/components/schemas/NestedElement' + title: Elements + type: array + required: + - destination + - elements + title: DataElementsTarget + type: object + DataItemSourceType: + enum: + - hda + - ldda + - hdca + - dce + - dc + title: DataItemSourceType + type: string + DatasetAssociationRoles: + properties: + access_dataset_roles: + default: [] + description: A list of roles that can access the dataset. The user has to + **have all these roles** in order to access this dataset. Users without + access permission **cannot** have other permissions on this dataset. If + there are no access roles set on the dataset it is considered **unrestricted**. + items: + items: + type: string + type: array + title: Access Roles + type: array + manage_dataset_roles: + default: [] + description: A list of roles that can manage permissions on the dataset. + Users with **any** of these roles can manage permissions of this dataset. + If you remove yourself you will lose the ability to manage this dataset + unless you are an admin. + items: + items: + type: string + type: array + title: Manage Roles + type: array + modify_item_roles: + default: [] + description: A list of roles that can modify the library item. This is a + library related permission. User with **any** of these roles can modify + name, metadata, and other information about this library item. + items: + items: + type: string + type: array + title: Modify Roles + type: array + title: DatasetAssociationRoles + type: object + DatasetCollectionAttributesResult: + properties: + dbkey: + description: TODO + title: Dbkey + type: string + dbkeys: + anyOf: + - items: + type: string + type: array + uniqueItems: true + - type: 'null' + title: Dbkeys + extension: + description: The dataset file extension. + examples: + - txt + title: Extension + type: string + extensions: + anyOf: + - items: + type: string + type: array + uniqueItems: true + - type: 'null' + title: Extensions + model_class: + const: HistoryDatasetCollectionAssociation + description: The name of the database model class. + title: Model class + type: string + tags: + $ref: '#/components/schemas/TagCollection' + required: + - dbkey + - extension + - model_class + - dbkeys + - extensions + - tags + title: DatasetCollectionAttributesResult + type: object + DatasetCollectionContentElements: + description: Represents a collection of elements contained in the dataset collection. + items: + $ref: '#/components/schemas/DCESummary' + title: DatasetCollectionContentElements + type: array + DatasetCollectionPopulatedState: + enum: + - new + - ok + - failed + title: DatasetCollectionPopulatedState + type: string + DatasetContentType: + description: For retrieving content from a structured dataset (e.g. HDF5) + enum: + - meta + - attr + - stats + - data + title: DatasetContentType + type: string + DatasetErrorMessage: + properties: + dataset: + allOf: + - $ref: '#/components/schemas/EncodedDatasetSourceId' + description: The encoded ID of the dataset and its source. + error_message: + description: The error message returned while processing this dataset. + title: Error Message + type: string + required: + - dataset + - error_message + title: DatasetErrorMessage + type: object + DatasetExtraFiles: + description: A list of extra files associated with a dataset. + items: + $ref: '#/components/schemas/ExtraFileEntry' + title: DatasetExtraFiles + type: array + DatasetInheritanceChain: + default: [] + items: + $ref: '#/components/schemas/DatasetInheritanceChainEntry' + title: DatasetInheritanceChain + type: array + DatasetInheritanceChainEntry: + properties: + dep: + description: Name of the source of the referenced dataset at this point + of the inheritance chain. + title: Dep + type: string + name: + description: Name of the referenced dataset + title: Name + type: string + required: + - name + - dep + title: DatasetInheritanceChainEntry + type: object + DatasetPermissions: + description: Role-based permissions for accessing and managing a dataset. + properties: + access: + default: [] + description: The set of roles (encoded IDs) that can access this dataset. + items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + title: Access + type: array + manage: + default: [] + description: The set of roles (encoded IDs) that can manage this dataset. + items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + title: Management + type: array + title: DatasetPermissions + type: object + DatasetSourceId: + properties: + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Id + type: string + src: + allOf: + - $ref: '#/components/schemas/DatasetSourceType' + description: The source of this dataset, either `hda` or `ldda` depending + of its origin. + title: Source + required: + - src + - id + title: DatasetSourceId + type: object + DatasetSourceType: + enum: + - hda + - ldda + title: DatasetSourceType + type: string + DatasetState: + enum: + - new + - upload + - queued + - running + - ok + - empty + - error + - paused + - setting_metadata + - failed_metadata + - deferred + - discarded + title: DatasetState + type: string + DatasetStorageDetails: + properties: + badges: + description: A list of badges describing object store properties for concrete + object store dataset is stored in. + items: + $ref: '#/components/schemas/BadgeDict' + title: Badges + type: array + dataset_state: + description: The model state of the supplied dataset instance. + title: Dataset State + type: string + description: + anyOf: + - type: string + - type: 'null' + description: A description of how this dataset is stored. + title: Description + hashes: + description: The file contents hashes associated with the supplied dataset + instance. + items: + type: object + title: Hashes + type: array + name: + anyOf: + - type: string + - type: 'null' + description: The display name of the destination ObjectStore for this dataset. + title: Name + object_store_id: + anyOf: + - type: string + - type: 'null' + description: The identifier of the destination ObjectStore for this dataset. + title: Object Store Id + percent_used: + anyOf: + - type: number + - type: 'null' + description: The percentage indicating how full the store is. + title: Percent Used + quota: + allOf: + - $ref: '#/components/schemas/ConcreteObjectStoreQuotaSourceDetails' + description: Information about quota sources around dataset storage. + relocatable: + description: Indicator of whether the objectstore for this dataset can be + switched by this user. + title: Relocatable + type: boolean + shareable: + description: Is this dataset shareable. + title: Shareable + type: boolean + sources: + description: The file sources associated with the supplied dataset instance. + items: + type: object + title: Sources + type: array + required: + - object_store_id + - name + - description + - percent_used + - dataset_state + - hashes + - sources + - shareable + - quota + - badges + - relocatable + title: DatasetStorageDetails + type: object + DatasetSummary: + properties: + create_time: + anyOf: + - format: date-time + type: string + - type: 'null' + description: The time and date this item was created. + title: Create Time + deleted: + title: Deleted + type: boolean + file_size: + title: File Size + type: integer + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Id + type: string + purgable: + title: Purgable + type: boolean + purged: + title: Purged + type: boolean + state: + allOf: + - $ref: '#/components/schemas/DatasetState' + description: The current state of this dataset. + title: State + total_size: + title: Total Size + type: integer + update_time: + anyOf: + - format: date-time + type: string + - type: 'null' + description: The last time and date this item was updated. + title: Update Time + uuid: + description: Universal unique identifier for this dataset. + format: uuid4 + title: UUID + type: string + required: + - id + - create_time + - update_time + - state + - deleted + - purged + - purgable + - file_size + - total_size + - uuid + title: DatasetSummary + type: object + DatasetSummaryList: + items: + $ref: '#/components/schemas/DatasetSummary' + title: DatasetSummaryList + type: array + DatasetTextContentDetails: + properties: + item_data: + anyOf: + - type: string + - type: 'null' + description: First chunk of text content (maximum 1MB) of the dataset. + title: Item Data + item_url: + description: URL to access this dataset. + title: Item Url + type: string + truncated: + description: Whether the text in `item_data` has been truncated or contains + the whole contents. + title: Truncated + type: boolean + required: + - item_data + - truncated + - item_url + title: DatasetTextContentDetails + type: object + DatasetValidatedState: + enum: + - unknown + - invalid + - ok + title: DatasetValidatedState + type: string + DatatypeConverter: + properties: + source: + description: Source type for conversion + examples: + - bam + title: Source + type: string + target: + description: Target type for conversion + examples: + - bai + title: Target + type: string + tool_id: + description: The converter tool identifier + examples: + - CONVERTER_Bam_Bai_0 + title: Tool identifier + type: string + required: + - source + - target + - tool_id + title: DatatypeConverter + type: object + DatatypeConverterList: + default: [] + items: + $ref: '#/components/schemas/DatatypeConverter' + title: DatatypeConverterList + type: array + DatatypeDetails: + properties: + composite_files: + anyOf: + - items: + $ref: '#/components/schemas/CompositeFileInfo' + type: array + - type: 'null' + description: A collection of files composing this data type + title: Composite files + description: + anyOf: + - type: string + - type: 'null' + description: A summary description for this data type + title: Description + description_url: + anyOf: + - format: uri + maxLength: 2083 + minLength: 1 + type: string + - type: 'null' + description: The URL to a detailed description for this datatype + examples: + - https://wiki.galaxyproject.org/Learn/Datatypes#Bed + title: Description URL + display_in_upload: + default: false + description: If True, the associated file extension will be displayed in + the `File Format` select list in the `Upload File from your computer` + tool in the `Get Data` tool section of the tool panel + title: Display in upload + type: boolean + extension: + description: "The data type\u2019s Dataset file extension" + examples: + - bed + title: Extension + type: string + upload_warning: + anyOf: + - type: string + - type: 'null' + description: End-user information regarding potential pitfalls with this + upload type. + title: Upload warning + required: + - extension + - description + - description_url + title: DatatypeDetails + type: object + DatatypeEDAMDetails: + properties: + definition: + anyOf: + - type: string + - type: 'null' + description: The EDAM definition + examples: + - Entry (gene) format of the NCBI database. + title: Definition + label: + anyOf: + - type: string + - type: 'null' + description: The EDAM label + examples: + - NCBI gene report format + title: Label + prefix_IRI: + description: The EDAM prefixed Resource Identifier + examples: + - format_1782 + title: Prefix IRI + type: string + required: + - prefix_IRI + - label + - definition + title: DatatypeEDAMDetails + type: object + DatatypesCombinedMap: + properties: + datatypes: + description: List of datatypes extensions + items: + type: string + title: Datatypes + type: array + datatypes_mapping: + allOf: + - $ref: '#/components/schemas/DatatypesMap' + description: Dictionaries for mapping datatype's extensions/classes with + their implementation classes + title: Datatypes Mapping + required: + - datatypes + - datatypes_mapping + title: DatatypesCombinedMap + type: object + DatatypesEDAMDetailsDict: + additionalProperties: + $ref: '#/components/schemas/DatatypeEDAMDetails' + default: {} + title: DatatypesEDAMDetailsDict + type: object + DatatypesMap: + properties: + class_to_classes: + additionalProperties: + additionalProperties: + type: boolean + type: object + description: Dictionary mapping datatype's classes with their base classes + title: Classes Map + type: object + ext_to_class_name: + additionalProperties: + type: string + description: Dictionary mapping datatype's extensions with implementation + classes + title: Extension Map + type: object + required: + - ext_to_class_name + - class_to_classes + title: DatatypesMap + type: object + DefaultQuota: + properties: + model_class: + const: DefaultQuotaAssociation + description: The name of the database model class. + title: Model class + type: string + type: + allOf: + - $ref: '#/components/schemas/DefaultQuotaTypes' + description: "The type of the default quota. Either one of:\n - `registered`:\ + \ the associated quota will affect registered users.\n - `unregistered`:\ + \ the associated quota will affect unregistered users.\n" + title: Type + required: + - model_class + - type + title: DefaultQuota + type: object + DefaultQuotaTypes: + enum: + - unregistered + - registered + title: DefaultQuotaTypes + type: string + DefaultQuotaValues: + enum: + - unregistered + - registered + - 'no' + title: DefaultQuotaValues + type: string + DeleteDatasetBatchPayload: + properties: + datasets: + description: The list of datasets IDs with their sources to be deleted/purged. + items: + $ref: '#/components/schemas/DatasetSourceId' + title: Datasets + type: array + purge: + anyOf: + - type: boolean + - type: 'null' + default: false + description: 'Whether to permanently delete from disk the specified datasets. + *Warning*: this is a destructive operation.' + title: Purge + required: + - datasets + title: DeleteDatasetBatchPayload + type: object + DeleteDatasetBatchResult: + properties: + errors: + anyOf: + - items: + $ref: '#/components/schemas/DatasetErrorMessage' + type: array + - type: 'null' + description: A list of dataset IDs and the corresponding error message if + something went wrong while processing the dataset. + title: Errors + success_count: + description: The number of datasets successfully processed. + title: Success Count + type: integer + required: + - success_count + title: DeleteDatasetBatchResult + type: object + DeleteHistoriesPayload: + properties: + ids: + description: List of history IDs to be deleted. + items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + title: IDs + type: array + purge: + default: false + description: Whether to definitely remove this history from disk. + title: Purge + type: boolean + required: + - ids + title: DeleteHistoriesPayload + type: object + DeleteHistoryContentPayload: + properties: + purge: + default: false + description: Whether to remove the dataset from storage. Datasets will only + be removed from storage once all HDAs or LDDAs that refer to this datasets + are deleted. + title: Purge + type: boolean + recursive: + default: false + description: When deleting a dataset collection, whether to also delete + containing datasets. + title: Recursive + type: boolean + stop_job: + default: false + description: Whether to stop the creating job if all the job's outputs are + deleted. + title: Stop Job + type: boolean + title: DeleteHistoryContentPayload + type: object + DeleteHistoryContentResult: + additionalProperties: true + description: 'Contains minimum information about the deletion state of a history + item. + + + Can also contain any other properties of the item.' + properties: + deleted: + description: True if the item was successfully deleted. + title: Deleted + type: boolean + id: + description: The encoded ID of the history item. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + purged: + anyOf: + - type: boolean + - type: 'null' + description: True if the item was successfully removed from disk. + title: Purged + required: + - id + - deleted + title: DeleteHistoryContentResult + type: object + DeleteHistoryPayload: + properties: + purge: + default: false + description: Whether to definitely remove this history from disk. + title: Purge + type: boolean + title: DeleteHistoryPayload + type: object + DeleteJobPayload: + properties: + message: + anyOf: + - type: string + - type: 'null' + description: Stop message + title: Job message + title: DeleteJobPayload + type: object + DeleteLibraryPayload: + properties: + undelete: + description: Whether to restore this previously deleted library. + title: Undelete + type: boolean + required: + - undelete + title: DeleteLibraryPayload + type: object + DeleteQuotaPayload: + properties: + purge: + default: false + description: Whether to also purge the Quota after deleting it. + title: Purge + type: boolean + title: DeleteQuotaPayload + type: object + DeletedCustomBuild: + properties: + message: + description: Confirmation of the custom build deletion. + title: Deletion message + type: string + required: + - message + title: DeletedCustomBuild + type: object + DetailedUserModel: + properties: + deleted: + description: ' User is deleted' + title: Deleted + type: boolean + email: + description: Email of the user + title: Email + type: string + id: + description: Encoded ID of the user + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + is_admin: + description: User is admin + title: Is admin + type: boolean + nice_total_disk_usage: + description: Size of all non-purged, unique datasets of the user in a nice + format. + title: Nice total disc usage + type: string + preferences: + description: Preferences of the user + title: Preferences + type: object + preferred_object_store_id: + anyOf: + - type: string + - type: 'null' + description: The ID of the object store that should be used to store new + datasets in this history. + title: Preferred Object Store ID + purged: + description: User is purged + title: Purged + type: boolean + quota: + description: Quota applicable to the user + title: Quota + type: string + quota_bytes: + description: Quota applicable to the user in bytes. + title: Quota in bytes + quota_percent: + description: Percentage of the storage quota applicable to the user. + title: Quota percent + tags_used: + description: Tags used by the user + items: + type: string + title: Tags used + type: array + total_disk_usage: + description: Size of all non-purged, unique datasets of the user in bytes. + title: Total disk usage + type: number + username: + description: The name of the user. + title: user_name + type: string + required: + - total_disk_usage + - nice_total_disk_usage + - id + - username + - email + - deleted + - is_admin + - purged + - preferences + - quota + - quota_bytes + - tags_used + title: DetailedUserModel + type: object + DisplayApp: + description: Basic linked information about an application that can display + certain datatypes. + properties: + label: + description: The label or title of the Display Application. + title: Label + type: string + links: + description: The collection of link details for this Display Application. + items: + $ref: '#/components/schemas/Hyperlink' + title: Links + type: array + required: + - label + - links + title: DisplayApp + type: object + DisplayApplication: + properties: + filename_: + title: 'Filename ' + type: string + id: + title: Id + type: string + links: + items: + $ref: '#/components/schemas/Link' + title: Links + type: array + name: + title: Name + type: string + version: + title: Version + type: string + required: + - id + - name + - version + - filename_ + - links + title: DisplayApplication + type: object + DrsObject: + properties: + access_methods: + anyOf: + - items: + $ref: '#/components/schemas/AccessMethod' + minItems: 1 + type: array + - type: 'null' + description: 'The list of access methods that can be used to fetch the `DrsObject`. + + Required for single blobs; optional for bundles.' + title: Access Methods + aliases: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: A list of strings that can be used to find other metadata about + this `DrsObject` from external metadata sources. These aliases can be + used to represent secondary accession numbers or external GUIDs. + title: Aliases + checksums: + description: 'The checksum of the `DrsObject`. At least one checksum must + be provided. + + For blobs, the checksum is computed over the bytes in the blob. + + For bundles, the checksum is computed over a sorted concatenation of the + checksums of its top-level contained objects (not recursive, names not + included). The list of checksums is sorted alphabetically (hex-code) before + concatenation and a further checksum is performed on the concatenated + checksum value. + + For example, if a bundle contains blobs with the following checksums: + + md5(blob1) = 72794b6d + + md5(blob2) = 5e089d29 + + Then the checksum of the bundle is: + + md5( concat( sort( md5(blob1), md5(blob2) ) ) ) + + = md5( concat( sort( 72794b6d, 5e089d29 ) ) ) + + = md5( concat( 5e089d29, 72794b6d ) ) + + = md5( 5e089d2972794b6d ) + + = f7a29a04' + items: + $ref: '#/components/schemas/Checksum' + minItems: 1 + title: Checksums + type: array + contents: + anyOf: + - items: + $ref: '#/components/schemas/ContentsObject' + type: array + - type: 'null' + description: 'If not set, this `DrsObject` is a single blob. + + If set, this `DrsObject` is a bundle containing the listed `ContentsObject` + s (some of which may be further nested).' + title: Contents + created_time: + description: 'Timestamp of content creation in RFC3339. + + (This is the creation time of the underlying content, not of the JSON + object.)' + format: date-time + title: Created Time + type: string + description: + anyOf: + - type: string + - type: 'null' + description: A human readable description of the `DrsObject`. + title: Description + id: + description: An identifier unique to this `DrsObject` + title: Id + type: string + mime_type: + anyOf: + - type: string + - type: 'null' + description: A string providing the mime-type of the `DrsObject`. + examples: + - application/json + title: Mime Type + name: + anyOf: + - type: string + - type: 'null' + description: 'A string that can be used to name a `DrsObject`. + + This string is made up of uppercase and lowercase letters, decimal digits, + hyphen, period, and underscore [A-Za-z0-9.-_]. See http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap03.html#tag_03_282[portable + filenames].' + title: Name + self_uri: + description: 'A drs:// hostname-based URI, as defined in the DRS documentation, + that tells clients how to access this object. + + The intent of this field is to make DRS objects self-contained, and therefore + easier for clients to store and pass around. For example, if you arrive + at this DRS JSON by resolving a compact identifier-based DRS URI, the + `self_uri` presents you with a hostname and properly encoded DRS ID for + use in subsequent `access` endpoint calls.' + examples: + - drs://drs.example.org/314159 + title: Self Uri + type: string + size: + description: 'For blobs, the blob size in bytes. + + For bundles, the cumulative size, in bytes, of items in the `contents` + field.' + title: Size + type: integer + updated_time: + anyOf: + - format: date-time + type: string + - type: 'null' + description: Timestamp of content update in RFC3339, identical to `created_time` + in systems that do not support updates. (This is the update time of the + underlying content, not of the JSON object.) + title: Updated Time + version: + anyOf: + - type: string + - type: 'null' + description: 'A string representing a version. + + (Some systems may use checksum, a RFC3339 timestamp, or an incrementing + version number.)' + title: Version + required: + - id + - self_uri + - size + - created_time + - checksums + title: DrsObject + type: object + ElementsFromType: + enum: + - archive + - bagit + - bagit_archive + - directory + title: ElementsFromType + type: string + EncodedDataItemSourceId: + properties: + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Id + type: string + src: + allOf: + - $ref: '#/components/schemas/DataItemSourceType' + description: The source of this dataset, either `hda`, `ldda`, `hdca`, `dce` + or `dc` depending of its origin. + title: Source + required: + - id + - src + title: EncodedDataItemSourceId + type: object + EncodedDatasetJobInfo: + properties: + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Id + type: string + src: + allOf: + - $ref: '#/components/schemas/DataItemSourceType' + description: The source of this dataset, either `hda`, `ldda`, `hdca`, `dce` + or `dc` depending of its origin. + title: Source + uuid: + anyOf: + - format: uuid4 + type: string + - type: 'null' + deprecated: true + description: Universal unique identifier for this dataset. + title: UUID + required: + - id + - src + title: EncodedDatasetJobInfo + type: object + EncodedDatasetSourceId: + properties: + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Id + type: string + src: + allOf: + - $ref: '#/components/schemas/DatasetSourceType' + description: The source of this dataset, either `hda` or `ldda` depending + of its origin. + title: Source + required: + - src + - id + title: EncodedDatasetSourceId + type: object + EncodedHdcaSourceId: + properties: + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Id + type: string + src: + const: hdca + description: The source of this dataset, which in the case of the model + can only be `hdca`. + title: Source + required: + - src + - id + title: EncodedHdcaSourceId + type: object + EncodedHistoryContentItem: + properties: + history_content_type: + allOf: + - $ref: '#/components/schemas/HistoryContentType' + description: The type of this item. + title: Content Type + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Id + type: string + required: + - history_content_type + - id + title: EncodedHistoryContentItem + type: object + EncodedJobDetails: + properties: + command_line: + anyOf: + - type: string + - type: 'null' + description: The command line produced by the job. Users can see this value + if allowed in the configuration, administrator can always see this value. + title: Command Line + command_version: + anyOf: + - type: string + - type: 'null' + description: Tool version indicated during job execution. + title: Command Version + copied_from_job_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: Reference to cached job if job execution was cached. + title: Copied from Job-ID + create_time: + description: The time and date this item was created. + format: date-time + title: Create Time + type: string + exit_code: + anyOf: + - type: integer + - type: 'null' + description: The exit code returned by the tool. Can be unset if the job + is not completed yet. + title: Exit Code + external_id: + anyOf: + - type: string + - type: 'null' + description: The job id used by the external job runner (Condor, Pulsar, + etc.). Only administrator can see this value. + title: External ID + galaxy_version: + anyOf: + - type: string + - type: 'null' + description: The (major) version of Galaxy used to create this job. + examples: + - '21.05' + title: Galaxy Version + handler: + anyOf: + - type: string + - type: 'null' + description: The job handler process assigned to handle this job. Only administrator + can see this value. + title: Job Handler + history_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: The encoded ID of the history associated with this item. + title: History ID + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Job ID + type: string + inputs: + additionalProperties: + $ref: '#/components/schemas/EncodedDatasetJobInfo' + default: {} + description: Dictionary mapping all the tool inputs (by name) to the corresponding + data references. + title: Inputs + type: object + job_runner_name: + anyOf: + - type: string + - type: 'null' + description: Name of the job runner plugin that handles this job. Only administrator + can see this value. + title: Job Runner Name + model_class: + const: Job + description: The name of the database model class. + title: Model class + type: string + output_collections: + additionalProperties: + $ref: '#/components/schemas/EncodedHdcaSourceId' + default: {} + description: '' + title: Output collections + type: object + outputs: + additionalProperties: + $ref: '#/components/schemas/EncodedDatasetJobInfo' + default: {} + description: Dictionary mapping all the tool outputs (by name) to the corresponding + data references. + title: Outputs + type: object + params: + description: Object containing all the parameters of the tool associated + with this job. The specific parameters depend on the tool itself. + title: Parameters + state: + allOf: + - $ref: '#/components/schemas/JobState' + description: Current state of the job. + title: State + tool_id: + description: Identifier of the tool that generated this job. + title: Tool ID + type: string + update_time: + description: The last time and date this item was updated. + format: date-time + title: Update Time + type: string + user_email: + anyOf: + - type: string + - type: 'null' + description: The email of the user that owns this job. Only the owner of + the job and administrators can see this value. + title: User Email + required: + - model_class + - id + - tool_id + - state + - create_time + - update_time + - params + title: EncodedJobDetails + type: object + EncodedJobParameterHistoryItem: + properties: + hid: + anyOf: + - type: integer + - type: 'null' + title: Hid + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Id + type: string + name: + title: Name + type: string + src: + allOf: + - $ref: '#/components/schemas/DataItemSourceType' + description: The source of this dataset, either `hda`, `ldda`, `hdca`, `dce` + or `dc` depending of its origin. + title: Source + required: + - id + - src + - name + title: EncodedJobParameterHistoryItem + type: object + ExportHistoryArchivePayload: + properties: + directory_uri: + anyOf: + - type: string + - type: 'null' + description: A writable directory destination where the history will be + exported using the `galaxy.files` URI infrastructure. + title: Directory URI + file_name: + anyOf: + - type: string + - type: 'null' + description: The name of the file containing the exported history. + title: File Name + force: + anyOf: + - type: boolean + - type: 'null' + description: Whether to force a rebuild of the history archive. + title: Force Rebuild + gzip: + anyOf: + - type: boolean + - type: 'null' + default: true + description: Whether to export as gzip archive. + title: GZip + include_deleted: + anyOf: + - type: boolean + - type: 'null' + default: false + description: Whether to include deleted datasets in the exported archive. + title: Include Deleted + include_hidden: + anyOf: + - type: boolean + - type: 'null' + default: false + description: Whether to include hidden datasets in the exported archive. + title: Include Hidden + title: ExportHistoryArchivePayload + type: object + ExportObjectMetadata: + properties: + request_data: + $ref: '#/components/schemas/ExportObjectRequestMetadata' + result_data: + anyOf: + - $ref: '#/components/schemas/ExportObjectResultMetadata' + - type: 'null' + required: + - request_data + title: ExportObjectMetadata + type: object + ExportObjectRequestMetadata: + properties: + object_id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Object Id + type: string + object_type: + $ref: '#/components/schemas/ExportObjectType' + payload: + anyOf: + - $ref: '#/components/schemas/WriteStoreToPayload' + - $ref: '#/components/schemas/ShortTermStoreExportPayload' + title: Payload + user_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + title: User Id + required: + - object_id + - object_type + - payload + title: ExportObjectRequestMetadata + type: object + ExportObjectResultMetadata: + properties: + error: + anyOf: + - type: string + - type: 'null' + title: Error + success: + title: Success + type: boolean + required: + - success + title: ExportObjectResultMetadata + type: object + ExportObjectType: + description: Types of objects that can be exported. + enum: + - history + - invocation + title: ExportObjectType + type: string + ExportRecordData: + description: Data of an export record associated with a history that was archived. + properties: + include_deleted: + default: false + description: Include file contents for deleted datasets (if include_files + is True). + title: Include deleted + type: boolean + include_files: + default: true + description: include materialized files in export when available + title: Include Files + type: boolean + include_hidden: + default: false + description: Include file contents for hidden datasets (if include_files + is True). + title: Include hidden + type: boolean + model_store_format: + allOf: + - $ref: '#/components/schemas/ModelStoreFormat' + default: tar.gz + description: format of model store to export + target_uri: + description: Galaxy Files URI to write mode store content to. + title: Target URI + type: string + required: + - target_uri + title: ExportRecordData + type: object + ExportTaskListResponse: + items: + $ref: '#/components/schemas/ObjectExportTaskResponse' + title: ExportTaskListResponse + type: array + ExtraFileEntry: + properties: + class: + allOf: + - $ref: '#/components/schemas/ExtraFilesEntryClass' + description: The class of this entry, either File or Directory. + path: + description: Relative path to the file or directory. + title: Path + type: string + required: + - class + - path + title: ExtraFileEntry + type: object + ExtraFiles: + properties: + fuzzy_root: + anyOf: + - type: boolean + - type: 'null' + default: true + description: Prevent Galaxy from checking for a single file in a directory + and re-interpreting the archive + title: Fuzzy Root + items_from: + anyOf: + - type: string + - type: 'null' + title: Items From + src: + $ref: '#/components/schemas/Src' + required: + - src + title: ExtraFiles + type: object + ExtraFilesEntryClass: + enum: + - Directory + - File + title: ExtraFilesEntryClass + type: string + FavoriteObject: + properties: + object_id: + description: The id of an object the user wants to favorite. + title: Object ID + type: string + required: + - object_id + title: FavoriteObject + type: object + FavoriteObjectType: + const: tools + title: FavoriteObjectType + type: string + FavoriteObjectsSummary: + properties: + tools: + description: The name of the tools the user favored. + items: + type: string + title: Favorite tools + type: array + required: + - tools + title: FavoriteObjectsSummary + type: object + FetchDataPayload: + additionalProperties: true + properties: + history_id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: History Id + type: string + targets: + items: + anyOf: + - $ref: '#/components/schemas/DataElementsTarget' + - $ref: '#/components/schemas/HdcaDataItemsTarget' + - $ref: '#/components/schemas/DataElementsFromTarget' + - $ref: '#/components/schemas/HdcaDataItemsFromTarget' + - $ref: '#/components/schemas/FtpImportTarget' + title: Targets + type: array + required: + - history_id + - targets + title: FetchDataPayload + type: object + FileDataElement: + additionalProperties: false + properties: + MD5: + anyOf: + - type: string + - type: 'null' + title: Md5 + auto_decompress: + default: false + description: Decompress compressed data before sniffing? + title: Auto Decompress + type: boolean + collection_type: + anyOf: + - type: string + - type: 'null' + title: Collection Type + created_from_basename: + anyOf: + - type: string + - type: 'null' + title: Created From Basename + dbkey: + default: '?' + title: Dbkey + type: string + deferred: + default: false + title: Deferred + type: boolean + description: + anyOf: + - type: string + - type: 'null' + title: Description + elements_from: + anyOf: + - $ref: '#/components/schemas/ElementsFromType' + - type: 'null' + ext: + default: auto + title: Ext + type: string + extra_files: + anyOf: + - $ref: '#/components/schemas/ExtraFiles' + - type: 'null' + info: + anyOf: + - type: string + - type: 'null' + title: Info + name: + anyOf: + - type: string + - type: integer + - type: number + - type: boolean + - type: 'null' + title: Name + space_to_tab: + default: false + title: Space To Tab + type: boolean + src: + const: files + title: Src + tags: + anyOf: + - items: + type: string + type: array + - type: 'null' + title: Tags + to_posix_lines: + default: false + title: To Posix Lines + type: boolean + required: + - src + title: FileDataElement + type: object + FileLibraryFolderItem: + properties: + can_manage: + title: Can Manage + type: boolean + create_time: + description: The time and date this item was created. + format: date-time + title: Create Time + type: string + date_uploaded: + format: date-time + title: Date Uploaded + type: string + deleted: + title: Deleted + type: boolean + file_ext: + title: File Ext + type: string + file_size: + title: File Size + type: string + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Id + type: string + is_private: + title: Is Private + type: boolean + is_unrestricted: + title: Is Unrestricted + type: boolean + ldda_id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Ldda Id + type: string + message: + anyOf: + - type: string + - type: 'null' + title: Message + name: + title: Name + type: string + raw_size: + title: Raw Size + type: integer + state: + allOf: + - $ref: '#/components/schemas/DatasetState' + description: The current state of this dataset. + title: State + tags: + $ref: '#/components/schemas/TagCollection' + type: + const: file + title: Type + update_time: + description: The last time and date this item was updated. + format: date-time + title: Update Time + type: string + required: + - name + - type + - create_time + - update_time + - can_manage + - deleted + - id + - file_ext + - date_uploaded + - is_unrestricted + - is_private + - state + - file_size + - raw_size + - ldda_id + - tags + title: FileLibraryFolderItem + type: object + FilesSourcePlugin: + properties: + browsable: + description: Whether this file source plugin can list items. + title: Browsable + type: boolean + doc: + description: Documentation or extended description for this plugin. + examples: + - Galaxy's library import directory + title: Documentation + type: string + id: + description: The `FilesSource` plugin identifier + examples: + - _import + title: ID + type: string + label: + description: The display label for this plugin. + examples: + - Library Import Directory + title: Label + type: string + requires_groups: + anyOf: + - type: string + - type: 'null' + description: Only users belonging to the groups specified here can access + this files source. + title: Requires groups + requires_roles: + anyOf: + - type: string + - type: 'null' + description: Only users with the roles specified here can access this files + source. + title: Requires roles + type: + description: The type of the plugin. + examples: + - gximport + title: Type + type: string + writable: + description: Whether this files source plugin allows write access. + examples: + - false + title: Writeable + type: boolean + required: + - id + - type + - label + - doc + - browsable + - writable + title: FilesSourcePlugin + type: object + FilesSourcePluginList: + default: [] + items: + anyOf: + - $ref: '#/components/schemas/BrowsableFilesSourcePlugin' + - $ref: '#/components/schemas/FilesSourcePlugin' + title: FilesSourcePluginList + type: array + FolderLibraryFolderItem: + properties: + can_manage: + title: Can Manage + type: boolean + can_modify: + title: Can Modify + type: boolean + create_time: + description: The time and date this item was created. + format: date-time + title: Create Time + type: string + deleted: + title: Deleted + type: boolean + description: + anyOf: + - type: string + - type: 'null' + default: '' + description: A detailed description of the library folder. + title: Description + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Id + type: string + name: + title: Name + type: string + type: + const: folder + title: Type + update_time: + description: The last time and date this item was updated. + format: date-time + title: Update Time + type: string + required: + - name + - type + - create_time + - update_time + - can_manage + - deleted + - id + - can_modify + title: FolderLibraryFolderItem + type: object + FtpImportElement: + additionalProperties: false + properties: + MD5: + anyOf: + - type: string + - type: 'null' + title: Md5 + auto_decompress: + default: false + description: Decompress compressed data before sniffing? + title: Auto Decompress + type: boolean + collection_type: + anyOf: + - type: string + - type: 'null' + title: Collection Type + created_from_basename: + anyOf: + - type: string + - type: 'null' + title: Created From Basename + dbkey: + default: '?' + title: Dbkey + type: string + deferred: + default: false + title: Deferred + type: boolean + description: + anyOf: + - type: string + - type: 'null' + title: Description + elements_from: + anyOf: + - $ref: '#/components/schemas/ElementsFromType' + - type: 'null' + ext: + default: auto + title: Ext + type: string + extra_files: + anyOf: + - $ref: '#/components/schemas/ExtraFiles' + - type: 'null' + ftp_path: + title: Ftp Path + type: string + info: + anyOf: + - type: string + - type: 'null' + title: Info + name: + anyOf: + - type: string + - type: integer + - type: number + - type: boolean + - type: 'null' + title: Name + space_to_tab: + default: false + title: Space To Tab + type: boolean + src: + const: ftp_import + title: Src + tags: + anyOf: + - items: + type: string + type: array + - type: 'null' + title: Tags + to_posix_lines: + default: false + title: To Posix Lines + type: boolean + required: + - src + - ftp_path + title: FtpImportElement + type: object + FtpImportTarget: + properties: + auto_decompress: + default: false + description: Decompress compressed data before sniffing? + title: Auto Decompress + type: boolean + collection_type: + anyOf: + - type: string + - type: 'null' + title: Collection Type + destination: + $ref: '#/components/schemas/HdcaDestination' + elements_from: + anyOf: + - $ref: '#/components/schemas/ElementsFromType' + - type: 'null' + ftp_path: + title: Ftp Path + type: string + name: + anyOf: + - type: string + - type: 'null' + title: Name + src: + const: ftp_import + title: Src + tags: + anyOf: + - items: + type: string + type: array + - type: 'null' + title: Tags + required: + - destination + - src + - ftp_path + title: FtpImportTarget + type: object + GroupCreatePayload: + description: Payload schema for creating a group. + properties: + name: + title: name of the group + type: string + role_ids: + default: [] + items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + title: role IDs + type: array + user_ids: + default: [] + items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + title: user IDs + type: array + required: + - name + title: GroupCreatePayload + type: object + GroupListResponse: + description: Response schema for listing groups. + items: + $ref: '#/components/schemas/GroupResponse' + title: GroupListResponse + type: array + GroupModel: + description: User group model + properties: + id: + description: Encoded group ID + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + model_class: + const: Group + description: The name of the database model class. + title: Model class + type: string + name: + description: The name of the group. + title: Name + type: string + required: + - model_class + - id + - name + title: GroupModel + type: object + GroupQuota: + properties: + group: + allOf: + - $ref: '#/components/schemas/GroupModel' + description: Information about a user group associated with a quota. + title: Group + model_class: + const: GroupQuotaAssociation + description: The name of the database model class. + title: Model class + type: string + required: + - model_class + - group + title: GroupQuota + type: object + GroupResponse: + description: Response schema for a group. + properties: + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: group ID + type: string + model_class: + const: Group + description: The name of the database model class. + title: Model class + type: string + name: + title: name of the group + type: string + roles_url: + anyOf: + - type: string + - type: 'null' + title: URL for the roles of the group + url: + title: URL for the group + type: string + users_url: + anyOf: + - type: string + - type: 'null' + title: URL for the users of the group + required: + - model_class + - id + - name + - url + title: GroupResponse + type: object + GroupRoleListResponse: + items: + $ref: '#/components/schemas/GroupRoleResponse' + title: GroupRoleListResponse + type: array + GroupRoleResponse: + properties: + id: + description: Encoded ID of the role + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + name: + description: Name of the role + title: Name + type: string + url: + deprecated: true + description: The relative URL to access this item. + title: URL + type: string + required: + - id + - name + - url + title: GroupRoleResponse + type: object + GroupUserListResponse: + items: + $ref: '#/components/schemas/GroupUserResponse' + title: GroupUserListResponse + type: array + GroupUserResponse: + properties: + email: + description: Email of the user + title: Email + type: string + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Id + type: string + url: + deprecated: true + description: The relative URL to access this item. + title: URL + type: string + required: + - id + - email + - url + title: GroupUserResponse + type: object + HDABasicInfo: + properties: + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Id + type: string + name: + title: Name + type: string + required: + - id + - name + title: HDABasicInfo + type: object + HDADetailed: + additionalProperties: true + description: History Dataset Association detailed information. + properties: + accessible: + description: Whether this item is accessible to the current user due to + permissions. + title: Accessible + type: boolean + annotation: + anyOf: + - type: string + - type: 'null' + description: An annotation to provide details or to help understand the + purpose and usage of this item. + title: Annotation + api_type: + const: file + default: file + deprecated: true + description: TODO + title: API Type + copied_from_ldda_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + title: Copied From Ldda Id + create_time: + anyOf: + - format: date-time + type: string + - type: 'null' + description: The time and date this item was created. + title: Create Time + created_from_basename: + anyOf: + - type: string + - type: 'null' + description: The basename of the output that produced this dataset. + title: Created from basename + creating_job: + description: The encoded ID of the job that created this dataset. + title: Creating Job ID + type: string + data_type: + description: The fully qualified name of the class implementing the data + type of this dataset. + examples: + - galaxy.datatypes.data.Text + title: Data Type + type: string + dataset_id: + description: The encoded ID of the dataset associated with this item. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Dataset ID + type: string + deleted: + description: Whether this item is marked as deleted. + title: Deleted + type: boolean + display_apps: + description: Contains new-style display app urls. + items: + $ref: '#/components/schemas/DisplayApp' + title: Display Applications + type: array + display_types: + description: Contains old-style display app urls. + items: + $ref: '#/components/schemas/DisplayApp' + title: Legacy Display Applications + type: array + download_url: + description: The URL to download this item from the server. + title: Download URL + type: string + extension: + anyOf: + - type: string + - type: 'null' + description: The extension of the dataset. + examples: + - txt + title: Extension + file_ext: + description: The extension of the file. + title: File extension + type: string + file_name: + anyOf: + - type: string + - type: 'null' + description: The full path to the dataset file. + title: File Name + file_size: + description: The file size in bytes. + title: File Size + type: integer + genome_build: + anyOf: + - type: string + - type: 'null' + default: '?' + description: TODO + title: Genome Build + hda_ldda: + allOf: + - $ref: '#/components/schemas/DatasetSourceType' + default: hda + description: Whether this dataset belongs to a history (HDA) or a library + (LDDA). + title: HDA or LDDA + hid: + description: The index position of this item in the History. + title: HID + type: integer + history_content_type: + const: dataset + description: This is always `dataset` for datasets. + title: History Content Type + history_id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: History ID + type: string + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Id + type: string + meta_files: + description: Collection of metadata files associated with this dataset. + items: + $ref: '#/components/schemas/MetadataFile' + title: Metadata Files + type: array + metadata: + anyOf: + - {} + - type: 'null' + description: The metadata associated with this dataset. + title: Metadata + metadata_data_lines: + default: 0 + description: TODO + title: Metadata Data Lines + type: integer + metadata_dbkey: + anyOf: + - type: string + - type: 'null' + default: '?' + description: TODO + title: Metadata DBKey + misc_blurb: + anyOf: + - type: string + - type: 'null' + description: TODO + title: Miscellaneous Blurb + misc_info: + anyOf: + - type: string + - type: 'null' + description: TODO + title: Miscellaneous Information + model_class: + const: HistoryDatasetAssociation + description: The name of the database model class. + title: Model class + type: string + name: + anyOf: + - type: string + - type: 'null' + description: The name of the item. + title: Name + peek: + anyOf: + - type: string + - type: 'null' + description: A few lines of contents from the start of the file. + title: Peek + permissions: + allOf: + - $ref: '#/components/schemas/DatasetPermissions' + description: Role-based access and manage control permissions for the dataset. + title: Permissions + purged: + description: Whether this dataset has been removed from disk. + title: Purged + type: boolean + rerunnable: + description: Whether the job creating this dataset can be run again. + title: Rerunnable + type: boolean + resubmitted: + description: Whether the job creating this dataset has been resubmitted. + title: Resubmitted + type: boolean + state: + allOf: + - $ref: '#/components/schemas/DatasetState' + description: The current state of this dataset. + title: State + tags: + $ref: '#/components/schemas/TagCollection' + type: + const: file + default: file + description: This is always `file` for datasets. + title: Type + type_id: + anyOf: + - type: string + - type: 'null' + description: The type and the encoded ID of this item. Used for caching. + examples: + - dataset-616e371b2cc6c62e + title: Type - ID + update_time: + anyOf: + - format: date-time + type: string + - type: 'null' + description: The last time and date this item was updated. + title: Update Time + url: + deprecated: true + description: The relative URL to access this item. + title: URL + type: string + uuid: + description: Universal unique identifier for this dataset. + format: uuid4 + title: UUID + type: string + validated_state: + allOf: + - $ref: '#/components/schemas/DatasetValidatedState' + description: The state of the datatype validation for this dataset. + title: Validated State + validated_state_message: + anyOf: + - type: string + - type: 'null' + description: The message with details about the datatype validation result + for this dataset. + title: Validated State Message + visible: + description: Whether this item is visible or hidden to the user by default. + title: Visible + type: boolean + visualizations: + description: The collection of visualizations that can be applied to this + dataset. + items: + $ref: '#/components/schemas/Visualization' + title: Visualizations + type: array + required: + - model_class + - id + - name + - history_id + - hid + - deleted + - visible + - create_time + - update_time + - url + - tags + - history_content_type + - dataset_id + - state + - extension + - purged + - accessible + - file_ext + - file_size + - resubmitted + - meta_files + - data_type + - creating_job + - rerunnable + - uuid + - permissions + - display_apps + - display_types + - visualizations + - validated_state + - annotation + - download_url + title: HDADetailed + type: object + HDAObject: + additionalProperties: true + description: History Dataset Association Object + properties: + copied_from_ldda_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + title: Copied From Ldda Id + hda_ldda: + allOf: + - $ref: '#/components/schemas/DatasetSourceType' + default: hda + description: Whether this dataset belongs to a history (HDA) or a library + (LDDA). + title: HDA or LDDA + history_id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: History ID + type: string + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: History Dataset Association ID + type: string + model_class: + const: HistoryDatasetAssociation + description: The name of the database model class. + title: Model class + type: string + state: + allOf: + - $ref: '#/components/schemas/DatasetState' + description: The current state of this dataset. + title: State + tags: + items: + type: string + title: Tags + type: array + required: + - model_class + - id + - state + - history_id + - tags + title: HDAObject + type: object + HDASummary: + additionalProperties: true + description: History Dataset Association summary information. + properties: + copied_from_ldda_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + title: Copied From Ldda Id + create_time: + anyOf: + - format: date-time + type: string + - type: 'null' + description: The time and date this item was created. + title: Create Time + dataset_id: + description: The encoded ID of the dataset associated with this item. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Dataset ID + type: string + deleted: + description: Whether this item is marked as deleted. + title: Deleted + type: boolean + extension: + anyOf: + - type: string + - type: 'null' + description: The extension of the dataset. + examples: + - txt + title: Extension + hid: + description: The index position of this item in the History. + title: HID + type: integer + history_content_type: + const: dataset + description: This is always `dataset` for datasets. + title: History Content Type + history_id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: History ID + type: string + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Id + type: string + name: + anyOf: + - type: string + - type: 'null' + description: The name of the item. + title: Name + purged: + description: Whether this dataset has been removed from disk. + title: Purged + type: boolean + state: + allOf: + - $ref: '#/components/schemas/DatasetState' + description: The current state of this dataset. + title: State + tags: + $ref: '#/components/schemas/TagCollection' + type: + description: The type of this item. + title: Type + type: string + type_id: + anyOf: + - type: string + - type: 'null' + description: The type and the encoded ID of this item. Used for caching. + examples: + - dataset-616e371b2cc6c62e + title: Type - ID + update_time: + anyOf: + - format: date-time + type: string + - type: 'null' + description: The last time and date this item was updated. + title: Update Time + url: + deprecated: true + description: The relative URL to access this item. + title: URL + type: string + visible: + description: Whether this item is visible or hidden to the user by default. + title: Visible + type: boolean + required: + - id + - name + - history_id + - hid + - deleted + - visible + - type + - create_time + - update_time + - url + - tags + - history_content_type + - dataset_id + - state + - extension + - purged + title: HDASummary + type: object + HDCADetailed: + additionalProperties: true + description: History Dataset Collection Association detailed information. + properties: + collection_id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Dataset Collection ID + type: string + collection_type: + description: The type of the collection, can be `list`, `paired`, or define + subcollections using `:` as separator like `list:paired` or `list:list`. + title: Collection Type + type: string + contents_url: + description: The relative URL to access the contents of this History. + title: Contents URL + type: string + create_time: + anyOf: + - format: date-time + type: string + - type: 'null' + description: The time and date this item was created. + title: Create Time + deleted: + description: Whether this item is marked as deleted. + title: Deleted + type: boolean + element_count: + anyOf: + - type: integer + - type: 'null' + description: The number of elements contained in the dataset collection. + It may be None or undefined if the collection could not be populated. + title: Element Count + elements: + default: [] + description: The summary information of each of the elements inside the + dataset collection. + items: + $ref: '#/components/schemas/DCESummary' + title: Elements + type: array + elements_datatypes: + description: A set containing all the different element datatypes in the + collection. + items: + type: string + title: Elements Datatypes + type: array + uniqueItems: true + hid: + description: The index position of this item in the History. + title: HID + type: integer + history_content_type: + const: dataset_collection + description: This is always `dataset_collection` for dataset collections. + title: History Content Type + history_id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: History ID + type: string + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Id + type: string + implicit_collection_jobs_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: Encoded ID for the ICJ object describing the collection of + jobs corresponding to this collection + title: Implicit Collection Jobs Id + job_source_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: The encoded ID of the Job that produced this dataset collection. + Used to track the state of the job. + title: Job Source ID + job_source_type: + anyOf: + - $ref: '#/components/schemas/JobSourceType' + - type: 'null' + description: The type of job (model class) that produced this dataset collection. + Used to track the state of the job. + title: Job Source Type + job_state_summary: + anyOf: + - $ref: '#/components/schemas/HDCJobStateSummary' + - type: 'null' + description: Overview of the job states working inside the dataset collection. + title: Job State Summary + model_class: + const: HistoryDatasetCollectionAssociation + description: The name of the database model class. + title: Model class + type: string + name: + anyOf: + - type: string + - type: 'null' + description: The name of the item. + title: Name + populated: + description: Whether the dataset collection elements (and any subcollections + elements) were successfully populated. + title: Populated + type: boolean + populated_state: + allOf: + - $ref: '#/components/schemas/DatasetCollectionPopulatedState' + description: 'Indicates the general state of the elements in the dataset + collection:- ''new'': new dataset collection, unpopulated elements.- ''ok'': + collection elements populated (HDAs may or may not have errors).- ''failed'': + some problem populating, won''t be populated.' + title: Populated State + populated_state_message: + anyOf: + - type: string + - type: 'null' + description: Optional message with further information in case the population + of the dataset collection failed. + title: Populated State Message + tags: + $ref: '#/components/schemas/TagCollection' + type: + const: collection + default: collection + description: This is always `collection` for dataset collections. + title: Type + type_id: + anyOf: + - type: string + - type: 'null' + description: The type and the encoded ID of this item. Used for caching. + examples: + - dataset-616e371b2cc6c62e + title: Type - ID + update_time: + anyOf: + - format: date-time + type: string + - type: 'null' + description: The last time and date this item was updated. + title: Update Time + url: + deprecated: true + description: The relative URL to access this item. + title: URL + type: string + visible: + description: Whether this item is visible or hidden to the user by default. + title: Visible + type: boolean + required: + - model_class + - id + - name + - history_id + - hid + - deleted + - visible + - create_time + - update_time + - url + - tags + - history_content_type + - collection_type + - populated_state + - contents_url + - collection_id + - elements_datatypes + title: HDCADetailed + type: object + HDCASummary: + additionalProperties: true + description: History Dataset Collection Association summary information. + properties: + collection_id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Dataset Collection ID + type: string + collection_type: + description: The type of the collection, can be `list`, `paired`, or define + subcollections using `:` as separator like `list:paired` or `list:list`. + title: Collection Type + type: string + contents_url: + description: The relative URL to access the contents of this History. + title: Contents URL + type: string + create_time: + anyOf: + - format: date-time + type: string + - type: 'null' + description: The time and date this item was created. + title: Create Time + deleted: + description: Whether this item is marked as deleted. + title: Deleted + type: boolean + element_count: + anyOf: + - type: integer + - type: 'null' + description: The number of elements contained in the dataset collection. + It may be None or undefined if the collection could not be populated. + title: Element Count + hid: + description: The index position of this item in the History. + title: HID + type: integer + history_content_type: + const: dataset_collection + description: This is always `dataset_collection` for dataset collections. + title: History Content Type + history_id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: History ID + type: string + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Id + type: string + job_source_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: The encoded ID of the Job that produced this dataset collection. + Used to track the state of the job. + title: Job Source ID + job_source_type: + anyOf: + - $ref: '#/components/schemas/JobSourceType' + - type: 'null' + description: The type of job (model class) that produced this dataset collection. + Used to track the state of the job. + title: Job Source Type + job_state_summary: + anyOf: + - $ref: '#/components/schemas/HDCJobStateSummary' + - type: 'null' + description: Overview of the job states working inside the dataset collection. + title: Job State Summary + model_class: + const: HistoryDatasetCollectionAssociation + description: The name of the database model class. + title: Model class + type: string + name: + anyOf: + - type: string + - type: 'null' + description: The name of the item. + title: Name + populated_state: + allOf: + - $ref: '#/components/schemas/DatasetCollectionPopulatedState' + description: 'Indicates the general state of the elements in the dataset + collection:- ''new'': new dataset collection, unpopulated elements.- ''ok'': + collection elements populated (HDAs may or may not have errors).- ''failed'': + some problem populating, won''t be populated.' + title: Populated State + populated_state_message: + anyOf: + - type: string + - type: 'null' + description: Optional message with further information in case the population + of the dataset collection failed. + title: Populated State Message + tags: + $ref: '#/components/schemas/TagCollection' + type: + const: collection + default: collection + description: This is always `collection` for dataset collections. + title: Type + type_id: + anyOf: + - type: string + - type: 'null' + description: The type and the encoded ID of this item. Used for caching. + examples: + - dataset-616e371b2cc6c62e + title: Type - ID + update_time: + anyOf: + - format: date-time + type: string + - type: 'null' + description: The last time and date this item was updated. + title: Update Time + url: + deprecated: true + description: The relative URL to access this item. + title: URL + type: string + visible: + description: Whether this item is visible or hidden to the user by default. + title: Visible + type: boolean + required: + - model_class + - id + - name + - history_id + - hid + - deleted + - visible + - create_time + - update_time + - url + - tags + - history_content_type + - collection_type + - populated_state + - contents_url + - collection_id + title: HDCASummary + type: object + HDCJobStateSummary: + description: Overview of the job states working inside a dataset collection. + properties: + all_jobs: + default: 0 + description: Total number of jobs associated with a dataset collection. + title: All jobs + type: integer + deleted: + default: 0 + description: Number of jobs in the `deleted` state. + title: Deleted jobs + type: integer + deleted_new: + default: 0 + description: Number of jobs in the `deleted_new` state. + title: Deleted new jobs + type: integer + error: + default: 0 + description: Number of jobs in the `error` state. + title: Jobs with errors + type: integer + failed: + default: 0 + description: Number of jobs in the `failed` state. + title: Failed jobs + type: integer + new: + default: 0 + description: Number of jobs in the `new` state. + title: New jobs + type: integer + ok: + default: 0 + description: Number of jobs in the `ok` state. + title: OK jobs + type: integer + paused: + default: 0 + description: Number of jobs in the `paused` state. + title: Paused jobs + type: integer + queued: + default: 0 + description: Number of jobs in the `queued` state. + title: Queued jobs + type: integer + resubmitted: + default: 0 + description: Number of jobs in the `resubmitted` state. + title: Resubmitted jobs + type: integer + running: + default: 0 + description: Number of jobs in the `running` state. + title: Running jobs + type: integer + skipped: + default: 0 + description: Number of jobs that were skipped due to conditional workflow + step execution. + title: Skipped jobs + type: integer + upload: + default: 0 + description: Number of jobs in the `upload` state. + title: Upload jobs + type: integer + waiting: + default: 0 + description: Number of jobs in the `waiting` state. + title: Waiting jobs + type: integer + title: HDCJobStateSummary + type: object + HTTPValidationError: + properties: + detail: + items: + $ref: '#/components/schemas/ValidationError' + title: Detail + type: array + title: HTTPValidationError + type: object + HashFunctionNameEnum: + description: Particular pieces of information that can be requested for a dataset. + enum: + - MD5 + - SHA-1 + - SHA-256 + - SHA-512 + title: HashFunctionNameEnum + type: string + HdaDestination: + properties: + type: + const: hdas + title: Type + required: + - type + title: HdaDestination + type: object + HdcaDataItemsFromTarget: + properties: + auto_decompress: + default: false + description: Decompress compressed data before sniffing? + title: Auto Decompress + type: boolean + collection_type: + anyOf: + - type: string + - type: 'null' + title: Collection Type + destination: + $ref: '#/components/schemas/HdcaDestination' + elements_from: + $ref: '#/components/schemas/ElementsFromType' + ftp_path: + anyOf: + - type: string + - type: 'null' + title: Ftp Path + name: + anyOf: + - type: string + - type: 'null' + title: Name + path: + anyOf: + - type: string + - type: 'null' + title: Path + server_dir: + anyOf: + - type: string + - type: 'null' + title: Server Dir + src: + $ref: '#/components/schemas/ItemsFromSrc' + tags: + anyOf: + - items: + type: string + type: array + - type: 'null' + title: Tags + url: + anyOf: + - type: string + - type: 'null' + title: Url + required: + - src + - destination + - elements_from + title: HdcaDataItemsFromTarget + type: object + HdcaDataItemsTarget: + properties: + auto_decompress: + default: false + description: Decompress compressed data before sniffing? + title: Auto Decompress + type: boolean + collection_type: + anyOf: + - type: string + - type: 'null' + title: Collection Type + destination: + $ref: '#/components/schemas/HdcaDestination' + elements: + items: + anyOf: + - discriminator: + mapping: + composite: '#/components/schemas/CompositeDataElement' + files: '#/components/schemas/FileDataElement' + ftp_import: '#/components/schemas/FtpImportElement' + pasted: '#/components/schemas/PastedDataElement' + path: '#/components/schemas/PathDataElement' + server_dir: '#/components/schemas/ServerDirElement' + url: '#/components/schemas/UrlDataElement' + propertyName: src + oneOf: + - $ref: '#/components/schemas/FileDataElement' + - $ref: '#/components/schemas/PastedDataElement' + - $ref: '#/components/schemas/UrlDataElement' + - $ref: '#/components/schemas/PathDataElement' + - $ref: '#/components/schemas/ServerDirElement' + - $ref: '#/components/schemas/FtpImportElement' + - $ref: '#/components/schemas/CompositeDataElement' + - $ref: '#/components/schemas/NestedElement' + title: Elements + type: array + name: + anyOf: + - type: string + - type: 'null' + title: Name + tags: + anyOf: + - items: + type: string + type: array + - type: 'null' + title: Tags + required: + - destination + - elements + title: HdcaDataItemsTarget + type: object + HdcaDestination: + properties: + type: + const: hdca + title: Type + required: + - type + title: HdcaDestination + type: object + HelpForumCategory: + additionalProperties: true + description: Model for a category in the help forum. + properties: {} + title: HelpForumCategory + type: object + HelpForumGroup: + additionalProperties: true + description: Model for a group in the help forum. + properties: {} + title: HelpForumGroup + type: object + HelpForumGroupedSearchResult: + additionalProperties: true + description: Model for a grouped search result. + properties: {} + title: HelpForumGroupedSearchResult + type: object + HelpForumPost: + additionalProperties: true + description: Model for a post in the help forum. + properties: + avatar_template: + description: The avatar template of the user. + title: Avatar Template + type: string + blurb: + description: The blurb of the post. + title: Blurb + type: string + created_at: + description: The creation date of the post. + title: Created At + type: string + id: + description: The ID of the post. + title: Id + type: integer + like_count: + description: The number of likes of the post. + title: Like Count + type: integer + name: + description: The name of the post. + title: Name + type: string + post_number: + description: The post number of the post. + title: Post Number + type: integer + topic_id: + description: The ID of the topic of the post. + title: Topic Id + type: integer + username: + description: The username of the post author. + title: Username + type: string + required: + - id + - name + - username + - avatar_template + - created_at + - like_count + - blurb + - post_number + - topic_id + title: HelpForumPost + type: object + HelpForumSearchResponse: + description: 'Response model for the help search API endpoint. + + + This model is based on the Discourse API response for the search endpoint.' + properties: + categories: + anyOf: + - items: + $ref: '#/components/schemas/HelpForumCategory' + type: array + - type: 'null' + title: Categories + grouped_search_result: + anyOf: + - $ref: '#/components/schemas/HelpForumGroupedSearchResult' + - type: 'null' + groups: + anyOf: + - items: + $ref: '#/components/schemas/HelpForumGroup' + type: array + - type: 'null' + title: Groups + posts: + anyOf: + - items: + $ref: '#/components/schemas/HelpForumPost' + type: array + - type: 'null' + title: Posts + tags: + anyOf: + - items: + $ref: '#/components/schemas/HelpForumTag' + type: array + - type: 'null' + title: Tags + topics: + anyOf: + - items: + $ref: '#/components/schemas/HelpForumTopic' + type: array + - type: 'null' + title: Topics + users: + anyOf: + - items: + $ref: '#/components/schemas/HelpForumUser' + type: array + - type: 'null' + title: Users + required: + - posts + - topics + - users + - categories + - tags + - groups + - grouped_search_result + title: HelpForumSearchResponse + type: object + HelpForumTag: + additionalProperties: true + description: Model for a tag in the help forum. + properties: {} + title: HelpForumTag + type: object + HelpForumTopic: + description: Model for a topic in the help forum compatible with Discourse API. + properties: + archetype: + description: The archetype of the topic. + title: Archetype + archived: + description: Whether the topic is archived. + title: Archived + type: boolean + bookmarked: + anyOf: + - type: boolean + - type: 'null' + description: Whether the topic is bookmarked. + title: Bookmarked + bumped: + description: Whether the topic was bumped. + title: Bumped + type: boolean + bumped_at: + description: The date of the last bump of the topic. + title: Bumped At + type: string + category_id: + description: The ID of the category of the topic. + title: Category Id + type: integer + closed: + description: Whether the topic is closed. + title: Closed + type: boolean + created_at: + description: The creation date of the topic. + title: Created At + type: string + fancy_title: + description: The fancy title of the topic. + title: Fancy Title + type: string + has_accepted_answer: + description: Whether the topic has an accepted answer. + title: Has Accepted Answer + type: boolean + highest_post_number: + description: The highest post number in the topic. + title: Highest Post Number + type: integer + id: + description: The ID of the topic. + title: Id + type: integer + last_posted_at: + description: The date of the last post in the topic. + title: Last Posted At + type: string + liked: + anyOf: + - type: boolean + - type: 'null' + description: Whether the topic is liked. + title: Liked + pinned: + description: Whether the topic is pinned. + title: Pinned + type: boolean + posts_count: + description: The number of posts in the topic. + title: Posts Count + type: integer + reply_count: + description: The number of replies in the topic. + title: Reply Count + type: integer + slug: + description: The slug of the topic. + title: Slug + type: string + tags: + description: The tags of the topic. + items: + type: string + title: Tags + type: array + tags_descriptions: + anyOf: + - {} + - type: 'null' + description: The descriptions of the tags of the topic. + title: Tags Descriptions + title: + description: The title of the topic. + title: Title + type: string + unpinned: + anyOf: + - type: boolean + - type: 'null' + description: Whether the topic is unpinned. + title: Unpinned + unseen: + description: Whether the topic is unseen. + title: Unseen + type: boolean + visible: + description: Whether the topic is visible. + title: Visible + type: boolean + required: + - id + - title + - fancy_title + - slug + - posts_count + - reply_count + - highest_post_number + - created_at + - last_posted_at + - bumped + - bumped_at + - archetype + - unseen + - pinned + - unpinned + - visible + - closed + - archived + - bookmarked + - liked + - tags + - tags_descriptions + - category_id + - has_accepted_answer + title: HelpForumTopic + type: object + HelpForumUser: + additionalProperties: true + description: Model for a user in the help forum. + properties: {} + title: HelpForumUser + type: object + HistoryContentBulkOperationPayload: + properties: + items: + anyOf: + - items: + $ref: '#/components/schemas/HistoryContentItem' + type: array + - type: 'null' + title: Items + operation: + $ref: '#/components/schemas/HistoryContentItemOperation' + params: + anyOf: + - $ref: '#/components/schemas/ChangeDatatypeOperationParams' + - $ref: '#/components/schemas/ChangeDbkeyOperationParams' + - $ref: '#/components/schemas/TagOperationParams' + - type: 'null' + title: Params + required: + - operation + title: HistoryContentBulkOperationPayload + type: object + HistoryContentBulkOperationResult: + properties: + errors: + items: + $ref: '#/components/schemas/BulkOperationItemError' + title: Errors + type: array + success_count: + title: Success Count + type: integer + required: + - success_count + - errors + title: HistoryContentBulkOperationResult + type: object + HistoryContentItem: + properties: + history_content_type: + allOf: + - $ref: '#/components/schemas/HistoryContentType' + description: The type of this item. + title: Content Type + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Id + type: string + required: + - history_content_type + - id + title: HistoryContentItem + type: object + HistoryContentItemOperation: + enum: + - hide + - unhide + - delete + - undelete + - purge + - change_datatype + - change_dbkey + - add_tags + - remove_tags + title: HistoryContentItemOperation + type: string + HistoryContentSource: + enum: + - hda + - hdca + - library + - library_folder + - new_collection + title: HistoryContentSource + type: string + HistoryContentStats: + properties: + total_matches: + description: The total number of items that match the search query without + any pagination + title: Total Matches + type: integer + required: + - total_matches + title: HistoryContentStats + type: object + HistoryContentType: + description: Available types of History contents. + enum: + - dataset + - dataset_collection + title: HistoryContentType + type: string + HistoryContentsResult: + description: 'List of history content items. + + Can contain different views and kinds of items.' + items: + anyOf: + - $ref: '#/components/schemas/HDADetailed' + - $ref: '#/components/schemas/HDASummary' + - $ref: '#/components/schemas/HDCADetailed' + - $ref: '#/components/schemas/HDCASummary' + - $ref: '#/components/schemas/CustomHistoryItem' + title: HistoryContentsResult + type: array + HistoryContentsWithStatsResult: + description: Includes stats with items counting + properties: + contents: + description: The items matching the search query. Only the items fitting + in the current page limit will be returned. + items: + anyOf: + - $ref: '#/components/schemas/HDADetailed' + - $ref: '#/components/schemas/HDASummary' + - $ref: '#/components/schemas/HDCADetailed' + - $ref: '#/components/schemas/HDCASummary' + - $ref: '#/components/schemas/CustomHistoryItem' + title: Contents + type: array + stats: + allOf: + - $ref: '#/components/schemas/HistoryContentStats' + description: Contains counting stats for the query. + title: Stats + required: + - stats + - contents + title: HistoryContentsWithStatsResult + type: object + HistoryDetailed: + additionalProperties: true + description: History detailed information. + properties: + annotation: + anyOf: + - type: string + - type: 'null' + description: An annotation to provide details or to help understand the + purpose and usage of this item. + title: Annotation + archived: + description: Whether this item has been archived and is no longer active. + title: Archived + type: boolean + contents_url: + description: The relative URL to access the contents of this History. + title: Contents URL + type: string + count: + description: The number of items in the history. + title: Count + type: integer + create_time: + description: The time and date this item was created. + format: date-time + title: Create Time + type: string + deleted: + description: Whether this item is marked as deleted. + title: Deleted + type: boolean + genome_build: + anyOf: + - type: string + - type: 'null' + default: '?' + description: TODO + title: Genome Build + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: History ID + type: string + importable: + description: Whether this History can be imported by other users with a + shared link. + title: Importable + type: boolean + model_class: + const: History + description: The name of the database model class. + title: Model class + type: string + name: + description: The name of the history. + title: Name + type: string + preferred_object_store_id: + anyOf: + - type: string + - type: 'null' + description: The ID of the object store that should be used to store new + datasets in this history. + title: Preferred Object Store ID + published: + description: Whether this resource is currently publicly available to all + users. + title: Published + type: boolean + purged: + description: Whether this item has been permanently removed. + title: Purged + type: boolean + size: + description: The total size of the contents of this history in bytes. + title: Size + type: integer + slug: + anyOf: + - type: string + - type: 'null' + description: Part of the URL to uniquely identify this History by link in + a readable way. + title: Slug + state: + allOf: + - $ref: '#/components/schemas/DatasetState' + description: The current state of the History based on the states of the + datasets it contains. + title: State + state_details: + additionalProperties: + type: integer + description: A dictionary keyed to possible dataset states and valued with + the number of datasets in this history that have those states. + title: State Counts + type: object + state_ids: + additionalProperties: + items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + type: array + description: A dictionary keyed to possible dataset states and valued with + lists containing the ids of each HDA in that state. + title: State IDs + type: object + tags: + $ref: '#/components/schemas/TagCollection' + update_time: + description: The last time and date this item was updated. + format: date-time + title: Update Time + type: string + url: + deprecated: true + description: The relative URL to access this item. + title: URL + type: string + user_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: The encoded ID of the user that owns this History. + title: User ID + username: + anyOf: + - type: string + - type: 'null' + description: Owner of the history + title: Username + username_and_slug: + anyOf: + - type: string + - type: 'null' + description: The relative URL in the form of /u/{username}/h/{slug} + title: Username and slug + required: + - model_class + - id + - name + - deleted + - purged + - archived + - url + - published + - count + - annotation + - tags + - update_time + - contents_url + - size + - create_time + - importable + - state + - state_ids + - state_details + title: HistoryDetailed + type: object + HistoryMinimal: + additionalProperties: true + description: Minimal History Response with optional fields + properties: + id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + title: Id + model_class: + const: History + description: The name of the database model class. + title: Model class + type: string + user_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: The encoded ID of the user that owns this History. + title: User ID + required: + - model_class + title: HistoryMinimal + type: object + HistorySummary: + additionalProperties: true + description: History summary information. + properties: + annotation: + anyOf: + - type: string + - type: 'null' + description: An annotation to provide details or to help understand the + purpose and usage of this item. + title: Annotation + archived: + description: Whether this item has been archived and is no longer active. + title: Archived + type: boolean + count: + description: The number of items in the history. + title: Count + type: integer + deleted: + description: Whether this item is marked as deleted. + title: Deleted + type: boolean + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: History ID + type: string + model_class: + const: History + description: The name of the database model class. + title: Model class + type: string + name: + description: The name of the history. + title: Name + type: string + preferred_object_store_id: + anyOf: + - type: string + - type: 'null' + description: The ID of the object store that should be used to store new + datasets in this history. + title: Preferred Object Store ID + published: + description: Whether this resource is currently publicly available to all + users. + title: Published + type: boolean + purged: + description: Whether this item has been permanently removed. + title: Purged + type: boolean + tags: + $ref: '#/components/schemas/TagCollection' + update_time: + description: The last time and date this item was updated. + format: date-time + title: Update Time + type: string + url: + deprecated: true + description: The relative URL to access this item. + title: URL + type: string + required: + - model_class + - id + - name + - deleted + - purged + - archived + - url + - published + - count + - annotation + - tags + - update_time + title: HistorySummary + type: object + Hyperlink: + description: Represents some text with an Hyperlink. + properties: + href: + description: Specifies the linked document, resource, or location. + format: uri + minLength: 1 + title: HRef + type: string + target: + description: Specifies where to open the linked document. + examples: + - _blank + title: Target + type: string + text: + description: The text placeholder for the link. + title: Text + type: string + required: + - target + - href + - text + title: Hyperlink + type: object + ImplicitCollectionJobsStateSummary: + properties: + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Id + type: string + model: + const: ImplicitCollectionJobs + description: The name of the database model class. + title: Model class + type: string + populated_state: + allOf: + - $ref: '#/components/schemas/DatasetCollectionPopulatedState' + description: 'Indicates the general state of the elements in the dataset + collection:- ''new'': new dataset collection, unpopulated elements.- ''ok'': + collection elements populated (HDAs may or may not have errors).- ''failed'': + some problem populating, won''t be populated.' + title: Populated State + states: + additionalProperties: + type: integer + default: {} + description: A dictionary of job states and the number of jobs in that state. + title: States + type: object + required: + - id + - populated_state + - model + title: ImplicitCollectionJobsStateSummary + type: object + ImportToolDataBundle: + properties: + source: + discriminator: + mapping: + hda: '#/components/schemas/ImportToolDataBundleDatasetSource' + ldda: '#/components/schemas/ImportToolDataBundleDatasetSource' + uri: '#/components/schemas/ImportToolDataBundleUriSource' + propertyName: src + oneOf: + - $ref: '#/components/schemas/ImportToolDataBundleDatasetSource' + - $ref: '#/components/schemas/ImportToolDataBundleUriSource' + title: Source + required: + - source + title: ImportToolDataBundle + type: object + ImportToolDataBundleDatasetSource: + properties: + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Id + type: string + src: + description: Indicates that the tool data should be resolved from a dataset. + enum: + - hda + - ldda + title: src + type: string + required: + - src + - id + title: ImportToolDataBundleDatasetSource + type: object + ImportToolDataBundleUriSource: + properties: + src: + const: uri + description: Indicates that the tool data should be resolved by a URI. + title: src + uri: + description: URI to fetch tool data bundle from (file:// URIs are fine because + this is an admin-only operation) + title: uri + type: string + required: + - src + - uri + title: ImportToolDataBundleUriSource + type: object + InputArguments: + properties: + dbkey: + anyOf: + - type: string + - type: 'null' + default: '?' + description: Sets the database key of the objects being fetched to Galaxy. + title: Database Key + file_type: + anyOf: + - type: string + - type: 'null' + default: auto + description: 'Sets the Galaxy datatype (e.g., `bam`) for the objects being + fetched to Galaxy. See the following link for a complete list of Galaxy + data types: https://galaxyproject.org/learn/datatypes/.' + title: File Type + space_to_tab: + anyOf: + - type: boolean + - type: 'null' + default: false + description: A boolean value ('true' or 'false') that sets if spaces should + be converted to tab in the objects being fetched to Galaxy. Applicable + only if `to_posix_lines` is True + title: Spaces to tabs + to_posix_lines: + anyOf: + - const: 'Yes' + - type: boolean + - type: 'null' + default: 'Yes' + description: A boolean value ('true' or 'false'); if 'Yes', converts universal + line endings to POSIX line endings. Set to 'False' if you upload a gzip, + bz2 or zip archive containing a binary file. + title: POSIX line endings + title: InputArguments + type: object + InstalledRepositoryToolShedStatus: + properties: + latest_installable_revision: + anyOf: + - type: string + - type: 'null' + description: Most recent version available on the tool shed + title: Latest installed revision + repository_deprecated: + anyOf: + - type: string + - type: 'null' + description: Repository has been depreciated on the tool shed + title: Repository deprecated + revision_update: + title: Revision Update + type: string + revision_upgrade: + anyOf: + - type: string + - type: 'null' + title: Revision Upgrade + required: + - latest_installable_revision + - revision_update + - repository_deprecated + title: InstalledRepositoryToolShedStatus + type: object + InstalledToolShedRepository: + properties: + changeset_revision: + description: Changeset revision of the repository - a mercurial commit hash + title: Changeset revision + type: string + ctx_rev: + anyOf: + - type: string + - type: 'null' + description: The linearized 0-based index of the changeset on the tool shed + (0, 1, 2,...) + title: Changeset revision number + deleted: + title: Deleted + type: boolean + dist_to_shed: + title: Dist To Shed + type: boolean + error_message: + default: Installation error message, the empty string means no error was + recorded + title: Error Message + type: string + id: + description: Encoded ID of the install tool shed repository. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + installed_changeset_revision: + description: Initially installed changeset revision. Used to construct path + to repository within Galaxies filesystem. Does not change if a repository + is updated. + title: Installed changeset revision + type: string + model_class: + const: ToolShedRepository + description: The name of the database model class. + title: Model class + type: string + name: + description: Name of repository + title: Name + type: string + owner: + description: Owner of repository + title: Owner + type: string + status: + title: Status + type: string + tool_shed: + description: Hostname of the tool shed this was installed from + title: Tool shed + type: string + tool_shed_status: + anyOf: + - $ref: '#/components/schemas/InstalledRepositoryToolShedStatus' + - type: 'null' + title: Latest updated status from the tool shed + uninstalled: + title: Uninstalled + type: boolean + required: + - model_class + - id + - status + - name + - owner + - deleted + - ctx_rev + - installed_changeset_revision + - tool_shed + - dist_to_shed + - uninstalled + - changeset_revision + - tool_shed_status + title: InstalledToolShedRepository + type: object + InvocationCancellationHistoryDeletedResponse: + properties: + history_id: + description: History ID of history that was deleted. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: History ID + type: string + reason: + const: history_deleted + title: Reason + required: + - reason + - history_id + title: InvocationCancellationHistoryDeletedResponse + type: object + InvocationCancellationReviewFailedResponse: + properties: + reason: + const: cancelled_on_review + title: Reason + workflow_step_id: + description: Workflow step id of paused step that did not pass review. + title: Workflow Step Id + type: integer + required: + - reason + - workflow_step_id + title: InvocationCancellationReviewFailedResponse + type: object + InvocationCancellationUserRequestResponse: + properties: + reason: + const: user_request + title: Reason + required: + - reason + title: InvocationCancellationUserRequestResponse + type: object + InvocationEvaluationWarningWorkflowOutputNotFoundResponse: + properties: + output_name: + description: Output that was designated as workflow output but that has + not been found + title: Output Name + type: string + reason: + const: workflow_output_not_found + title: Reason + workflow_step_id: + title: Workflow step id of step that caused a warning. + type: integer + required: + - reason + - workflow_step_id + - output_name + title: InvocationEvaluationWarningWorkflowOutputNotFoundResponse + type: object + InvocationFailureCollectionFailedResponse: + properties: + dependent_workflow_step_id: + description: Workflow step id of step that caused failure. + title: Dependent Workflow Step Id + type: integer + hdca_id: + description: HistoryDatasetCollectionAssociation ID that relates to failure. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: HistoryDatasetCollectionAssociation ID + type: string + reason: + const: collection_failed + title: Reason + workflow_step_id: + description: Workflow step id of step that failed. + title: Workflow Step Id + type: integer + required: + - reason + - workflow_step_id + - hdca_id + - dependent_workflow_step_id + title: InvocationFailureCollectionFailedResponse + type: object + InvocationFailureDatasetFailedResponse: + properties: + dependent_workflow_step_id: + anyOf: + - type: integer + - type: 'null' + description: Workflow step id of step that caused failure. + title: Dependent Workflow Step Id + hda_id: + description: HistoryDatasetAssociation ID that relates to failure. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: HistoryDatasetAssociation ID + type: string + reason: + const: dataset_failed + title: Reason + workflow_step_id: + description: Workflow step id of step that failed. + title: Workflow Step Id + type: integer + required: + - reason + - workflow_step_id + - hda_id + title: InvocationFailureDatasetFailedResponse + type: object + InvocationFailureExpressionEvaluationFailedResponse: + properties: + details: + anyOf: + - type: string + - type: 'null' + description: May contain details to help troubleshoot this problem. + title: Details + reason: + const: expression_evaluation_failed + title: Reason + workflow_step_id: + description: Workflow step id of step that failed. + title: Workflow Step Id + type: integer + required: + - reason + - workflow_step_id + title: InvocationFailureExpressionEvaluationFailedResponse + type: object + InvocationFailureJobFailedResponse: + properties: + dependent_workflow_step_id: + description: Workflow step id of step that caused failure. + title: Dependent Workflow Step Id + type: integer + job_id: + description: Job ID that relates to failure. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Job ID + type: string + reason: + const: job_failed + title: Reason + workflow_step_id: + description: Workflow step id of step that failed. + title: Workflow Step Id + type: integer + required: + - reason + - workflow_step_id + - job_id + - dependent_workflow_step_id + title: InvocationFailureJobFailedResponse + type: object + InvocationFailureOutputNotFoundResponse: + properties: + dependent_workflow_step_id: + description: Workflow step id of step that caused failure. + title: Dependent Workflow Step Id + type: integer + output_name: + title: Tool or module output name that was referenced but not produced + type: string + reason: + const: output_not_found + title: Reason + workflow_step_id: + description: Workflow step id of step that failed. + title: Workflow Step Id + type: integer + required: + - reason + - workflow_step_id + - output_name + - dependent_workflow_step_id + title: InvocationFailureOutputNotFoundResponse + type: object + InvocationFailureWhenNotBooleanResponse: + properties: + details: + description: Contains details to help troubleshoot this problem. + title: Details + type: string + reason: + const: when_not_boolean + title: Reason + workflow_step_id: + description: Workflow step id of step that failed. + title: Workflow Step Id + type: integer + required: + - reason + - workflow_step_id + - details + title: InvocationFailureWhenNotBooleanResponse + type: object + InvocationInput: + properties: + id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: The encoded ID of the dataset/dataset collection. + title: ID + label: + anyOf: + - type: string + - type: 'null' + description: Label of the workflow step associated with the input dataset/dataset + collection. + title: Label + src: + anyOf: + - const: hda + - const: hdca + description: Source type of the input dataset/dataset collection. + title: Source + workflow_step_id: + description: The encoded ID of the workflow step associated with the dataset/dataset + collection. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Workflow step ID + type: string + required: + - workflow_step_id + - src + title: InvocationInput + type: object + InvocationInputParameter: + properties: + label: + description: Label of the workflow step associated with the input parameter. + title: Label + type: string + parameter_value: + description: Value of the input parameter. + title: Parameter value + workflow_step_id: + description: The encoded ID of the workflow step associated with the input + parameter. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Workflow step ID + type: string + required: + - parameter_value + - label + - workflow_step_id + title: InvocationInputParameter + type: object + InvocationJobsResponse: + properties: + id: + description: The encoded ID of the workflow invocation. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + model: + const: WorkflowInvocation + title: Model + populated_state: + allOf: + - $ref: '#/components/schemas/JobState' + description: The absolute state of all the jobs related to the Invocation. + title: Populated state + states: + additionalProperties: + type: integer + description: The states of all the jobs related to the Invocation. + title: States + type: object + required: + - id + - states + - populated_state + - model + title: InvocationJobsResponse + type: object + InvocationOutput: + properties: + id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: The encoded ID of the dataset/dataset collection. + title: ID + src: + const: hda + description: Source model of the output dataset. + title: Source + workflow_step_id: + description: The encoded ID of the workflow step associated with the dataset/dataset + collection. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Workflow step ID + type: string + required: + - workflow_step_id + - src + title: InvocationOutput + type: object + InvocationOutputCollection: + properties: + id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: The encoded ID of the dataset/dataset collection. + title: ID + src: + const: hdca + description: Source model of the output dataset collection. + title: Source + workflow_step_id: + description: The encoded ID of the workflow step associated with the dataset/dataset + collection. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Workflow step ID + type: string + required: + - workflow_step_id + - src + title: InvocationOutputCollection + type: object + InvocationReport: + description: Report describing workflow invocation + properties: + errors: + anyOf: + - type: object + - type: 'null' + description: Errors associated with the invocation. + title: Errors + generate_time: + anyOf: + - type: string + - type: 'null' + description: The version of Galaxy this object was generated with. + title: Galaxy Version + generate_version: + anyOf: + - type: string + - type: 'null' + description: The version of Galaxy this object was generated with. + title: Galaxy Version + histories: + anyOf: + - type: object + - type: 'null' + description: Histories associated with the invocation. + title: Histories + history_dataset_collections: + anyOf: + - type: object + - type: 'null' + description: History dataset collections associated with the invocation. + title: History dataset collections + history_datasets: + anyOf: + - type: object + - type: 'null' + description: History datasets associated with the invocation. + title: History datasets + id: + description: The workflow this invocation has been triggered for. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Workflow ID + type: string + invocation_markdown: + anyOf: + - type: string + - type: 'null' + description: Raw galaxy-flavored markdown contents of the report. + title: Markdown + invocations: + anyOf: + - type: object + - type: 'null' + description: Other invocations associated with the invocation. + title: Invocations + jobs: + anyOf: + - type: object + - type: 'null' + description: Jobs associated with the invocation. + title: Jobs + markdown: + anyOf: + - type: string + - type: 'null' + description: Raw galaxy-flavored markdown contents of the report. + title: Markdown + model_class: + const: Report + description: The name of the database model class. + title: Model class + type: string + render_format: + const: markdown + default: markdown + description: Format of the invocation report. + title: Render format + title: + description: The name of the report. + title: Title + type: string + username: + description: The name of the user who owns this report. + title: Username + type: string + workflows: + anyOf: + - type: object + - type: 'null' + description: Workflows associated with the invocation. + title: Workflows + required: + - model_class + - id + - username + - title + title: InvocationReport + type: object + InvocationSerializationView: + enum: + - element + - collection + title: InvocationSerializationView + type: string + InvocationSortByEnum: + enum: + - create_time + - update_time + - None + title: InvocationSortByEnum + type: string + InvocationState: + enum: + - new + - ready + - scheduled + - cancelled + - cancelling + - failed + title: InvocationState + type: string + InvocationStep: + description: Information about workflow invocation step + properties: + action: + anyOf: + - type: boolean + - type: 'null' + description: Whether to take action on the invocation step. + title: Action + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation Step ID + type: string + job_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + title: Job Id + jobs: + default: [] + description: Jobs associated with the workflow invocation step. + items: + $ref: '#/components/schemas/JobBaseModel' + title: Jobs + type: array + model_class: + const: WorkflowInvocationStep + description: The name of the database model class. + title: Model class + type: string + order_index: + description: The index of the workflow step in the workflow. + title: Order index + type: integer + output_collections: + additionalProperties: + $ref: '#/components/schemas/InvocationStepCollectionOutput' + default: {} + description: The dataset collection outputs of the workflow invocation step. + title: Output collections + type: object + outputs: + additionalProperties: + $ref: '#/components/schemas/InvocationStepOutput' + default: {} + description: The outputs of the workflow invocation step. + title: Outputs + type: object + state: + anyOf: + - $ref: '#/components/schemas/InvocationStepState' + - $ref: '#/components/schemas/JobState' + - type: 'null' + description: Describes where in the scheduling process the workflow invocation + step is. + title: State of the invocation step + subworkflow_invocation_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + title: Subworkflow Invocation Id + update_time: + anyOf: + - format: date-time + type: string + - type: 'null' + description: The last time and date this item was updated. + title: Update Time + workflow_step_id: + description: The encoded ID of the workflow step associated with this workflow + invocation step. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Workflow step ID + type: string + workflow_step_label: + anyOf: + - type: string + - type: 'null' + description: The label of the workflow step + title: Step label + workflow_step_uuid: + anyOf: + - format: uuid4 + type: string + - type: 'null' + description: Universal unique identifier of the workflow step. + title: UUID + required: + - model_class + - id + - update_time + - job_id + - workflow_step_id + - subworkflow_invocation_id + - action + - order_index + title: InvocationStep + type: object + InvocationStepCollectionOutput: + properties: + id: + description: Dataset Collection ID of the workflow step output. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Dataset Collection ID + type: string + src: + const: hdca + default: hdca + description: The source model of the output. + title: src + required: + - id + title: InvocationStepCollectionOutput + type: object + InvocationStepJobsResponseCollectionJobsModel: + properties: + id: + description: The encoded ID of the workflow invocation. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + model: + const: ImplicitCollectionJobs + title: Model + populated_state: + allOf: + - $ref: '#/components/schemas/JobState' + description: The absolute state of all the jobs related to the Invocation. + title: Populated state + states: + additionalProperties: + type: integer + description: The states of all the jobs related to the Invocation. + title: States + type: object + required: + - id + - states + - populated_state + - model + title: InvocationStepJobsResponseCollectionJobsModel + type: object + InvocationStepJobsResponseJobModel: + properties: + id: + description: The encoded ID of the workflow invocation. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + model: + const: Job + title: Model + populated_state: + allOf: + - $ref: '#/components/schemas/JobState' + description: The absolute state of all the jobs related to the Invocation. + title: Populated state + states: + additionalProperties: + type: integer + description: The states of all the jobs related to the Invocation. + title: States + type: object + required: + - id + - states + - populated_state + - model + title: InvocationStepJobsResponseJobModel + type: object + InvocationStepJobsResponseStepModel: + properties: + id: + description: The encoded ID of the workflow invocation. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + model: + const: WorkflowInvocationStep + title: Model + populated_state: + allOf: + - $ref: '#/components/schemas/JobState' + description: The absolute state of all the jobs related to the Invocation. + title: Populated state + states: + additionalProperties: + type: integer + description: The states of all the jobs related to the Invocation. + title: States + type: object + required: + - id + - states + - populated_state + - model + title: InvocationStepJobsResponseStepModel + type: object + InvocationStepOutput: + properties: + id: + description: Dataset ID of the workflow step output. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Dataset ID + type: string + src: + const: hda + default: hda + description: The source model of the output. + title: src + uuid: + anyOf: + - format: uuid4 + type: string + - type: 'null' + description: Universal unique identifier of the workflow step output dataset. + title: UUID + required: + - id + title: InvocationStepOutput + type: object + InvocationStepState: + enum: + - new + - ready + - scheduled + title: InvocationStepState + type: string + InvocationUnexpectedFailureResponse: + properties: + details: + anyOf: + - type: string + - type: 'null' + description: May contains details to help troubleshoot this problem. + title: Details + reason: + const: unexpected_failure + title: Reason + workflow_step_id: + anyOf: + - type: integer + - type: 'null' + description: Workflow step id of step that failed. + title: Workflow Step Id + required: + - reason + title: InvocationUnexpectedFailureResponse + type: object + InvocationUpdatePayload: + properties: + action: + description: Whether to take action on the invocation step. + title: Action + type: boolean + required: + - action + title: InvocationUpdatePayload + type: object + ItemTagsCreatePayload: + description: Payload schema for creating an item tag. + properties: + value: + anyOf: + - type: string + - type: 'null' + title: value of the item tag + title: ItemTagsCreatePayload + type: object + ItemTagsListResponse: + description: Response schema for listing item tags. + items: + $ref: '#/components/schemas/ItemTagsResponse' + title: ItemTagsListResponse + type: array + ItemTagsPayload: + properties: + item_class: + allOf: + - $ref: '#/components/schemas/TaggableItemClass' + description: The name of the class of the item that will be tagged. + title: Item class + item_id: + description: The `encoded identifier` of the item whose tags will be updated. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Item ID + type: string + item_tags: + anyOf: + - $ref: '#/components/schemas/TagCollection' + - type: 'null' + description: The list of tags that will replace the current tags associated + with the item. + title: Item tags + required: + - item_id + - item_class + title: ItemTagsPayload + type: object + ItemTagsResponse: + description: Response schema for showing an item tag. + properties: + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: item tag ID + type: string + model_class: + title: model class + type: string + user_tname: + title: name of the item tag + type: string + user_value: + anyOf: + - type: string + - type: 'null' + title: value of the item tag + required: + - model_class + - id + - user_tname + title: ItemTagsResponse + type: object + ItemsFromSrc: + enum: + - url + - files + - path + - ftp_import + - server_dir + title: ItemsFromSrc + type: string + JobBaseModel: + properties: + create_time: + description: The time and date this item was created. + format: date-time + title: Create Time + type: string + exit_code: + anyOf: + - type: integer + - type: 'null' + description: The exit code returned by the tool. Can be unset if the job + is not completed yet. + title: Exit Code + galaxy_version: + anyOf: + - type: string + - type: 'null' + description: The (major) version of Galaxy used to create this job. + examples: + - '21.05' + title: Galaxy Version + history_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: The encoded ID of the history associated with this item. + title: History ID + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Job ID + type: string + model_class: + const: Job + description: The name of the database model class. + title: Model class + type: string + state: + allOf: + - $ref: '#/components/schemas/JobState' + description: Current state of the job. + title: State + tool_id: + description: Identifier of the tool that generated this job. + title: Tool ID + type: string + update_time: + description: The last time and date this item was updated. + format: date-time + title: Update Time + type: string + required: + - model_class + - id + - tool_id + - state + - create_time + - update_time + title: JobBaseModel + type: object + JobDestinationParams: + additionalProperties: true + properties: + Handler: + anyOf: + - type: string + - type: 'null' + description: Name of the process that handled the job. + title: Handler + Runner: + anyOf: + - type: string + - type: 'null' + description: Job runner class + title: Runner + Runner Job ID: + anyOf: + - type: string + - type: 'null' + description: ID assigned to submitted job by external job running system + title: Runner Job ID + title: JobDestinationParams + type: object + JobDisplayParametersSummary: + properties: + has_parameter_errors: + description: The job has parameter errors + title: Has parameter errors + type: boolean + outputs: + additionalProperties: + items: + $ref: '#/components/schemas/JobOutput' + type: array + description: Dictionary mapping all the tool outputs (by name) with the + corresponding dataset information in a nested format. + title: Outputs + type: object + parameters: + description: The parameters of the job in a nested format. + items: + $ref: '#/components/schemas/JobParameter' + title: Parameters + type: array + required: + - parameters + - has_parameter_errors + - outputs + title: JobDisplayParametersSummary + type: object + JobErrorSummary: + properties: + messages: + description: The error messages for the specified job. + items: + items: + type: string + type: array + title: Error messages + type: array + required: + - messages + title: JobErrorSummary + type: object + JobExportHistoryArchiveListResponse: + items: + $ref: '#/components/schemas/JobExportHistoryArchiveModel' + title: JobExportHistoryArchiveListResponse + type: array + JobExportHistoryArchiveModel: + properties: + download_url: + description: Relative API URL to download the exported history archive. + title: Download URL + type: string + external_download_latest_url: + description: Fully qualified URL to download the latests version of the + exported history archive. + format: uri + minLength: 1 + title: External Download Latest URL + type: string + external_download_permanent_url: + description: Fully qualified URL to download this particular version of + the exported history archive. + format: uri + minLength: 1 + title: External Download Permanent URL + type: string + id: + description: The encoded database ID of the export request. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + job_id: + description: The encoded database ID of the job that generated this history + export archive. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Job ID + type: string + preparing: + description: Whether the archive is currently being built or in preparation. + title: Preparing + type: boolean + ready: + description: Whether the export has completed successfully and the archive + is ready + title: Ready + type: boolean + up_to_date: + description: False, if a new export archive should be generated. + title: Up to Date + type: boolean + required: + - id + - ready + - preparing + - up_to_date + - job_id + - download_url + - external_download_latest_url + - external_download_permanent_url + title: JobExportHistoryArchiveModel + type: object + JobIdResponse: + description: Contains the ID of the job associated with a particular request. + properties: + job_id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Job ID + type: string + required: + - job_id + title: JobIdResponse + type: object + JobImportHistoryResponse: + properties: + create_time: + description: The time and date this item was created. + format: date-time + title: Create Time + type: string + exit_code: + anyOf: + - type: integer + - type: 'null' + description: The exit code returned by the tool. Can be unset if the job + is not completed yet. + title: Exit Code + galaxy_version: + anyOf: + - type: string + - type: 'null' + description: The (major) version of Galaxy used to create this job. + examples: + - '21.05' + title: Galaxy Version + history_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: The encoded ID of the history associated with this item. + title: History ID + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Job ID + type: string + message: + description: Text message containing information about the history import. + title: Message + type: string + model_class: + const: Job + description: The name of the database model class. + title: Model class + type: string + state: + allOf: + - $ref: '#/components/schemas/JobState' + description: Current state of the job. + title: State + tool_id: + description: Identifier of the tool that generated this job. + title: Tool ID + type: string + update_time: + description: The last time and date this item was updated. + format: date-time + title: Update Time + type: string + required: + - model_class + - id + - tool_id + - state + - create_time + - update_time + - message + title: JobImportHistoryResponse + type: object + JobIndexSortByEnum: + enum: + - create_time + - update_time + title: JobIndexSortByEnum + type: string + JobIndexViewEnum: + enum: + - collection + - admin_job_list + title: JobIndexViewEnum + type: string + JobInputAssociation: + properties: + dataset: + allOf: + - $ref: '#/components/schemas/EncodedDataItemSourceId' + description: Reference to the associated item. + title: dataset + name: + description: Name of the job input parameter. + title: name + type: string + required: + - name + - dataset + title: JobInputAssociation + type: object + JobInputSummary: + properties: + has_duplicate_inputs: + description: Job has duplicate inputs. + title: Duplicate inputs + type: boolean + has_empty_inputs: + description: Job has empty inputs. + title: Empty inputs + type: boolean + required: + - has_empty_inputs + - has_duplicate_inputs + title: JobInputSummary + type: object + JobLock: + properties: + active: + description: If active, jobs will not dispatch + title: Job lock status + type: boolean + required: + - active + title: JobLock + type: object + JobMetric: + example: + name: start_epoch + plugin: core + raw_value: '1614261340.0000000' + title: Job Start Time + value: '2021-02-25 14:55:40' + properties: + name: + description: The name of the metric variable. + title: Name + type: string + plugin: + description: The instrumenter plugin that generated this metric. + title: Plugin + type: string + raw_value: + description: The raw value of the metric as a string. + title: Raw Value + type: string + title: + description: A descriptive title for this metric. + title: Title + type: string + value: + description: The textual representation of the metric value. + title: Value + type: string + required: + - title + - value + - plugin + - name + - raw_value + title: JobMetric + type: object + JobMetricCollection: + default: [] + description: Represents a collection of metrics associated with a Job. + items: + $ref: '#/components/schemas/JobMetric' + title: JobMetricCollection + type: array + JobOutput: + properties: + label: + description: The output label + title: Output label + value: + allOf: + - $ref: '#/components/schemas/EncodedDataItemSourceId' + description: The associated dataset. + title: Dataset + required: + - label + - value + title: JobOutput + type: object + JobOutputAssociation: + properties: + dataset: + allOf: + - $ref: '#/components/schemas/EncodedDataItemSourceId' + description: Reference to the associated item. + title: dataset + name: + description: Name of the job output parameter. + title: name + type: string + required: + - name + - dataset + title: JobOutputAssociation + type: object + JobParameter: + properties: + depth: + description: The depth of the job parameter. + title: Depth + type: integer + notes: + anyOf: + - type: string + - type: 'null' + description: Notes associated with the job parameter. + title: Notes + text: + description: Text associated with the job parameter. + title: Text + type: string + value: + anyOf: + - items: + $ref: '#/components/schemas/EncodedJobParameterHistoryItem' + type: array + - type: number + - type: integer + - type: boolean + - type: string + - type: 'null' + description: The values of the job parameter + title: Value + required: + - text + - depth + title: JobParameter + type: object + JobSourceType: + description: Available types of job sources (model classes) that produce dataset + collections. + enum: + - Job + - ImplicitCollectionJobs + - WorkflowInvocation + title: JobSourceType + type: string + JobState: + enum: + - new + - resubmitted + - upload + - waiting + - queued + - running + - ok + - error + - failed + - paused + - deleting + - deleted + - stop + - stopped + - skipped + title: JobState + type: string + JobStateSummary: + properties: + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Id + type: string + model: + const: Job + description: The name of the database model class. + title: Model class + type: string + populated_state: + allOf: + - $ref: '#/components/schemas/DatasetCollectionPopulatedState' + description: 'Indicates the general state of the elements in the dataset + collection:- ''new'': new dataset collection, unpopulated elements.- ''ok'': + collection elements populated (HDAs may or may not have errors).- ''failed'': + some problem populating, won''t be populated.' + title: Populated State + states: + additionalProperties: + type: integer + default: {} + description: A dictionary of job states and the number of jobs in that state. + title: States + type: object + required: + - id + - populated_state + - model + title: JobStateSummary + type: object + JobSummary: + description: Basic information about a job. + properties: + command_line: + anyOf: + - type: string + - type: 'null' + description: The command line produced by the job. Users can see this value + if allowed in the configuration, administrator can always see this value. + title: Command Line + create_time: + description: The time and date this item was created. + format: date-time + title: Create Time + type: string + exit_code: + anyOf: + - type: integer + - type: 'null' + description: The exit code returned by the tool. Can be unset if the job + is not completed yet. + title: Exit Code + external_id: + anyOf: + - type: string + - type: 'null' + description: The job id used by the external job runner (Condor, Pulsar, + etc.). Only administrator can see this value. + title: External ID + galaxy_version: + anyOf: + - type: string + - type: 'null' + description: The (major) version of Galaxy used to create this job. + examples: + - '21.05' + title: Galaxy Version + handler: + anyOf: + - type: string + - type: 'null' + description: The job handler process assigned to handle this job. Only administrator + can see this value. + title: Job Handler + history_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: The encoded ID of the history associated with this item. + title: History ID + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Job ID + type: string + job_runner_name: + anyOf: + - type: string + - type: 'null' + description: Name of the job runner plugin that handles this job. Only administrator + can see this value. + title: Job Runner Name + model_class: + const: Job + description: The name of the database model class. + title: Model class + type: string + state: + allOf: + - $ref: '#/components/schemas/JobState' + description: Current state of the job. + title: State + tool_id: + description: Identifier of the tool that generated this job. + title: Tool ID + type: string + update_time: + description: The last time and date this item was updated. + format: date-time + title: Update Time + type: string + user_email: + anyOf: + - type: string + - type: 'null' + description: The email of the user that owns this job. Only the owner of + the job and administrators can see this value. + title: User Email + required: + - model_class + - id + - tool_id + - state + - create_time + - update_time + title: JobSummary + type: object + LabelValuePair: + description: Generic Label/Value pair model. + properties: + label: + description: The label of the item. + title: Label + type: string + value: + description: The value of the item. + title: Value + type: string + required: + - label + - value + title: LabelValuePair + type: object + LegacyLibraryPermissionsPayload: + properties: + LIBRARY_ACCESS_in: + anyOf: + - items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + type: array + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + default: [] + description: A list of role encoded IDs defining roles that should have + access permission on the library. + title: Access IDs + LIBRARY_ADD_in: + anyOf: + - items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + type: array + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + default: [] + description: A list of role encoded IDs defining roles that should have + manage permission on the library. + title: Manage IDs + LIBRARY_MANAGE_in: + anyOf: + - items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + type: array + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + default: [] + description: A list of role encoded IDs defining roles that should have + modify permission on the library. + title: Modify IDs + LIBRARY_MODIFY_in: + anyOf: + - items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + type: array + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + default: [] + description: A list of role encoded IDs defining roles that should be able + to add items to the library. + title: Add IDs + title: LegacyLibraryPermissionsPayload + type: object + LibraryAvailablePermissions: + properties: + page: + description: Current page. + title: Page + type: integer + page_limit: + description: Maximum number of items per page. + title: Page Limit + type: integer + roles: + description: A list available roles that can be assigned to a particular + permission. + items: + $ref: '#/components/schemas/BasicRoleModel' + title: Roles + type: array + total: + description: Total number of items + title: Total + type: integer + required: + - roles + - page + - page_limit + - total + title: LibraryAvailablePermissions + type: object + LibraryCurrentPermissions: + properties: + access_library_role_list: + description: A list containing pairs of role names and corresponding encoded + IDs which have access to the Library. + items: + items: + type: string + type: array + title: Access Role List + type: array + add_library_item_role_list: + description: A list containing pairs of role names and corresponding encoded + IDs which can add items to the Library. + items: + items: + type: string + type: array + title: Add Role List + type: array + manage_library_role_list: + description: A list containing pairs of role names and corresponding encoded + IDs which can manage the Library. + items: + items: + type: string + type: array + title: Manage Role List + type: array + modify_library_role_list: + description: A list containing pairs of role names and corresponding encoded + IDs which can modify the Library. + items: + items: + type: string + type: array + title: Modify Role List + type: array + required: + - access_library_role_list + - modify_library_role_list + - manage_library_role_list + - add_library_item_role_list + title: LibraryCurrentPermissions + type: object + LibraryDestination: + properties: + description: + anyOf: + - type: string + - type: 'null' + description: Description for library to create + title: Description + name: + description: Must specify a library name + title: Name + type: string + synopsis: + anyOf: + - type: string + - type: 'null' + description: Description for library to create + title: Synopsis + type: + const: library + title: Type + required: + - type + - name + title: LibraryDestination + type: object + LibraryFolderContentsIndexResult: + properties: + folder_contents: + items: + discriminator: + mapping: + file: '#/components/schemas/FileLibraryFolderItem' + folder: '#/components/schemas/FolderLibraryFolderItem' + propertyName: type + oneOf: + - $ref: '#/components/schemas/FileLibraryFolderItem' + - $ref: '#/components/schemas/FolderLibraryFolderItem' + title: Folder Contents + type: array + metadata: + $ref: '#/components/schemas/LibraryFolderMetadata' + required: + - metadata + - folder_contents + title: LibraryFolderContentsIndexResult + type: object + LibraryFolderCurrentPermissions: + properties: + add_library_item_role_list: + description: A list containing pairs of role names and corresponding encoded + IDs which can add items to the Library folder. + items: + items: + type: string + type: array + title: Add Role List + type: array + manage_folder_role_list: + description: A list containing pairs of role names and corresponding encoded + IDs which can manage the Library folder. + items: + items: + type: string + type: array + title: Manage Role List + type: array + modify_folder_role_list: + description: A list containing pairs of role names and corresponding encoded + IDs which can modify the Library folder. + items: + items: + type: string + type: array + title: Modify Role List + type: array + required: + - modify_folder_role_list + - manage_folder_role_list + - add_library_item_role_list + title: LibraryFolderCurrentPermissions + type: object + LibraryFolderDestination: + properties: + library_folder_id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Library Folder Id + type: string + type: + const: library_folder + title: Type + required: + - type + - library_folder_id + title: LibraryFolderDestination + type: object + LibraryFolderDetails: + properties: + deleted: + description: Whether this folder is marked as deleted. + title: Deleted + type: boolean + description: + anyOf: + - type: string + - type: 'null' + default: '' + description: A detailed description of the library folder. + title: Description + genome_build: + anyOf: + - type: string + - type: 'null' + default: '?' + description: TODO + title: Genome Build + id: + description: Encoded ID of the library folder. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + item_count: + description: A detailed description of the library folder. + title: Item Count + type: integer + library_path: + default: [] + description: The list of folder names composing the path to this folder. + items: + type: string + title: Path + type: array + model_class: + const: LibraryFolder + description: The name of the database model class. + title: Model class + type: string + name: + description: The name of the library folder. + title: Name + type: string + parent_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: Encoded ID of the parent folder. Empty if it's the root folder. + title: Parent Folder ID + parent_library_id: + description: Encoded ID of the Library this folder belongs to. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Parent Library ID + type: string + update_time: + description: The last time and date this item was updated. + format: date-time + title: Update Time + type: string + required: + - model_class + - id + - name + - item_count + - parent_library_id + - update_time + - deleted + title: LibraryFolderDetails + type: object + LibraryFolderMetadata: + properties: + can_add_library_item: + title: Can Add Library Item + type: boolean + can_modify_folder: + title: Can Modify Folder + type: boolean + folder_description: + title: Folder Description + type: string + folder_name: + title: Folder Name + type: string + full_path: + items: + maxItems: 2 + minItems: 2 + prefixItems: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: string + type: array + title: Full Path + type: array + parent_library_id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Parent Library Id + type: string + total_rows: + title: Total Rows + type: integer + required: + - parent_library_id + - folder_name + - folder_description + - total_rows + - can_modify_folder + - can_add_library_item + - full_path + title: LibraryFolderMetadata + type: object + LibraryFolderPermissionAction: + const: set_permissions + title: LibraryFolderPermissionAction + type: string + LibraryFolderPermissionsPayload: + properties: + action: + anyOf: + - $ref: '#/components/schemas/LibraryFolderPermissionAction' + - type: 'null' + description: Indicates what action should be performed on the library folder. + title: Action + add_ids[]: + anyOf: + - items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + type: array + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + default: [] + description: A list of role encoded IDs defining roles that should be able + to add items to the library. + title: Add IDs + manage_ids[]: + anyOf: + - items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + type: array + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + default: [] + description: A list of role encoded IDs defining roles that should have + manage permission on the library. + title: Manage IDs + modify_ids[]: + anyOf: + - items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + type: array + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + default: [] + description: A list of role encoded IDs defining roles that should have + modify permission on the library. + title: Modify IDs + title: LibraryFolderPermissionsPayload + type: object + LibraryLegacySummary: + properties: + create_time: + description: The time and date this item was created. + format: date-time + title: Create Time + type: string + deleted: + description: Whether this Library has been deleted. + title: Deleted + type: boolean + description: + anyOf: + - type: string + - type: 'null' + default: '' + description: A detailed description of the Library. + title: Description + id: + description: Encoded ID of the Library. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + model_class: + const: Library + description: The name of the database model class. + title: Model class + type: string + name: + description: The name of the Library. + title: Name + type: string + root_folder_id: + description: Encoded ID of the Library's base folder. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Root Folder ID + type: string + synopsis: + anyOf: + - type: string + - type: 'null' + description: A short text describing the contents of the Library. + title: Description + required: + - model_class + - id + - name + - root_folder_id + - create_time + - deleted + title: LibraryLegacySummary + type: object + LibraryPermissionAction: + enum: + - set_permissions + - remove_restrictions + title: LibraryPermissionAction + type: string + LibraryPermissionScope: + enum: + - current + - available + title: LibraryPermissionScope + type: string + LibraryPermissionsPayload: + properties: + access_ids[]: + anyOf: + - items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + type: array + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + default: [] + description: A list of role encoded IDs defining roles that should have + access permission on the library. + title: Access IDs + action: + anyOf: + - $ref: '#/components/schemas/LibraryPermissionAction' + - type: 'null' + description: Indicates what action should be performed on the Library. + title: Action + add_ids[]: + anyOf: + - items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + type: array + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + default: [] + description: A list of role encoded IDs defining roles that should be able + to add items to the library. + title: Add IDs + manage_ids[]: + anyOf: + - items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + type: array + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + default: [] + description: A list of role encoded IDs defining roles that should have + manage permission on the library. + title: Manage IDs + modify_ids[]: + anyOf: + - items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + type: array + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + default: [] + description: A list of role encoded IDs defining roles that should have + modify permission on the library. + title: Modify IDs + title: LibraryPermissionsPayload + type: object + LibrarySummary: + properties: + can_user_add: + description: Whether the current user can add contents to this Library. + title: Can User Add + type: boolean + can_user_manage: + description: Whether the current user can manage the Library and its contents. + title: Can User Manage + type: boolean + can_user_modify: + description: Whether the current user can modify this Library. + title: Can User Modify + type: boolean + create_time: + description: The time and date this item was created. + format: date-time + title: Create Time + type: string + create_time_pretty: + description: Nice time representation of the creation date. + examples: + - 2 months ago + title: Create Time Pretty + type: string + deleted: + description: Whether this Library has been deleted. + title: Deleted + type: boolean + description: + anyOf: + - type: string + - type: 'null' + default: '' + description: A detailed description of the Library. + title: Description + id: + description: Encoded ID of the Library. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + model_class: + const: Library + description: The name of the database model class. + title: Model class + type: string + name: + description: The name of the Library. + title: Name + type: string + public: + description: Whether this Library has been deleted. + title: Public + type: boolean + root_folder_id: + description: Encoded ID of the Library's base folder. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Root Folder ID + type: string + synopsis: + anyOf: + - type: string + - type: 'null' + description: A short text describing the contents of the Library. + title: Description + required: + - model_class + - id + - name + - root_folder_id + - create_time + - deleted + - create_time_pretty + - public + - can_user_add + - can_user_modify + - can_user_manage + title: LibrarySummary + type: object + LibrarySummaryList: + default: [] + items: + $ref: '#/components/schemas/LibrarySummary' + title: LibrarySummaryList + type: array + LicenseMetadataModel: + properties: + detailsUrl: + description: URL to the SPDX json details for this license + examples: + - http://spdx.org/licenses/Apache-2.0.json + format: uri + maxLength: 2083 + minLength: 1 + title: Details URL + type: string + isDeprecatedLicenseId: + description: True if the entire license is deprecated + examples: + - false + title: Deprecated License + type: boolean + isOsiApproved: + description: Indicates if the [OSI](https://opensource.org/) has approved + the license + examples: + - true + title: OSI approved + type: boolean + licenseId: + description: SPDX Identifier + examples: + - Apache-2.0 + title: Identifier + type: string + name: + description: Full name of the license + examples: + - Apache License 2.0 + title: Name + type: string + recommended: + description: True if this license is recommended to be used + title: Recommended + type: boolean + reference: + description: Reference to the HTML format for the license file + examples: + - ./Apache-2.0.html + title: Reference + type: string + referenceNumber: + description: '*Deprecated* - this field is generated and is no longer in + use' + title: Reference number + type: integer + seeAlso: + description: Cross reference URL pointing to additional copies of the license + items: + format: uri + maxLength: 2083 + minLength: 1 + type: string + title: Reference URLs + type: array + spdxUrl: + examples: + - https://spdx.org/licenses/Apache-2.0.html + format: uri + maxLength: 2083 + minLength: 1 + title: SPDX URL + type: string + url: + description: License URL + examples: + - http://www.apache.org/licenses/LICENSE-2.0 + format: uri + maxLength: 2083 + minLength: 1 + title: URL + type: string + required: + - licenseId + - name + - reference + - referenceNumber + - isDeprecatedLicenseId + - isOsiApproved + - seeAlso + - detailsUrl + - recommended + - url + - spdxUrl + title: LicenseMetadataModel + type: object + LimitedUserModel: + description: This is used when config options (expose_user_name and expose_user_email) + are in place. + properties: + email: + anyOf: + - type: string + - type: 'null' + title: Email + id: + description: Encoded ID of the user + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + username: + anyOf: + - type: string + - type: 'null' + title: Username + required: + - id + title: LimitedUserModel + type: object + Link: + properties: + name: + title: Name + type: string + required: + - name + title: Link + type: object + ListJstreeResponse: + default: [] + deprecated: true + items: {} + title: ListJstreeResponse + type: array + ListUriResponse: + default: [] + items: + discriminator: + mapping: + Directory: '#/components/schemas/RemoteDirectory' + File: '#/components/schemas/RemoteFile' + propertyName: class + oneOf: + - $ref: '#/components/schemas/RemoteFile' + - $ref: '#/components/schemas/RemoteDirectory' + title: ListUriResponse + type: array + MandatoryNotificationCategory: + const: broadcast + description: 'These notification categories cannot be opt-out by the user. + + + The user will always receive notifications from these categories.' + title: MandatoryNotificationCategory + type: string + MaterializeDatasetInstanceAPIRequest: + properties: + content: + description: 'Depending on the `source` it can be: + + - The encoded id of the source library dataset + + - The encoded id of the HDA + + ' + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Content + type: string + source: + allOf: + - $ref: '#/components/schemas/DatasetSourceType' + description: The source of the content. Can be other history element to + be copied or library elements. + title: Source + required: + - source + - content + title: MaterializeDatasetInstanceAPIRequest + type: object + MessageNotificationContent: + properties: + category: + const: message + default: message + title: Category + message: + description: The message of the notification (supports Markdown). + title: Message + type: string + subject: + description: The subject of the notification. + title: Subject + type: string + required: + - subject + - message + title: MessageNotificationContent + type: object + MetadataFile: + description: Metadata file associated with a dataset. + properties: + download_url: + description: The URL to download this item from the server. + title: Download URL + type: string + file_type: + description: TODO + title: File Type + type: string + required: + - file_type + - download_url + title: MetadataFile + type: object + Metric: + properties: + args: + description: A JSON string containing an array of extra data. + title: Arguments + type: string + level: + description: An integer representing the metric's log level. + title: Level + type: integer + namespace: + description: Label indicating the source of the metric. + title: Namespace + type: string + time: + description: The timestamp in ISO format. + examples: + - '2021-01-23T18:25:43.511Z' + title: Timestamp + type: string + required: + - namespace + - time + - level + - args + title: Metric + type: object + ModelStoreFormat: + description: Available types of model stores for export. + enum: + - tgz + - tar + - tar.gz + - bag.zip + - bag.tar + - bag.tgz + - rocrate.zip + - bco.json + title: ModelStoreFormat + type: string + NestedElement: + additionalProperties: false + properties: + MD5: + anyOf: + - type: string + - type: 'null' + title: Md5 + auto_decompress: + default: false + description: Decompress compressed data before sniffing? + title: Auto Decompress + type: boolean + collection_type: + anyOf: + - type: string + - type: 'null' + title: Collection Type + created_from_basename: + anyOf: + - type: string + - type: 'null' + title: Created From Basename + dbkey: + default: '?' + title: Dbkey + type: string + deferred: + default: false + title: Deferred + type: boolean + description: + anyOf: + - type: string + - type: 'null' + title: Description + elements: + items: + anyOf: + - discriminator: + mapping: + composite: '#/components/schemas/CompositeDataElement' + files: '#/components/schemas/FileDataElement' + ftp_import: '#/components/schemas/FtpImportElement' + pasted: '#/components/schemas/PastedDataElement' + path: '#/components/schemas/PathDataElement' + server_dir: '#/components/schemas/ServerDirElement' + url: '#/components/schemas/UrlDataElement' + propertyName: src + oneOf: + - $ref: '#/components/schemas/FileDataElement' + - $ref: '#/components/schemas/PastedDataElement' + - $ref: '#/components/schemas/UrlDataElement' + - $ref: '#/components/schemas/PathDataElement' + - $ref: '#/components/schemas/ServerDirElement' + - $ref: '#/components/schemas/FtpImportElement' + - $ref: '#/components/schemas/CompositeDataElement' + - $ref: '#/components/schemas/NestedElement' + title: Elements + type: array + elements_from: + anyOf: + - $ref: '#/components/schemas/ElementsFromType' + - type: 'null' + ext: + default: auto + title: Ext + type: string + extra_files: + anyOf: + - $ref: '#/components/schemas/ExtraFiles' + - type: 'null' + info: + anyOf: + - type: string + - type: 'null' + title: Info + name: + anyOf: + - type: string + - type: integer + - type: number + - type: boolean + - type: 'null' + title: Name + space_to_tab: + default: false + title: Space To Tab + type: boolean + tags: + anyOf: + - items: + type: string + type: array + - type: 'null' + title: Tags + to_posix_lines: + default: false + title: To Posix Lines + type: boolean + required: + - elements + title: NestedElement + type: object + NewSharedItemNotificationContent: + properties: + category: + const: new_shared_item + default: new_shared_item + title: Category + item_name: + description: The name of the shared item. + title: Item name + type: string + item_type: + description: The type of the shared item. + enum: + - history + - workflow + - visualization + - page + title: Item type + type: string + owner_name: + description: The name of the owner of the shared item. + title: Owner name + type: string + slug: + description: The slug of the shared item. Used for the link to the item. + title: Slug + type: string + required: + - item_type + - item_name + - owner_name + - slug + title: NewSharedItemNotificationContent + type: object + NotificationBroadcastUpdateRequest: + description: A notification update request specific for broadcasting. + properties: + content: + anyOf: + - $ref: '#/components/schemas/BroadcastNotificationContent' + - type: 'null' + description: The content of the broadcast notification. Broadcast notifications + are displayed prominently to all users and can contain action links to + redirect the user to a specific page. + title: Content + expiration_time: + anyOf: + - format: date-time + type: string + - type: 'null' + description: The time when the notification should expire. By default it + will expire after 6 months. Expired notifications will be permanently + deleted. + title: Expiration time + publication_time: + anyOf: + - format: date-time + type: string + - type: 'null' + description: The time when the notification should be published. Notifications + can be created and then scheduled to be published at a later time. + title: Publication time + source: + anyOf: + - type: string + - type: 'null' + description: The source of the notification. Represents the agent that created + the notification. + title: Source + variant: + anyOf: + - $ref: '#/components/schemas/NotificationVariant' + - type: 'null' + description: The variant of the notification. Used to express the importance + of the notification. + title: Variant + title: NotificationBroadcastUpdateRequest + type: object + NotificationCategorySettings: + description: The settings for a notification category. + properties: + channels: + allOf: + - $ref: '#/components/schemas/NotificationChannelSettings' + default: + push: true + description: The channels that the user wants to receive notifications from + for this category. + title: Channels + enabled: + default: true + description: Whether the user wants to receive notifications for this category. + title: Enabled + type: boolean + title: NotificationCategorySettings + type: object + NotificationChannelSettings: + description: The settings for each channel of a notification category. + properties: + push: + default: true + description: Whether the user wants to receive push notifications in the + browser for this category. + title: Push + type: boolean + title: NotificationChannelSettings + type: object + NotificationCreateData: + description: Basic common fields for all notification create requests. + properties: + category: + anyOf: + - $ref: '#/components/schemas/MandatoryNotificationCategory' + - $ref: '#/components/schemas/PersonalNotificationCategory' + description: The category of the notification. Represents the type of the + notification. E.g. 'message' or 'new_shared_item'. + title: Category + content: + description: The content of the notification. The structure depends on the + category. + discriminator: + mapping: + broadcast: '#/components/schemas/BroadcastNotificationContent' + message: '#/components/schemas/MessageNotificationContent' + new_shared_item: '#/components/schemas/NewSharedItemNotificationContent' + propertyName: category + oneOf: + - $ref: '#/components/schemas/MessageNotificationContent' + - $ref: '#/components/schemas/NewSharedItemNotificationContent' + - $ref: '#/components/schemas/BroadcastNotificationContent' + title: Content + expiration_time: + anyOf: + - format: date-time + type: string + - type: 'null' + description: The time when the notification should expire. By default it + will expire after 6 months. Expired notifications will be permanently + deleted. + title: Expiration time + publication_time: + anyOf: + - format: date-time + type: string + - type: 'null' + description: The time when the notification should be published. Notifications + can be created and then scheduled to be published at a later time. + title: Publication time + source: + description: The source of the notification. Represents the agent that created + the notification. E.g. 'galaxy' or 'admin'. + title: Source + type: string + variant: + allOf: + - $ref: '#/components/schemas/NotificationVariant' + description: The variant of the notification. Represents the intent or relevance + of the notification. E.g. 'info' or 'urgent'. + title: Variant + required: + - source + - category + - variant + - content + title: NotificationCreateData + type: object + NotificationCreateRequest: + description: Contains the recipients and the notification to create. + properties: + notification: + allOf: + - $ref: '#/components/schemas/NotificationCreateData' + description: The notification to create. The structure depends on the category. + title: Notification + recipients: + allOf: + - $ref: '#/components/schemas/NotificationRecipients' + description: The recipients of the notification. Can be a combination of + users, groups and roles. + title: Recipients + required: + - recipients + - notification + title: NotificationCreateRequest + type: object + NotificationCreatedResponse: + properties: + notification: + allOf: + - $ref: '#/components/schemas/NotificationResponse' + description: The notification that was created. The structure depends on + the category. + title: Notification + total_notifications_sent: + description: The total number of notifications that were sent to the recipients. + title: Total notifications sent + type: integer + required: + - total_notifications_sent + - notification + title: NotificationCreatedResponse + type: object + NotificationRecipients: + description: The recipients of a notification. Can be a combination of users, + groups and roles. + properties: + group_ids: + default: [] + description: The list of encoded group IDs of the groups that should receive + the notification. + items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + title: Group IDs + type: array + role_ids: + default: [] + description: The list of encoded role IDs of the roles that should receive + the notification. + items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + title: Role IDs + type: array + user_ids: + default: [] + description: The list of encoded user IDs of the users that should receive + the notification. + items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + title: User IDs + type: array + title: NotificationRecipients + type: object + NotificationResponse: + description: Basic common fields for all notification responses. + properties: + category: + anyOf: + - $ref: '#/components/schemas/MandatoryNotificationCategory' + - $ref: '#/components/schemas/PersonalNotificationCategory' + description: The category of the notification. Represents the type of the + notification. E.g. 'message' or 'new_shared_item'. + title: Category + content: + description: The content of the notification. The structure depends on the + category. + discriminator: + mapping: + broadcast: '#/components/schemas/BroadcastNotificationContent' + message: '#/components/schemas/MessageNotificationContent' + new_shared_item: '#/components/schemas/NewSharedItemNotificationContent' + propertyName: category + oneOf: + - $ref: '#/components/schemas/MessageNotificationContent' + - $ref: '#/components/schemas/NewSharedItemNotificationContent' + - $ref: '#/components/schemas/BroadcastNotificationContent' + title: Content + create_time: + description: The time when the notification was created. + format: date-time + title: Create time + type: string + expiration_time: + anyOf: + - format: date-time + type: string + - type: 'null' + description: The time when the notification will expire. If not set, the + notification will never expire. Expired notifications will be permanently + deleted. + title: Expiration time + id: + description: The encoded ID of the notification. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + publication_time: + description: The time when the notification was published. Notifications + can be created and then published at a later time. + format: date-time + title: Publication time + type: string + source: + description: The source of the notification. Represents the agent that created + the notification. E.g. 'galaxy' or 'admin'. + title: Source + type: string + update_time: + description: The time when the notification was last updated. + format: date-time + title: Update time + type: string + variant: + allOf: + - $ref: '#/components/schemas/NotificationVariant' + description: The variant of the notification. Represents the intent or relevance + of the notification. E.g. 'info' or 'urgent'. + title: Variant + required: + - id + - source + - category + - variant + - create_time + - update_time + - publication_time + - content + title: NotificationResponse + type: object + NotificationStatusSummary: + description: A summary of the notification status for a user. Contains only + updates since a particular timestamp. + properties: + broadcasts: + description: The list of updated broadcasts. + items: + $ref: '#/components/schemas/BroadcastNotificationResponse' + title: Broadcasts + type: array + notifications: + description: The list of updated notifications for the user. + items: + $ref: '#/components/schemas/UserNotificationResponse' + title: Notifications + type: array + total_unread_count: + description: The total number of unread notifications for the user. + title: Total unread count + type: integer + required: + - total_unread_count + - notifications + - broadcasts + title: NotificationStatusSummary + type: object + NotificationVariant: + description: The notification variant communicates the intent or relevance of + the notification. + enum: + - info + - warning + - urgent + title: NotificationVariant + type: string + NotificationsBatchRequest: + properties: + notification_ids: + description: The list of encoded notification IDs of the notifications that + should be updated. + items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + title: Notification IDs + type: array + required: + - notification_ids + title: NotificationsBatchRequest + type: object + NotificationsBatchUpdateResponse: + description: The response of a batch update request. + properties: + updated_count: + description: The number of notifications that were updated. + title: Updated count + type: integer + required: + - updated_count + title: NotificationsBatchUpdateResponse + type: object + ObjectExportTaskResponse: + properties: + create_time: + description: The time and date this item was created. + format: date-time + title: Create Time + type: string + export_metadata: + anyOf: + - $ref: '#/components/schemas/ExportObjectMetadata' + - type: 'null' + id: + description: The encoded database ID of the export request. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + preparing: + description: Whether the archive is currently being built or in preparation. + title: Preparing + type: boolean + ready: + description: Whether the export has completed successfully and the archive + is ready + title: Ready + type: boolean + task_uuid: + description: The identifier of the task processing the export. + format: uuid4 + title: Task ID + type: string + up_to_date: + description: False, if a new export archive should be generated. + title: Up to Date + type: boolean + required: + - id + - ready + - preparing + - up_to_date + - task_uuid + - create_time + title: ObjectExportTaskResponse + type: object + Organization: + properties: + name: + description: Name of the organization responsible for the service + examples: + - My organization + title: Name + type: string + url: + description: URL of the website of the organization (RFC 3986 format) + examples: + - https://example.com + format: uri + minLength: 1 + title: Url + type: string + required: + - name + - url + title: Organization + type: object + PageContentFormat: + enum: + - markdown + - html + title: PageContentFormat + type: string + PageDetails: + additionalProperties: true + properties: + content: + anyOf: + - type: string + - type: 'null' + default: '' + description: Raw text contents of the last page revision (type dependent + on content_format). + title: Content + content_format: + allOf: + - $ref: '#/components/schemas/PageContentFormat' + default: html + description: Either `markdown` or `html`. + title: Content format + create_time: + description: The time and date this item was created. + format: date-time + title: Create Time + type: string + deleted: + description: Whether this Page has been deleted. + title: Deleted + type: boolean + email_hash: + description: The encoded email of the user. + title: Encoded email + type: string + generate_time: + anyOf: + - type: string + - type: 'null' + description: The version of Galaxy this object was generated with. + title: Galaxy Version + generate_version: + anyOf: + - type: string + - type: 'null' + description: The version of Galaxy this object was generated with. + title: Galaxy Version + id: + description: Encoded ID of the Page. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + importable: + description: Whether this Page can be imported. + title: Importable + type: boolean + latest_revision_id: + description: The encoded ID of the last revision of this Page. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Latest revision ID + type: string + model_class: + const: Page + description: The name of the database model class. + title: Model class + type: string + published: + description: Whether this Page has been published. + title: Published + type: boolean + revision_ids: + description: The history with the encoded ID of each revision of the Page. + items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + title: List of revisions + type: array + slug: + description: The title slug for the page URL, must be unique. + pattern: ^[a-z0-9\-]+$ + title: Identifier + type: string + tags: + $ref: '#/components/schemas/TagCollection' + title: + description: The name of the page. + title: Title + type: string + update_time: + description: The last time and date this item was updated. + format: date-time + title: Update Time + type: string + username: + description: The name of the user owning this Page. + title: Username + type: string + required: + - model_class + - title + - slug + - id + - username + - email_hash + - published + - importable + - deleted + - latest_revision_id + - revision_ids + - create_time + - update_time + - tags + title: PageDetails + type: object + PageSummary: + properties: + create_time: + description: The time and date this item was created. + format: date-time + title: Create Time + type: string + deleted: + description: Whether this Page has been deleted. + title: Deleted + type: boolean + email_hash: + description: The encoded email of the user. + title: Encoded email + type: string + id: + description: Encoded ID of the Page. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + importable: + description: Whether this Page can be imported. + title: Importable + type: boolean + latest_revision_id: + description: The encoded ID of the last revision of this Page. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Latest revision ID + type: string + model_class: + const: Page + description: The name of the database model class. + title: Model class + type: string + published: + description: Whether this Page has been published. + title: Published + type: boolean + revision_ids: + description: The history with the encoded ID of each revision of the Page. + items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + title: List of revisions + type: array + slug: + description: The title slug for the page URL, must be unique. + pattern: ^[a-z0-9\-]+$ + title: Identifier + type: string + tags: + $ref: '#/components/schemas/TagCollection' + title: + description: The name of the page. + title: Title + type: string + update_time: + description: The last time and date this item was updated. + format: date-time + title: Update Time + type: string + username: + description: The name of the user owning this Page. + title: Username + type: string + required: + - model_class + - title + - slug + - id + - username + - email_hash + - published + - importable + - deleted + - latest_revision_id + - revision_ids + - create_time + - update_time + - tags + title: PageSummary + type: object + PageSummaryList: + default: [] + items: + $ref: '#/components/schemas/PageSummary' + title: PageSummaryList + type: array + PastedDataElement: + additionalProperties: false + properties: + MD5: + anyOf: + - type: string + - type: 'null' + title: Md5 + auto_decompress: + default: false + description: Decompress compressed data before sniffing? + title: Auto Decompress + type: boolean + collection_type: + anyOf: + - type: string + - type: 'null' + title: Collection Type + created_from_basename: + anyOf: + - type: string + - type: 'null' + title: Created From Basename + dbkey: + default: '?' + title: Dbkey + type: string + deferred: + default: false + title: Deferred + type: boolean + description: + anyOf: + - type: string + - type: 'null' + title: Description + elements_from: + anyOf: + - $ref: '#/components/schemas/ElementsFromType' + - type: 'null' + ext: + default: auto + title: Ext + type: string + extra_files: + anyOf: + - $ref: '#/components/schemas/ExtraFiles' + - type: 'null' + info: + anyOf: + - type: string + - type: 'null' + title: Info + name: + anyOf: + - type: string + - type: integer + - type: number + - type: boolean + - type: 'null' + title: Name + paste_content: + anyOf: + - type: string + - type: integer + - type: number + - type: boolean + description: Content to upload + title: Paste Content + space_to_tab: + default: false + title: Space To Tab + type: boolean + src: + const: pasted + title: Src + tags: + anyOf: + - items: + type: string + type: array + - type: 'null' + title: Tags + to_posix_lines: + default: false + title: To Posix Lines + type: boolean + required: + - src + - paste_content + title: PastedDataElement + type: object + PathDataElement: + additionalProperties: false + properties: + MD5: + anyOf: + - type: string + - type: 'null' + title: Md5 + auto_decompress: + default: false + description: Decompress compressed data before sniffing? + title: Auto Decompress + type: boolean + collection_type: + anyOf: + - type: string + - type: 'null' + title: Collection Type + created_from_basename: + anyOf: + - type: string + - type: 'null' + title: Created From Basename + dbkey: + default: '?' + title: Dbkey + type: string + deferred: + default: false + title: Deferred + type: boolean + description: + anyOf: + - type: string + - type: 'null' + title: Description + elements_from: + anyOf: + - $ref: '#/components/schemas/ElementsFromType' + - type: 'null' + ext: + default: auto + title: Ext + type: string + extra_files: + anyOf: + - $ref: '#/components/schemas/ExtraFiles' + - type: 'null' + info: + anyOf: + - type: string + - type: 'null' + title: Info + link_data_only: + anyOf: + - type: boolean + - type: 'null' + title: Link Data Only + name: + anyOf: + - type: string + - type: integer + - type: number + - type: boolean + - type: 'null' + title: Name + path: + title: Path + type: string + space_to_tab: + default: false + title: Space To Tab + type: boolean + src: + const: path + title: Src + tags: + anyOf: + - items: + type: string + type: array + - type: 'null' + title: Tags + to_posix_lines: + default: false + title: To Posix Lines + type: boolean + required: + - src + - path + title: PathDataElement + type: object + PersonalNotificationCategory: + description: 'These notification categories can be opt-out by the user and will + be + + displayed in the notification preferences.' + enum: + - message + - new_shared_item + title: PersonalNotificationCategory + type: string + PluginKind: + description: Enum to distinguish between different kinds or categories of plugins. + enum: + - rfs + - drs + - rdm + - stock + title: PluginKind + type: string + PrepareStoreDownloadPayload: + properties: + bco_merge_history_metadata: + default: false + description: When reading tags/annotations to generate BCO object include + history metadata. + title: Bco Merge History Metadata + type: boolean + bco_override_algorithmic_error: + anyOf: + - additionalProperties: + type: string + type: object + - type: 'null' + description: Override algorithmic error for 'error domain' when generating + BioCompute object. + title: Bco Override Algorithmic Error + bco_override_empirical_error: + anyOf: + - additionalProperties: + type: string + type: object + - type: 'null' + description: Override empirical error for 'error domain' when generating + BioCompute object. + title: Bco Override Empirical Error + bco_override_environment_variables: + anyOf: + - additionalProperties: + type: string + type: object + - type: 'null' + description: Override environment variables for 'execution_domain' when + generating BioCompute object. + title: Bco Override Environment Variables + bco_override_xref: + anyOf: + - items: + $ref: '#/components/schemas/XrefItem' + type: array + - type: 'null' + description: Override xref for 'description domain' when generating BioCompute + object. + title: Bco Override Xref + include_deleted: + default: false + description: Include file contents for deleted datasets (if include_files + is True). + title: Include deleted + type: boolean + include_files: + default: true + description: include materialized files in export when available + title: Include Files + type: boolean + include_hidden: + default: false + description: Include file contents for hidden datasets (if include_files + is True). + title: Include hidden + type: boolean + model_store_format: + allOf: + - $ref: '#/components/schemas/ModelStoreFormat' + default: tar.gz + description: format of model store to export + title: PrepareStoreDownloadPayload + type: object + QuotaDetails: + properties: + bytes: + description: The amount, expressed in bytes, of this Quota. + title: Bytes + type: integer + default: + default: [] + description: A list indicating which types of default user quotas, if any, + are associated with this quota. + items: + $ref: '#/components/schemas/DefaultQuota' + title: Default + type: array + description: + description: Detailed text description for this Quota. + title: Description + type: string + display_amount: + description: Human-readable representation of the `amount` field. + title: Display Amount + type: string + groups: + default: [] + description: A list of specific groups of users associated with this quota. + items: + $ref: '#/components/schemas/GroupQuota' + title: Groups + type: array + id: + description: The `encoded identifier` of the quota. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + model_class: + const: Quota + description: The name of the database model class. + title: Model class + type: string + name: + description: The name of the quota. This must be unique within a Galaxy + instance. + title: Name + type: string + operation: + allOf: + - $ref: '#/components/schemas/QuotaOperation' + default: '=' + description: 'Quotas can have one of three `operations`:- `=` : The quota + is exactly the amount specified- `+` : The amount specified will be added + to the amounts of the user''s other associated quota definitions- `-` + : The amount specified will be subtracted from the amounts of the user''s + other associated quota definitions' + title: Operation + quota_source_label: + anyOf: + - type: string + - type: 'null' + description: Quota source label + title: Quota Source Label + users: + default: [] + description: A list of specific users associated with this quota. + items: + $ref: '#/components/schemas/UserQuota' + title: Users + type: array + required: + - model_class + - id + - name + - description + - bytes + - display_amount + title: QuotaDetails + type: object + QuotaModel: + properties: + enabled: + title: Enabled + type: boolean + source: + anyOf: + - type: string + - type: 'null' + title: Source + required: + - enabled + title: QuotaModel + type: object + QuotaOperation: + enum: + - '=' + - + + - '-' + title: QuotaOperation + type: string + QuotaSummary: + description: Contains basic information about a Quota + properties: + id: + description: The `encoded identifier` of the quota. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + model_class: + const: Quota + description: The name of the database model class. + title: Model class + type: string + name: + description: The name of the quota. This must be unique within a Galaxy + instance. + title: Name + type: string + quota_source_label: + anyOf: + - type: string + - type: 'null' + description: Quota source label + title: Quota Source Label + url: + deprecated: true + description: The relative URL to get this particular Quota details from + the rest API. + title: URL + type: string + required: + - model_class + - id + - name + - url + title: QuotaSummary + type: object + QuotaSummaryList: + default: [] + items: + $ref: '#/components/schemas/QuotaSummary' + title: QuotaSummaryList + type: array + ReloadFeedback: + properties: + failed: + items: + anyOf: + - type: string + - type: 'null' + title: Failed + type: array + message: + title: Message + type: string + reloaded: + items: + anyOf: + - type: string + - type: 'null' + title: Reloaded + type: array + required: + - message + - reloaded + - failed + title: ReloadFeedback + type: object + RemoteDirectory: + properties: + class: + const: Directory + title: Class + name: + description: The name of the entry. + title: Name + type: string + path: + description: The path of the entry. + title: Path + type: string + uri: + description: The URI of the entry. + title: URI + type: string + required: + - name + - uri + - path + - class + title: RemoteDirectory + type: object + RemoteFile: + properties: + class: + const: File + title: Class + ctime: + description: The creation time of the file. + title: Creation time + type: string + name: + description: The name of the entry. + title: Name + type: string + path: + description: The path of the entry. + title: Path + type: string + size: + description: The size of the file in bytes. + title: Size + type: integer + uri: + description: The URI of the entry. + title: URI + type: string + required: + - name + - uri + - path + - class + - size + - ctime + title: RemoteFile + type: object + RemoteFilesDisableMode: + enum: + - folders + - files + title: RemoteFilesDisableMode + type: string + RemoteFilesFormat: + enum: + - flat + - jstree + - uri + title: RemoteFilesFormat + type: string + RemoteUserCreationPayload: + properties: + remote_user_email: + description: Email of the user + title: Email + type: string + required: + - remote_user_email + title: RemoteUserCreationPayload + type: object + ReportJobErrorPayload: + properties: + dataset_id: + description: The History Dataset Association ID related to the error. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: History Dataset Association ID + type: string + email: + anyOf: + - type: string + - type: 'null' + description: Email address for communication with the user. Only required + for anonymous users. + title: Email + message: + anyOf: + - type: string + - type: 'null' + description: The optional message sent with the error report. + title: Message + required: + - dataset_id + title: ReportJobErrorPayload + type: object + RequestDataType: + description: Particular pieces of information that can be requested for a dataset. + enum: + - state + - converted_datasets_state + - data + - features + - raw_data + - track_config + - genome_data + - in_use_state + title: RequestDataType + type: string + Requirement: + description: Available types of job sources (model classes) that produce dataset + collections. + enum: + - logged_in + - new_history + - admin + title: Requirement + type: string + RoleDefinitionModel: + properties: + description: + description: Description of the role + title: Description + type: string + group_ids: + anyOf: + - items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + type: array + - type: 'null' + default: [] + title: Group IDs + name: + description: Name of the role + title: Name + type: string + user_ids: + anyOf: + - items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + type: array + - type: 'null' + default: [] + title: User IDs + required: + - name + - description + title: RoleDefinitionModel + type: object + RoleListResponse: + items: + $ref: '#/components/schemas/RoleModelResponse' + title: RoleListResponse + type: array + RoleModelResponse: + properties: + description: + anyOf: + - description: Description of the role + title: Description + type: string + - type: 'null' + title: Description + id: + description: Encoded ID of the role + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + model_class: + const: Role + description: The name of the database model class. + title: Model class + type: string + name: + description: Name of the role + title: Name + type: string + type: + description: Type or category of the role + title: Type + type: string + url: + deprecated: true + description: The relative URL to access this item. + title: URL + type: string + required: + - model_class + - id + - name + - type + - description + - url + title: RoleModelResponse + type: object + RootModel_Dict_str__int__: + additionalProperties: + type: integer + title: RootModel[Dict[str, int]] + type: object + SearchJobsPayload: + additionalProperties: true + properties: + inputs: + description: The inputs of the job. + title: Inputs + type: object + state: + anyOf: + - $ref: '#/components/schemas/JobState' + - type: 'null' + description: Current state of the job. + title: State + tool_id: + description: The tool ID related to the job. + title: Tool ID + type: string + required: + - tool_id + - inputs + title: SearchJobsPayload + type: object + ServerDirElement: + additionalProperties: false + properties: + MD5: + anyOf: + - type: string + - type: 'null' + title: Md5 + auto_decompress: + default: false + description: Decompress compressed data before sniffing? + title: Auto Decompress + type: boolean + collection_type: + anyOf: + - type: string + - type: 'null' + title: Collection Type + created_from_basename: + anyOf: + - type: string + - type: 'null' + title: Created From Basename + dbkey: + default: '?' + title: Dbkey + type: string + deferred: + default: false + title: Deferred + type: boolean + description: + anyOf: + - type: string + - type: 'null' + title: Description + elements_from: + anyOf: + - $ref: '#/components/schemas/ElementsFromType' + - type: 'null' + ext: + default: auto + title: Ext + type: string + extra_files: + anyOf: + - $ref: '#/components/schemas/ExtraFiles' + - type: 'null' + info: + anyOf: + - type: string + - type: 'null' + title: Info + link_data_only: + anyOf: + - type: boolean + - type: 'null' + title: Link Data Only + name: + anyOf: + - type: string + - type: integer + - type: number + - type: boolean + - type: 'null' + title: Name + server_dir: + title: Server Dir + type: string + space_to_tab: + default: false + title: Space To Tab + type: boolean + src: + const: server_dir + title: Src + tags: + anyOf: + - items: + type: string + type: array + - type: 'null' + title: Tags + to_posix_lines: + default: false + title: To Posix Lines + type: boolean + required: + - src + - server_dir + title: ServerDirElement + type: object + Service: + properties: + contactUrl: + anyOf: + - format: uri + minLength: 1 + type: string + - type: 'null' + description: URL of the contact for the provider of this service, e.g. a + link to a contact form (RFC 3986 format), or an email (RFC 2368 format). + examples: + - mailto:support@example.com + title: Contacturl + createdAt: + anyOf: + - format: date-time + type: string + - type: 'null' + description: Timestamp describing when the service was first deployed and + available (RFC 3339 format) + examples: + - '2019-06-04T12:58:19Z' + title: Createdat + description: + anyOf: + - type: string + - type: 'null' + description: Description of the service. Should be human readable and provide + information about the service. + examples: + - This service provides... + title: Description + documentationUrl: + anyOf: + - format: uri + minLength: 1 + type: string + - type: 'null' + description: URL of the documentation of this service (RFC 3986 format). + This should help someone learn how to use your service, including any + specifics required to access data, e.g. authentication. + examples: + - https://docs.myservice.example.com + title: Documentationurl + environment: + anyOf: + - type: string + - type: 'null' + description: Environment the service is running in. Use this to distinguish + between production, development and testing/staging deployments. Suggested + values are prod, test, dev, staging. However this is advised and not enforced. + examples: + - test + title: Environment + id: + description: Unique ID of this service. Reverse domain name notation is + recommended, though not required. The identifier should attempt to be + globally unique so it can be used in downstream aggregator services e.g. + Service Registry. + examples: + - org.ga4gh.myservice + title: Id + type: string + name: + description: Name of this service. Should be human readable. + examples: + - My project + title: Name + type: string + organization: + allOf: + - $ref: '#/components/schemas/Organization' + description: Organization providing the service + type: + $ref: '#/components/schemas/ServiceType' + updatedAt: + anyOf: + - format: date-time + type: string + - type: 'null' + description: Timestamp describing when the service was last updated (RFC + 3339 format) + examples: + - '2019-06-04T12:58:19Z' + title: Updatedat + version: + description: Version of the service being described. Semantic versioning + is recommended, but other identifiers, such as dates or commit hashes, + are also allowed. The version should be changed whenever the service is + updated. + examples: + - 1.0.0 + title: Version + type: string + required: + - id + - name + - type + - organization + - version + title: Service + type: object + ServiceType: + properties: + artifact: + description: Name of the API or GA4GH specification implemented. Official + GA4GH types should be assigned as part of standards approval process. + Custom artifacts are supported. + examples: + - beacon + title: Artifact + type: string + group: + description: Namespace in reverse domain name format. Use `org.ga4gh` for + implementations compliant with official GA4GH specifications. For services + with custom APIs not standardized by GA4GH, or implementations diverging + from official GA4GH specifications, use a different namespace (e.g. your + organization's reverse domain name). + examples: + - org.ga4gh + title: Group + type: string + version: + description: Version of the API or specification. GA4GH specifications use + semantic versioning. + examples: + - 1.0.0 + title: Version + type: string + required: + - group + - artifact + - version + title: ServiceType + type: object + SetSlugPayload: + properties: + new_slug: + description: The slug that will be used to access this shared item. + title: New Slug + type: string + required: + - new_slug + title: SetSlugPayload + type: object + ShareHistoryExtra: + properties: + accessible_count: + default: 0 + description: The number of datasets in the history that are public or accessible + by all the target users. + title: Accessible Count + type: integer + can_change: + default: [] + description: A collection of datasets that are not accessible by one or + more of the target users and that can be made accessible for others by + the user sharing the history. + items: + $ref: '#/components/schemas/HDABasicInfo' + title: Can Change + type: array + can_share: + default: false + description: Indicates whether the resource can be directly shared or requires + further actions. + title: Can Share + type: boolean + cannot_change: + default: [] + description: A collection of datasets that are not accessible by one or + more of the target users and that cannot be made accessible for others + by the user sharing the history. + items: + $ref: '#/components/schemas/HDABasicInfo' + title: Cannot Change + type: array + title: ShareHistoryExtra + type: object + ShareHistoryWithStatus: + properties: + email_hash: + anyOf: + - type: string + - type: 'null' + description: Encoded owner email. + title: Encoded Email + errors: + default: [] + description: Collection of messages indicating that the resource was not + shared with some (or all users) due to an error. + items: + type: string + title: Errors + type: array + extra: + allOf: + - $ref: '#/components/schemas/ShareHistoryExtra' + description: Optional extra information about this shareable resource that + may be of interest. The contents of this field depend on the particular + resource. + title: Extra + id: + description: The encoded ID of the resource to be shared. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + importable: + description: Whether this resource can be published using a link. + title: Importable + type: boolean + published: + description: Whether this resource is currently published. + title: Published + type: boolean + title: + description: The title or name of the resource. + title: Title + type: string + username: + anyOf: + - type: string + - type: 'null' + description: The owner's username. + title: Username + username_and_slug: + anyOf: + - type: string + - type: 'null' + description: The relative URL in the form of /u/{username}/{resource_single_char}/{slug} + title: Username and slug + users_shared_with: + default: [] + description: The list of encoded ids for users the resource has been shared. + items: + $ref: '#/components/schemas/UserEmail' + title: Users shared with + type: array + required: + - id + - title + - importable + - published + - extra + title: ShareHistoryWithStatus + type: object + ShareWithExtra: + properties: + can_share: + default: false + description: Indicates whether the resource can be directly shared or requires + further actions. + title: Can Share + type: boolean + title: ShareWithExtra + type: object + ShareWithPayload: + properties: + share_option: + anyOf: + - $ref: '#/components/schemas/SharingOptions' + - type: 'null' + description: "User choice for sharing resources which its contents may be\ + \ restricted:\n - None: The user did not choose anything yet or no option\ + \ is needed.\n - make_public: The contents of the resource will be made\ + \ publicly accessible.\n - make_accessible_to_shared: This will automatically\ + \ create a new `sharing role` allowing protected contents to be accessed\ + \ only by the desired users.\n - no_changes: This won't change the current\ + \ permissions for the contents. The user which this resource will be shared\ + \ may not be able to access all its contents.\n" + title: Share Option + user_ids: + description: A collection of encoded IDs (or email addresses) of users that + this resource will be shared with. + items: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: string + title: User Identifiers + type: array + required: + - user_ids + title: ShareWithPayload + type: object + ShareWithStatus: + properties: + email_hash: + anyOf: + - type: string + - type: 'null' + description: Encoded owner email. + title: Encoded Email + errors: + default: [] + description: Collection of messages indicating that the resource was not + shared with some (or all users) due to an error. + items: + type: string + title: Errors + type: array + extra: + anyOf: + - $ref: '#/components/schemas/ShareWithExtra' + - type: 'null' + description: Optional extra information about this shareable resource that + may be of interest. The contents of this field depend on the particular + resource. + title: Extra + id: + description: The encoded ID of the resource to be shared. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + importable: + description: Whether this resource can be published using a link. + title: Importable + type: boolean + published: + description: Whether this resource is currently published. + title: Published + type: boolean + title: + description: The title or name of the resource. + title: Title + type: string + username: + anyOf: + - type: string + - type: 'null' + description: The owner's username. + title: Username + username_and_slug: + anyOf: + - type: string + - type: 'null' + description: The relative URL in the form of /u/{username}/{resource_single_char}/{slug} + title: Username and slug + users_shared_with: + default: [] + description: The list of encoded ids for users the resource has been shared. + items: + $ref: '#/components/schemas/UserEmail' + title: Users shared with + type: array + required: + - id + - title + - importable + - published + title: ShareWithStatus + type: object + SharingOptions: + description: Options for sharing resources that may have restricted access to + all or part of their contents. + enum: + - make_public + - make_accessible_to_shared + - no_changes + title: SharingOptions + type: string + SharingStatus: + properties: + email_hash: + anyOf: + - type: string + - type: 'null' + description: Encoded owner email. + title: Encoded Email + id: + description: The encoded ID of the resource to be shared. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + importable: + description: Whether this resource can be published using a link. + title: Importable + type: boolean + published: + description: Whether this resource is currently published. + title: Published + type: boolean + title: + description: The title or name of the resource. + title: Title + type: string + username: + anyOf: + - type: string + - type: 'null' + description: The owner's username. + title: Username + username_and_slug: + anyOf: + - type: string + - type: 'null' + description: The relative URL in the form of /u/{username}/{resource_single_char}/{slug} + title: Username and slug + users_shared_with: + default: [] + description: The list of encoded ids for users the resource has been shared. + items: + $ref: '#/components/schemas/UserEmail' + title: Users shared with + type: array + required: + - id + - title + - importable + - published + title: SharingStatus + type: object + ShortTermStoreExportPayload: + properties: + duration: + anyOf: + - type: integer + - type: number + - type: 'null' + title: Duration + include_deleted: + default: false + description: Include file contents for deleted datasets (if include_files + is True). + title: Include deleted + type: boolean + include_files: + default: true + description: include materialized files in export when available + title: Include Files + type: boolean + include_hidden: + default: false + description: Include file contents for hidden datasets (if include_files + is True). + title: Include hidden + type: boolean + model_store_format: + allOf: + - $ref: '#/components/schemas/ModelStoreFormat' + default: tar.gz + description: format of model store to export + short_term_storage_request_id: + format: uuid + title: Short Term Storage Request Id + type: string + required: + - short_term_storage_request_id + title: ShortTermStoreExportPayload + type: object + ShowFullJobResponse: + properties: + command_line: + anyOf: + - type: string + - type: 'null' + description: The command line produced by the job. Users can see this value + if allowed in the configuration, administrator can always see this value. + title: Command Line + command_version: + anyOf: + - type: string + - type: 'null' + description: Tool version indicated during job execution. + title: Command Version + copied_from_job_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: Reference to cached job if job execution was cached. + title: Copied from Job-ID + create_time: + description: The time and date this item was created. + format: date-time + title: Create Time + type: string + dependencies: + anyOf: + - items: {} + type: array + - type: 'null' + description: The dependencies of the job. + title: Job dependencies + exit_code: + anyOf: + - type: integer + - type: 'null' + description: The exit code returned by the tool. Can be unset if the job + is not completed yet. + title: Exit Code + external_id: + anyOf: + - type: string + - type: 'null' + description: The job id used by the external job runner (Condor, Pulsar, + etc.). Only administrator can see this value. + title: External ID + galaxy_version: + anyOf: + - type: string + - type: 'null' + description: The (major) version of Galaxy used to create this job. + examples: + - '21.05' + title: Galaxy Version + handler: + anyOf: + - type: string + - type: 'null' + description: The job handler process assigned to handle this job. Only administrator + can see this value. + title: Job Handler + history_id: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + - type: 'null' + description: The encoded ID of the history associated with this item. + title: History ID + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Job ID + type: string + inputs: + additionalProperties: + $ref: '#/components/schemas/EncodedDatasetJobInfo' + default: {} + description: Dictionary mapping all the tool inputs (by name) to the corresponding + data references. + title: Inputs + type: object + job_messages: + anyOf: + - items: {} + type: array + - type: 'null' + description: List with additional information and possible reasons for a + failed job. + title: Job Messages + job_metrics: + anyOf: + - $ref: '#/components/schemas/JobMetricCollection' + - type: 'null' + description: Collections of metrics provided by `JobInstrumenter` plugins + on a particular job. Only administrators can see these metrics. + title: Job Metrics + job_runner_name: + anyOf: + - type: string + - type: 'null' + description: Name of the job runner plugin that handles this job. Only administrator + can see this value. + title: Job Runner Name + job_stderr: + anyOf: + - type: string + - type: 'null' + description: The captured standard error of the job execution. + title: Job Standard Error + job_stdout: + anyOf: + - type: string + - type: 'null' + description: The captured standard output of the job execution. + title: Job Standard Output + model_class: + const: Job + description: The name of the database model class. + title: Model class + type: string + output_collections: + additionalProperties: + $ref: '#/components/schemas/EncodedHdcaSourceId' + default: {} + description: '' + title: Output collections + type: object + outputs: + additionalProperties: + $ref: '#/components/schemas/EncodedDatasetJobInfo' + default: {} + description: Dictionary mapping all the tool outputs (by name) to the corresponding + data references. + title: Outputs + type: object + params: + description: Object containing all the parameters of the tool associated + with this job. The specific parameters depend on the tool itself. + title: Parameters + state: + allOf: + - $ref: '#/components/schemas/JobState' + description: Current state of the job. + title: State + stderr: + anyOf: + - type: string + - type: 'null' + description: Combined tool and job standard error streams. + title: Standard Error + stdout: + anyOf: + - type: string + - type: 'null' + description: Combined tool and job standard output streams. + title: Standard Output + tool_id: + description: Identifier of the tool that generated this job. + title: Tool ID + type: string + tool_stderr: + anyOf: + - type: string + - type: 'null' + description: The captured standard error of the tool executed by the job. + title: Tool Standard Error + tool_stdout: + anyOf: + - type: string + - type: 'null' + description: The captured standard output of the tool executed by the job. + title: Tool Standard Output + update_time: + description: The last time and date this item was updated. + format: date-time + title: Update Time + type: string + user_email: + anyOf: + - type: string + - type: 'null' + description: The email of the user that owns this job. Only the owner of + the job and administrators can see this value. + title: User Email + required: + - model_class + - id + - tool_id + - state + - create_time + - update_time + - params + title: ShowFullJobResponse + type: object + Src: + enum: + - url + - pasted + - files + - path + - composite + - ftp_import + - server_dir + title: Src + type: string + StorageItemCleanupError: + properties: + error: + title: Error + type: string + item_id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Item Id + type: string + required: + - item_id + - error + title: StorageItemCleanupError + type: object + StorageItemsCleanupResult: + properties: + errors: + items: + $ref: '#/components/schemas/StorageItemCleanupError' + title: Errors + type: array + success_item_count: + title: Success Item Count + type: integer + total_free_bytes: + title: Total Free Bytes + type: integer + total_item_count: + title: Total Item Count + type: integer + required: + - total_item_count + - success_item_count + - total_free_bytes + - errors + title: StorageItemsCleanupResult + type: object + StoreExportPayload: + properties: + include_deleted: + default: false + description: Include file contents for deleted datasets (if include_files + is True). + title: Include deleted + type: boolean + include_files: + default: true + description: include materialized files in export when available + title: Include Files + type: boolean + include_hidden: + default: false + description: Include file contents for hidden datasets (if include_files + is True). + title: Include hidden + type: boolean + model_store_format: + allOf: + - $ref: '#/components/schemas/ModelStoreFormat' + default: tar.gz + description: format of model store to export + title: StoreExportPayload + type: object + StoredItem: + properties: + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Id + type: string + name: + title: Name + type: string + size: + title: Size + type: integer + type: + anyOf: + - const: history + - const: dataset + title: Type + update_time: + description: The last time and date this item was updated. + format: date-time + title: Update Time + type: string + required: + - id + - name + - type + - size + - update_time + title: StoredItem + type: object + StoredItemOrderBy: + description: Available options for sorting Stored Items results. + enum: + - name-asc + - name-dsc + - size-asc + - size-dsc + - update_time-asc + - update_time-dsc + title: StoredItemOrderBy + type: string + SuitableConverter: + properties: + name: + description: The name of the converter. + title: Name + type: string + original_type: + description: The type to convert from. + title: Original Type + type: string + target_type: + description: The type to convert to. + title: Target Type + type: string + tool_id: + description: The ID of the tool that can perform the type conversion. + title: Tool Id + type: string + required: + - tool_id + - name + - target_type + - original_type + title: SuitableConverter + type: object + SuitableConverters: + description: Collection of converters that can be used on a particular dataset + collection. + items: + $ref: '#/components/schemas/SuitableConverter' + title: SuitableConverters + type: array + SupportedType: + enum: + - None + - BasicAuth + - BearerAuth + - PassportAuth + title: SupportedType + type: string + TagCollection: + description: Represents the collection of tags associated with an item. + items: + pattern: ^([^\s.:])+(.[^\s.:]+)*(:[^\s.:]+)?$ + type: string + title: TagCollection + type: array + TagOperationParams: + properties: + tags: + items: + type: string + title: Tags + type: array + type: + anyOf: + - const: add_tags + - const: remove_tags + title: Type + required: + - type + - tags + title: TagOperationParams + type: object + TaggableItemClass: + enum: + - History + - HistoryDatasetAssociation + - HistoryDatasetCollectionAssociation + - LibraryDatasetDatasetAssociation + - Page + - StoredWorkflow + - Visualization + title: TaggableItemClass + type: string + TaskState: + description: Enum representing the possible states of a task. + enum: + - PENDING + - STARTED + - RETRY + - FAILURE + - SUCCESS + title: TaskState + type: string + ToolDataDetails: + properties: + columns: + description: A list of column names + examples: + - value + - dbkey + - name + - path + items: + type: string + title: Columns + type: array + fields: + default: [] + description: '' + items: + items: + type: string + type: array + title: Fields + type: array + model_class: + description: The name of class modelling this tool data + examples: + - TabularToolDataTable + title: Model class + type: string + name: + description: The name of this tool data entry + examples: + - all_fasta + title: Name + type: string + required: + - name + - model_class + - columns + title: ToolDataDetails + type: object + ToolDataEntry: + properties: + model_class: + description: The name of class modelling this tool data + examples: + - TabularToolDataTable + title: Model class + type: string + name: + description: The name of this tool data entry + examples: + - all_fasta + title: Name + type: string + required: + - name + - model_class + title: ToolDataEntry + type: object + ToolDataEntryList: + items: + $ref: '#/components/schemas/ToolDataEntry' + title: ToolDataEntryList + type: array + ToolDataField: + properties: + base_dir: + description: A list of directories where the data files are stored + items: + type: string + title: Base directories + type: array + fields: + additionalProperties: + type: string + description: '' + title: Fields + type: object + files: + additionalProperties: + type: integer + description: A dictionary of file names and their size in bytes + examples: + - file.txt: 136 + title: Files + type: object + fingerprint: + description: SHA1 Hash + examples: + - 22b45237a85c2b3f474bf66888c534387ffe0ced + title: Fingerprint + type: string + model_class: + description: The name of class modelling this tool data field + examples: + - TabularToolDataField + title: Model class + type: string + name: + description: The name of the field + title: Name + type: string + required: + - name + - model_class + - fields + - base_dir + - files + - fingerprint + title: ToolDataField + type: object + ToolDataItem: + properties: + values: + description: A `\t` (TAB) separated list of column __contents__. You must + specify a value for each of the columns of the data table. + examples: + - "value\tdbkey\tname\tpath" + title: Values + type: string + required: + - values + title: ToolDataItem + type: object + Tour: + properties: + description: + description: Tour description + title: Description + type: string + id: + description: Tour identifier + title: Identifier + type: string + name: + description: Name of tour + title: Name + type: string + requirements: + description: Requirements to run the tour. + items: + $ref: '#/components/schemas/Requirement' + title: Requirements + type: array + tags: + description: Topic topic tags + items: + type: string + title: Tags + type: array + required: + - name + - description + - tags + - requirements + - id + title: Tour + type: object + TourDetails: + properties: + description: + description: Tour description + title: Description + type: string + name: + description: Name of tour + title: Name + type: string + requirements: + description: Requirements to run the tour. + items: + $ref: '#/components/schemas/Requirement' + title: Requirements + type: array + steps: + description: Tour steps + items: + $ref: '#/components/schemas/TourStep' + title: Steps + type: array + tags: + description: Topic topic tags + items: + type: string + title: Tags + type: array + title_default: + anyOf: + - type: string + - type: 'null' + description: Default title for each step + title: Default title + required: + - name + - description + - tags + - requirements + - steps + title: TourDetails + type: object + TourList: + default: [] + items: + $ref: '#/components/schemas/Tour' + title: TourList + type: array + TourStep: + properties: + content: + anyOf: + - type: string + - type: 'null' + description: Text shown to the user + title: Content + element: + anyOf: + - type: string + - type: 'null' + description: CSS selector for the element to be described/clicked + title: Element + placement: + anyOf: + - type: string + - type: 'null' + description: Placement of the text box relative to the selected element + title: Placement + postclick: + anyOf: + - type: boolean + - items: + type: string + type: array + - type: 'null' + description: Elements that receive a click() event after the step is shown + title: Post-click + preclick: + anyOf: + - type: boolean + - items: + type: string + type: array + - type: 'null' + description: Elements that receive a click() event before the step is shown + title: Pre-click + textinsert: + anyOf: + - type: string + - type: 'null' + description: Text to insert if element is a text box (e.g. tool search or + upload) + title: Text-insert + title: + anyOf: + - type: string + - type: 'null' + description: Title displayed in the header of the step container + title: Title + title: TourStep + type: object + UndeleteHistoriesPayload: + properties: + ids: + description: List of history IDs to be undeleted. + items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + title: IDs + type: array + required: + - ids + title: UndeleteHistoriesPayload + type: object + UpdateCollectionAttributePayload: + additionalProperties: false + description: Contains attributes that can be updated for all elements in a dataset + collection. + properties: + dbkey: + description: TODO + title: Dbkey + type: string + required: + - dbkey + title: UpdateCollectionAttributePayload + type: object + UpdateContentItem: + additionalProperties: true + description: Used for updating a particular history item. All fields are optional. + properties: + history_content_type: + allOf: + - $ref: '#/components/schemas/HistoryContentType' + description: The type of this item. + title: Content Type + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Id + type: string + required: + - history_content_type + - id + title: UpdateContentItem + type: object + UpdateHistoryContentsBatchPayload: + additionalProperties: true + description: Contains property values that will be updated for all the history + `items` provided. + example: + items: + - history_content_type: dataset + id: string + visible: false + properties: + items: + description: A list of content items to update with the changes. + items: + $ref: '#/components/schemas/UpdateContentItem' + title: Items + type: array + required: + - items + title: UpdateHistoryContentsBatchPayload + type: object + UpdateHistoryContentsPayload: + additionalProperties: true + description: Can contain arbitrary/dynamic fields that will be updated for a + particular history item. + example: + annotation: Test + visible: false + properties: + annotation: + anyOf: + - type: string + - type: 'null' + description: A user-defined annotation for this item. + title: Annotation + deleted: + anyOf: + - type: boolean + - type: 'null' + description: Whether this item is marked as deleted. + title: Deleted + name: + anyOf: + - type: string + - type: 'null' + description: The new name of the item. + title: Name + tags: + anyOf: + - $ref: '#/components/schemas/TagCollection' + - type: 'null' + description: A list of tags to add to this item. + title: Tags + visible: + anyOf: + - type: boolean + - type: 'null' + description: Whether this item is visible in the history. + title: Visible + title: UpdateHistoryContentsPayload + type: object + UpdateLibraryFolderPayload: + properties: + description: + anyOf: + - type: string + - type: 'null' + description: The new description of the library folder. + title: Description + name: + anyOf: + - type: string + - type: 'null' + description: The new name of the library folder. + title: Name + title: UpdateLibraryFolderPayload + type: object + UpdateLibraryPayload: + properties: + description: + anyOf: + - type: string + - type: 'null' + description: A detailed description of the Library. Leave unset to keep + the existing. + title: Description + name: + anyOf: + - type: string + - type: 'null' + description: The new name of the Library. Leave unset to keep the existing. + title: Name + synopsis: + anyOf: + - type: string + - type: 'null' + description: A short text describing the contents of the Library. Leave + unset to keep the existing. + title: Synopsis + title: UpdateLibraryPayload + type: object + UpdateObjectStoreIdPayload: + properties: + object_store_id: + description: Object store ID to update to, it must be an object store with + the same device ID as the target dataset currently. + title: Object Store Id + type: string + required: + - object_store_id + title: UpdateObjectStoreIdPayload + type: object + UpdateQuotaParams: + properties: + amount: + anyOf: + - type: string + - type: 'null' + description: Quota size (E.g. ``10000MB``, ``99 gb``, ``0.2T``, ``unlimited``) + title: Amount + default: + anyOf: + - $ref: '#/components/schemas/DefaultQuotaValues' + - type: 'null' + description: Whether or not this is a default quota. Valid values are ``no``, + ``unregistered``, ``registered``. Calling this method with ``default="no"`` + on a non-default quota will throw an error. Not passing this parameter + is equivalent to passing ``no``. + title: Default + description: + anyOf: + - type: string + - type: 'null' + description: Detailed text description for this Quota. + title: Description + in_groups: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: A list of group IDs or names to associate with this quota. + title: Groups + in_users: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: A list of user IDs or user emails to associate with this quota. + title: Users + name: + anyOf: + - type: string + - type: 'null' + description: The new name of the quota. This must be unique within a Galaxy + instance. + title: Name + operation: + allOf: + - $ref: '#/components/schemas/QuotaOperation' + default: '=' + description: One of (``+``, ``-``, ``=``). If you wish to change this value, + you must also provide the ``amount``, otherwise it will not take effect. + title: Operation + title: UpdateQuotaParams + type: object + UpdateUserNotificationPreferencesRequest: + description: Contains the new notification preferences of a user. + examples: + - preferences: + message: + channels: + push: true + enabled: true + new_shared_item: + channels: + push: true + enabled: true + properties: + preferences: + additionalProperties: + $ref: '#/components/schemas/NotificationCategorySettings' + description: The new notification preferences of the user. + title: Preferences + type: object + required: + - preferences + title: UpdateUserNotificationPreferencesRequest + type: object + UrlDataElement: + additionalProperties: false + properties: + MD5: + anyOf: + - type: string + - type: 'null' + title: Md5 + auto_decompress: + default: false + description: Decompress compressed data before sniffing? + title: Auto Decompress + type: boolean + collection_type: + anyOf: + - type: string + - type: 'null' + title: Collection Type + created_from_basename: + anyOf: + - type: string + - type: 'null' + title: Created From Basename + dbkey: + default: '?' + title: Dbkey + type: string + deferred: + default: false + title: Deferred + type: boolean + description: + anyOf: + - type: string + - type: 'null' + title: Description + elements_from: + anyOf: + - $ref: '#/components/schemas/ElementsFromType' + - type: 'null' + ext: + default: auto + title: Ext + type: string + extra_files: + anyOf: + - $ref: '#/components/schemas/ExtraFiles' + - type: 'null' + info: + anyOf: + - type: string + - type: 'null' + title: Info + name: + anyOf: + - type: string + - type: integer + - type: number + - type: boolean + - type: 'null' + title: Name + space_to_tab: + default: false + title: Space To Tab + type: boolean + src: + const: url + title: Src + tags: + anyOf: + - items: + type: string + type: array + - type: 'null' + title: Tags + to_posix_lines: + default: false + title: To Posix Lines + type: boolean + url: + description: URL to upload + title: Url + type: string + required: + - src + - url + title: UrlDataElement + type: object + UserBeaconSetting: + properties: + enabled: + description: True if beacon sharing is enabled + title: Enabled + type: boolean + required: + - enabled + title: UserBeaconSetting + type: object + UserCreationPayload: + properties: + email: + description: Email of the user + title: Email + type: string + password: + description: The password of the user. + title: user_password + type: string + username: + description: The name of the user. + title: user_name + type: string + required: + - password + - email + - username + title: UserCreationPayload + type: object + UserDeletionPayload: + properties: + purge: + description: Purge the user + title: Purge user + type: boolean + required: + - purge + title: UserDeletionPayload + type: object + UserEmail: + properties: + email: + description: The email of the user. + title: Email + type: string + id: + description: The encoded ID of the user. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: User ID + type: string + required: + - id + - email + title: UserEmail + type: object + UserModel: + description: User in a transaction context. + properties: + active: + description: User is active + title: Active + type: boolean + deleted: + description: ' User is deleted' + title: Deleted + type: boolean + email: + description: Email of the user + title: Email + type: string + id: + description: Encoded ID of the user + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + last_password_change: + anyOf: + - format: date-time + type: string + - type: 'null' + description: '' + title: Last password change + model_class: + const: User + description: The name of the database model class. + title: Model class + type: string + username: + description: The name of the user. + title: user_name + type: string + required: + - model_class + - id + - username + - email + - deleted + - active + - last_password_change + title: UserModel + type: object + UserNotificationListResponse: + description: A list of user notifications. + items: + $ref: '#/components/schemas/UserNotificationResponse' + title: UserNotificationListResponse + type: array + UserNotificationPreferences: + description: Contains the full notification preferences of a user. + examples: + - preferences: + message: + channels: + push: true + enabled: true + new_shared_item: + channels: + push: true + enabled: true + properties: + preferences: + additionalProperties: + $ref: '#/components/schemas/NotificationCategorySettings' + description: The notification preferences of the user. + title: Preferences + type: object + required: + - preferences + title: UserNotificationPreferences + type: object + UserNotificationResponse: + description: A notification response specific to the user. + properties: + category: + allOf: + - $ref: '#/components/schemas/PersonalNotificationCategory' + description: The category of the notification. Represents the type of the + notification. E.g. 'message' or 'new_shared_item'. + title: Category + content: + description: The content of the notification. The structure depends on the + category. + discriminator: + mapping: + broadcast: '#/components/schemas/BroadcastNotificationContent' + message: '#/components/schemas/MessageNotificationContent' + new_shared_item: '#/components/schemas/NewSharedItemNotificationContent' + propertyName: category + oneOf: + - $ref: '#/components/schemas/MessageNotificationContent' + - $ref: '#/components/schemas/NewSharedItemNotificationContent' + - $ref: '#/components/schemas/BroadcastNotificationContent' + title: Content + create_time: + description: The time when the notification was created. + format: date-time + title: Create time + type: string + deleted: + description: Whether the notification is marked as deleted by the user. + Deleted notifications don't show up in the notification list. + title: Deleted + type: boolean + expiration_time: + anyOf: + - format: date-time + type: string + - type: 'null' + description: The time when the notification will expire. If not set, the + notification will never expire. Expired notifications will be permanently + deleted. + title: Expiration time + id: + description: The encoded ID of the notification. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + publication_time: + description: The time when the notification was published. Notifications + can be created and then published at a later time. + format: date-time + title: Publication time + type: string + seen_time: + anyOf: + - format: date-time + type: string + - type: 'null' + description: The time when the notification was seen by the user. If not + set, the notification was not seen yet. + title: Seen time + source: + description: The source of the notification. Represents the agent that created + the notification. E.g. 'galaxy' or 'admin'. + title: Source + type: string + update_time: + description: The time when the notification was last updated. + format: date-time + title: Update time + type: string + variant: + allOf: + - $ref: '#/components/schemas/NotificationVariant' + description: The variant of the notification. Represents the intent or relevance + of the notification. E.g. 'info' or 'urgent'. + title: Variant + required: + - id + - source + - category + - variant + - create_time + - update_time + - publication_time + - content + - deleted + title: UserNotificationResponse + type: object + UserNotificationUpdateRequest: + description: A notification update request specific to the user. + properties: + deleted: + anyOf: + - type: boolean + - type: 'null' + description: Whether the notification should be marked as deleted by the + user. If not set, the notification will not be changed. + title: Deleted + seen: + anyOf: + - type: boolean + - type: 'null' + description: Whether the notification should be marked as seen by the user. + If not set, the notification will not be changed. + title: Seen + title: UserNotificationUpdateRequest + type: object + UserNotificationsBatchUpdateRequest: + description: A batch update request specific for user notifications. + properties: + changes: + allOf: + - $ref: '#/components/schemas/UserNotificationUpdateRequest' + description: The changes that should be applied to the notifications. Only + the fields that are set will be changed. + title: Changes + notification_ids: + description: The list of encoded notification IDs of the notifications that + should be updated. + items: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + type: string + title: Notification IDs + type: array + required: + - notification_ids + - changes + title: UserNotificationsBatchUpdateRequest + type: object + UserQuota: + properties: + model_class: + const: UserQuotaAssociation + description: The name of the database model class. + title: Model class + type: string + user: + allOf: + - $ref: '#/components/schemas/UserModel' + description: Information about a user associated with a quota. + title: User + required: + - model_class + - user + title: UserQuota + type: object + UserQuotaUsage: + properties: + quota: + anyOf: + - type: string + - type: 'null' + title: Quota + quota_bytes: + anyOf: + - type: integer + - type: 'null' + title: Quota Bytes + quota_percent: + anyOf: + - type: number + - type: 'null' + title: Quota Percent + quota_source_label: + anyOf: + - type: string + - type: 'null' + title: Quota Source Label + total_disk_usage: + title: Total Disk Usage + type: number + required: + - total_disk_usage + title: UserQuotaUsage + type: object + ValidationError: + properties: + loc: + items: + anyOf: + - type: string + - type: integer + title: Location + type: array + msg: + title: Message + type: string + type: + title: Error Type + type: string + required: + - loc + - msg + - type + title: ValidationError + type: object + Visualization: + properties: {} + title: Visualization + type: object + VisualizationSummary: + additionalProperties: true + properties: + annotation: + anyOf: + - type: string + - type: 'null' + description: The annotation of this Visualization. + title: Annotation + create_time: + anyOf: + - format: date-time + type: string + - type: 'null' + description: The time and date this item was created. + title: Create Time + dbkey: + anyOf: + - type: string + - type: 'null' + description: The database key of the visualization. + title: DbKey + deleted: + description: Whether this Visualization has been deleted. + title: Deleted + type: boolean + id: + description: Encoded ID of the Visualization. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + importable: + description: Whether this Visualization can be imported. + title: Importable + type: boolean + published: + description: Whether this Visualization has been published. + title: Published + type: boolean + tags: + anyOf: + - $ref: '#/components/schemas/TagCollection' + - type: 'null' + description: A list of tags to add to this item. + title: Tags + title: + description: The name of the visualization. + title: Title + type: string + type: + description: The type of the visualization. + title: Type + type: string + update_time: + anyOf: + - format: date-time + type: string + - type: 'null' + description: The last time and date this item was updated. + title: Update Time + username: + description: The name of the user owning this Visualization. + title: Username + type: string + required: + - id + - deleted + - importable + - published + - tags + - title + - type + - username + - create_time + - update_time + title: VisualizationSummary + type: object + VisualizationSummaryList: + default: [] + items: + $ref: '#/components/schemas/VisualizationSummary' + title: VisualizationSummaryList + type: array + WorkflowInvocationCollectionView: + properties: + create_time: + description: The time and date this item was created. + format: date-time + title: Create Time + type: string + history_id: + description: The encoded ID of the history associated with the invocation. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: History ID + type: string + id: + description: The encoded ID of the workflow invocation. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + model_class: + const: WorkflowInvocation + description: The name of the database model class. + title: Model class + type: string + state: + allOf: + - $ref: '#/components/schemas/InvocationState' + description: State of workflow invocation. + title: Invocation state + update_time: + description: The last time and date this item was updated. + format: date-time + title: Update Time + type: string + uuid: + anyOf: + - format: uuid4 + type: string + - format: uuid1 + type: string + - type: 'null' + description: Universal unique identifier of the workflow invocation. + title: UUID + workflow_id: + description: The encoded Workflow ID associated with the invocation. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Workflow ID + type: string + required: + - model_class + - id + - create_time + - update_time + - workflow_id + - history_id + - state + title: WorkflowInvocationCollectionView + type: object + WorkflowInvocationElementView: + properties: + create_time: + description: The time and date this item was created. + format: date-time + title: Create Time + type: string + history_id: + description: The encoded ID of the history associated with the invocation. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: History ID + type: string + id: + description: The encoded ID of the workflow invocation. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: ID + type: string + input_step_parameters: + additionalProperties: + $ref: '#/components/schemas/InvocationInputParameter' + description: Input step parameters of the workflow invocation. + title: Input step parameters + type: object + inputs: + additionalProperties: + $ref: '#/components/schemas/InvocationInput' + description: Input datasets/dataset collections of the workflow invocation. + title: Inputs + type: object + messages: + description: A list of messages about why the invocation did not succeed. + items: + discriminator: + mapping: + cancelled_on_review: '#/components/schemas/InvocationCancellationReviewFailedResponse' + collection_failed: '#/components/schemas/InvocationFailureCollectionFailedResponse' + dataset_failed: '#/components/schemas/InvocationFailureDatasetFailedResponse' + expression_evaluation_failed: '#/components/schemas/InvocationFailureExpressionEvaluationFailedResponse' + history_deleted: '#/components/schemas/InvocationCancellationHistoryDeletedResponse' + job_failed: '#/components/schemas/InvocationFailureJobFailedResponse' + output_not_found: '#/components/schemas/InvocationFailureOutputNotFoundResponse' + unexpected_failure: '#/components/schemas/InvocationUnexpectedFailureResponse' + user_request: '#/components/schemas/InvocationCancellationUserRequestResponse' + when_not_boolean: '#/components/schemas/InvocationFailureWhenNotBooleanResponse' + workflow_output_not_found: '#/components/schemas/InvocationEvaluationWarningWorkflowOutputNotFoundResponse' + propertyName: reason + oneOf: + - $ref: '#/components/schemas/InvocationCancellationReviewFailedResponse' + - $ref: '#/components/schemas/InvocationCancellationHistoryDeletedResponse' + - $ref: '#/components/schemas/InvocationCancellationUserRequestResponse' + - $ref: '#/components/schemas/InvocationFailureDatasetFailedResponse' + - $ref: '#/components/schemas/InvocationFailureCollectionFailedResponse' + - $ref: '#/components/schemas/InvocationFailureJobFailedResponse' + - $ref: '#/components/schemas/InvocationFailureOutputNotFoundResponse' + - $ref: '#/components/schemas/InvocationFailureExpressionEvaluationFailedResponse' + - $ref: '#/components/schemas/InvocationFailureWhenNotBooleanResponse' + - $ref: '#/components/schemas/InvocationUnexpectedFailureResponse' + - $ref: '#/components/schemas/InvocationEvaluationWarningWorkflowOutputNotFoundResponse' + title: Messages + type: array + model_class: + const: WorkflowInvocation + description: The name of the database model class. + title: Model class + type: string + output_collections: + additionalProperties: + $ref: '#/components/schemas/InvocationOutputCollection' + description: Output dataset collections of the workflow invocation. + title: Output collections + type: object + output_values: + description: Output values of the workflow invocation. + title: Output values + type: object + outputs: + additionalProperties: + $ref: '#/components/schemas/InvocationOutput' + description: Output datasets of the workflow invocation. + title: Outputs + type: object + state: + allOf: + - $ref: '#/components/schemas/InvocationState' + description: State of workflow invocation. + title: Invocation state + steps: + description: Steps of the workflow invocation. + items: + $ref: '#/components/schemas/InvocationStep' + title: Steps + type: array + update_time: + description: The last time and date this item was updated. + format: date-time + title: Update Time + type: string + uuid: + anyOf: + - format: uuid4 + type: string + - format: uuid1 + type: string + - type: 'null' + description: Universal unique identifier of the workflow invocation. + title: UUID + workflow_id: + description: The encoded Workflow ID associated with the invocation. + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Workflow ID + type: string + required: + - model_class + - id + - create_time + - update_time + - workflow_id + - history_id + - state + - steps + - inputs + - input_step_parameters + - outputs + - output_collections + - output_values + - messages + title: WorkflowInvocationElementView + type: object + WorkflowInvocationResponse: + anyOf: + - $ref: '#/components/schemas/WorkflowInvocationElementView' + - $ref: '#/components/schemas/WorkflowInvocationCollectionView' + title: WorkflowInvocationResponse + WorkflowInvocationStateSummary: + properties: + id: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Id + type: string + model: + const: WorkflowInvocation + description: The name of the database model class. + title: Model class + type: string + populated_state: + allOf: + - $ref: '#/components/schemas/DatasetCollectionPopulatedState' + description: 'Indicates the general state of the elements in the dataset + collection:- ''new'': new dataset collection, unpopulated elements.- ''ok'': + collection elements populated (HDAs may or may not have errors).- ''failed'': + some problem populating, won''t be populated.' + title: Populated State + states: + additionalProperties: + type: integer + default: {} + description: A dictionary of job states and the number of jobs in that state. + title: States + type: object + required: + - id + - populated_state + - model + title: WorkflowInvocationStateSummary + type: object + WriteInvocationStoreToPayload: + properties: + bco_merge_history_metadata: + default: false + description: When reading tags/annotations to generate BCO object include + history metadata. + title: Bco Merge History Metadata + type: boolean + bco_override_algorithmic_error: + anyOf: + - additionalProperties: + type: string + type: object + - type: 'null' + description: Override algorithmic error for 'error domain' when generating + BioCompute object. + title: Bco Override Algorithmic Error + bco_override_empirical_error: + anyOf: + - additionalProperties: + type: string + type: object + - type: 'null' + description: Override empirical error for 'error domain' when generating + BioCompute object. + title: Bco Override Empirical Error + bco_override_environment_variables: + anyOf: + - additionalProperties: + type: string + type: object + - type: 'null' + description: Override environment variables for 'execution_domain' when + generating BioCompute object. + title: Bco Override Environment Variables + bco_override_xref: + anyOf: + - items: + $ref: '#/components/schemas/XrefItem' + type: array + - type: 'null' + description: Override xref for 'description domain' when generating BioCompute + object. + title: Bco Override Xref + include_deleted: + default: false + description: Include file contents for deleted datasets (if include_files + is True). + title: Include deleted + type: boolean + include_files: + default: true + description: include materialized files in export when available + title: Include Files + type: boolean + include_hidden: + default: false + description: Include file contents for hidden datasets (if include_files + is True). + title: Include hidden + type: boolean + model_store_format: + allOf: + - $ref: '#/components/schemas/ModelStoreFormat' + default: tar.gz + description: format of model store to export + target_uri: + description: Galaxy Files URI to write mode store content to. + title: Target URI + type: string + required: + - target_uri + title: WriteInvocationStoreToPayload + type: object + WriteStoreToPayload: + properties: + include_deleted: + default: false + description: Include file contents for deleted datasets (if include_files + is True). + title: Include deleted + type: boolean + include_files: + default: true + description: include materialized files in export when available + title: Include Files + type: boolean + include_hidden: + default: false + description: Include file contents for hidden datasets (if include_files + is True). + title: Include hidden + type: boolean + model_store_format: + allOf: + - $ref: '#/components/schemas/ModelStoreFormat' + default: tar.gz + description: format of model store to export + target_uri: + description: Galaxy Files URI to write mode store content to. + title: Target URI + type: string + required: + - target_uri + title: WriteStoreToPayload + type: object + XrefItem: + properties: + access_time: + description: Date and time the external reference was accessed + format: date-time + title: Access Time + type: string + ids: + description: List of reference identifiers + items: + type: string + title: Ids + type: array + name: + description: Name of external reference + examples: + - PubChem-compound + title: Name + type: string + namespace: + description: External resource vendor prefix + examples: + - pubchem.compound + title: Namespace + type: string + required: + - namespace + - name + - ids + - access_time + title: XrefItem + type: object + securitySchemes: + APIKeyCookie: + in: cookie + name: galaxysession + type: apiKey + APIKeyHeader: + in: header + name: x-api-key + type: apiKey + APIKeyQuery: + in: query + name: key + type: apiKey + HTTPBearer: + scheme: bearer + type: http +info: + license: + name: MIT + url: https://github.com/galaxyproject/galaxy/blob/dev/LICENSE.txt + title: Galaxy API + version: 0.1.0 +openapi: 3.1.0 +paths: + /api/authenticate/baseauth: + get: + operationId: get_api_key_api_authenticate_baseauth_get + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/APIKeyResponse' + description: Successful Response + summary: Returns returns an API key for authenticated user based on BaseAuth + headers. + tags: + - authenticate + - authenticate + /api/cloud/storage/get: + post: + deprecated: true + operationId: get_api_cloud_storage_get_post + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/CloudObjects' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DatasetSummaryList' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Gets given objects from a given cloud-based bucket to a Galaxy history. + tags: + - cloud + - cloud + /api/cloud/storage/send: + post: + deprecated: true + operationId: send_api_cloud_storage_send_post + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/CloudDatasets' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/CloudDatasetsResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Sends given dataset(s) in a given history to a given cloud-based bucket. + tags: + - cloud + - cloud + /api/configuration: + get: + description: 'Return an object containing exposable configuration settings. + + + A more complete list is returned if the user is an admin. + + Pass in `view` and a comma-seperated list of keys to control which + + configuration settings are returned.' + operationId: index_api_configuration_get + parameters: + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + title: Response Index Api Configuration Get + type: object + description: Object containing exposable configuration settings + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return an object containing exposable configuration settings + tags: + - configuration + - configuration + /api/configuration/decode/{encoded_id}: + get: + description: Decode a given id. + operationId: decode_id_api_configuration_decode__encoded_id__get + parameters: + - description: Encoded id to be decoded + in: path + name: encoded_id + required: true + schema: + description: Encoded id to be decoded + title: Encoded id + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + additionalProperties: + type: integer + title: Response Decode Id Api Configuration Decode Encoded Id Get + type: object + description: Decoded id + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Decode a given id + tags: + - configuration + - configuration + /api/configuration/dynamic_tool_confs: + get: + description: Return dynamic tool configuration files. + operationId: dynamic_tool_confs_api_configuration_dynamic_tool_confs_get + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + additionalProperties: + type: string + type: object + title: Response Dynamic Tool Confs Api Configuration Dynamic Tool + Confs Get + type: array + description: Dynamic tool configuration files + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return dynamic tool configuration files + tags: + - configuration + - configuration + /api/configuration/encode/{decoded_id}: + get: + description: Decode a given id. + operationId: encode_id_api_configuration_encode__decoded_id__get + parameters: + - description: Decoded id to be encoded + in: path + name: decoded_id + required: true + schema: + description: Decoded id to be encoded + title: Decoded id + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + additionalProperties: + type: string + title: Response Encode Id Api Configuration Encode Decoded Id Get + type: object + description: Encoded id + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Encode a given id + tags: + - configuration + - configuration + /api/configuration/tool_lineages: + get: + description: Return tool lineages for tools that have them. + operationId: tool_lineages_api_configuration_tool_lineages_get + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + additionalProperties: + type: object + type: object + title: Response Tool Lineages Api Configuration Tool Lineages Get + type: array + description: Tool lineages for tools that have them + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return tool lineages for tools that have them + tags: + - configuration + - configuration + /api/configuration/toolbox: + put: + description: Reload the Galaxy toolbox (but not individual tools). + operationId: reload_toolbox_api_configuration_toolbox_put + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Reload the Galaxy toolbox (but not individual tools) + tags: + - configuration + - configuration + /api/dataset_collection_element/{dce_id}: + get: + operationId: content_api_dataset_collection_element__dce_id__get + parameters: + - description: The encoded ID of the dataset collection element. + in: path + name: dce_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DCESummary' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Content + tags: + - dataset collections + - dataset collections + /api/dataset_collections: + post: + operationId: create_api_dataset_collections_post + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/CreateNewCollectionPayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/HDCADetailed' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Create a new dataset collection instance. + tags: + - dataset collections + - dataset collections + /api/dataset_collections/{hdca_id}/contents/{parent_id}: + get: + operationId: contents_dataset_collection_api_dataset_collections__hdca_id__contents__parent_id__get + parameters: + - description: The ID of the `HDCA`. + in: path + name: hdca_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: Parent collection ID describing what collection the contents + belongs to. + in: path + name: parent_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The type of collection instance. Either `history` (default) or + `library`. + in: query + name: instance_type + required: false + schema: + default: history + description: The type of collection instance. Either `history` (default) + or `library`. + enum: + - history + - library + title: Instance Type + type: string + - description: The maximum number of content elements to return. + in: query + name: limit + required: false + schema: + anyOf: + - type: integer + - type: 'null' + description: The maximum number of content elements to return. + title: Limit + - description: The number of content elements that will be skipped before returning. + in: query + name: offset + required: false + schema: + anyOf: + - type: integer + - type: 'null' + description: The number of content elements that will be skipped before + returning. + title: Offset + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DatasetCollectionContentElements' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns direct child contents of indicated dataset collection parent + ID. + tags: + - dataset collections + - dataset collections + /api/dataset_collections/{id}: + get: + operationId: show_api_dataset_collections__id__get + parameters: + - description: The ID of the `HDCA`. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The type of collection instance. Either `history` (default) or + `library`. + in: query + name: instance_type + required: false + schema: + default: history + description: The type of collection instance. Either `history` (default) + or `library`. + enum: + - history + - library + title: Instance Type + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/HDCADetailed' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns detailed information about the given collection. + tags: + - dataset collections + - dataset collections + /api/dataset_collections/{id}/attributes: + get: + operationId: attributes_api_dataset_collections__id__attributes_get + parameters: + - description: The ID of the `HDCA`. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The type of collection instance. Either `history` (default) or + `library`. + in: query + name: instance_type + required: false + schema: + default: history + description: The type of collection instance. Either `history` (default) + or `library`. + enum: + - history + - library + title: Instance Type + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DatasetCollectionAttributesResult' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns `dbkey`/`extension` attributes for all the collection elements. + tags: + - dataset collections + - dataset collections + /api/dataset_collections/{id}/copy: + post: + operationId: copy_api_dataset_collections__id__copy_post + parameters: + - description: The ID of the `HDCA`. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/UpdateCollectionAttributePayload' + required: true + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Copy the given collection datasets to a new collection using a new + `dbkey` attribute. + tags: + - dataset collections + - dataset collections + /api/dataset_collections/{id}/download: + get: + description: 'Download the content of a history dataset collection as a `zip` + archive + + while maintaining approximate collection structure.' + operationId: dataset_collections__download + parameters: + - description: The ID of the `HDCA`. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Download the content of a dataset collection as a `zip` archive. + tags: + - histories + - histories + - dataset collections + /api/dataset_collections/{id}/prepare_download: + post: + description: 'The history dataset collection will be written as a `zip` archive + to the + + returned short term storage object. Progress tracking this file''s creation + + can be tracked with the short_term_storage API.' + operationId: prepare_collection_download_api_dataset_collections__id__prepare_download_post + parameters: + - description: The ID of the `HDCA`. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/AsyncFile' + description: Short term storage reference for async monitoring of this download. + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + '501': + description: Required asynchronous tasks required for this operation not + available. + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Prepare an short term storage object that the collection will be downloaded + to. + tags: + - histories + - histories + - dataset collections + /api/dataset_collections/{id}/suitable_converters: + get: + operationId: suitable_converters_api_dataset_collections__id__suitable_converters_get + parameters: + - description: The ID of the `HDCA`. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The type of collection instance. Either `history` (default) or + `library`. + in: query + name: instance_type + required: false + schema: + default: history + description: The type of collection instance. Either `history` (default) + or `library`. + enum: + - history + - library + title: Instance Type + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/SuitableConverters' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns a list of applicable converters for all datatypes in the given + collection. + tags: + - dataset collections + - dataset collections + /api/datasets: + delete: + description: 'Deletes or purges a batch of datasets. + + **Warning**: only the ownership of the datasets (and upload state for HDAs) + is checked, + + no other checks or restrictions are made.' + operationId: delete_batch_api_datasets_delete + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/DeleteDatasetBatchPayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DeleteDatasetBatchResult' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Deletes or purges a batch of datasets. + tags: + - datasets + - datasets + get: + operationId: index_api_datasets_get + parameters: + - description: Optional identifier of a History. Use it to restrict the search + within a particular History. + in: query + name: history_id + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: Optional identifier of a History. Use it to restrict the search + within a particular History. + title: History Id + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: Generally a property name to filter by followed by an (often + optional) hyphen and operator string. + in: query + name: q + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: Generally a property name to filter by followed by an (often + optional) hyphen and operator string. + examples: + - create_time-gt + title: Filter Query + - description: The value to filter by. + in: query + name: qv + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: The value to filter by. + examples: + - '2015-01-29' + title: Filter Value + - description: Starts at the beginning skip the first ( offset - 1 ) items and + begin returning at the Nth item + in: query + name: offset + required: false + schema: + anyOf: + - minimum: 0 + type: integer + - type: 'null' + default: 0 + description: Starts at the beginning skip the first ( offset - 1 ) items + and begin returning at the Nth item + title: Offset + - description: The maximum number of items to return. + in: query + name: limit + required: false + schema: + anyOf: + - minimum: 1 + type: integer + - type: 'null' + description: The maximum number of items to return. + title: Limit + - description: String containing one of the valid ordering attributes followed + (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. + Orders can be stacked as a comma-separated list of values. + in: query + name: order + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: String containing one of the valid ordering attributes followed + (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. + Orders can be stacked as a comma-separated list of values. + title: Order + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + anyOf: + - $ref: '#/components/schemas/HDADetailed' + - $ref: '#/components/schemas/HDASummary' + - $ref: '#/components/schemas/HDCADetailed' + - $ref: '#/components/schemas/HDCASummary' + - $ref: '#/components/schemas/CustomHistoryItem' + title: Response Index Api Datasets Get + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Search datasets or collections using a query system. + tags: + - datasets + - datasets + /api/datasets/{dataset_id}: + get: + description: '**Note**: Due to the multipurpose nature of this endpoint, which + can receive a wild variety of parameters + + and return different kinds of responses, the documentation here will be limited. + + To get more information please check the source code.' + operationId: show_api_datasets__dataset_id__get + parameters: + - description: The ID of the History Dataset. + in: path + name: dataset_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The type of information about the dataset to be requested. + in: query + name: hda_ldda + required: false + schema: + allOf: + - $ref: '#/components/schemas/DatasetSourceType' + default: hda + description: The type of information about the dataset to be requested. + title: Hda Ldda + - description: The type of information about the dataset to be requested. Each + of these values may require additional parameters in the request and may + return different responses. + in: query + name: data_type + required: false + schema: + anyOf: + - $ref: '#/components/schemas/RequestDataType' + - type: 'null' + description: The type of information about the dataset to be requested. + Each of these values may require additional parameters in the request + and may return different responses. + title: Data Type + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Displays information about and/or content of a dataset. + tags: + - datasets + - datasets + /api/datasets/{dataset_id}/content/{content_type}: + get: + operationId: get_structured_content_api_datasets__dataset_id__content__content_type__get + parameters: + - description: The ID of the History Dataset. + in: path + name: dataset_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - in: path + name: content_type + required: true + schema: + $ref: '#/components/schemas/DatasetContentType' + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Retrieve information about the content of a dataset. + tags: + - datasets + - datasets + /api/datasets/{dataset_id}/converted: + get: + description: 'Return a map of ` : ` containing + all the *existing* converted datasets.' + operationId: converted_api_datasets__dataset_id__converted_get + parameters: + - description: The ID of the History Dataset. + in: path + name: dataset_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ConvertedDatasetsMap' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return a a map with all the existing converted datasets associated + with this instance. + tags: + - datasets + - datasets + /api/datasets/{dataset_id}/converted/{ext}: + get: + description: 'Return information about datasets made by converting this dataset + to a new format. + + + If there is no existing converted dataset for the format in `ext`, one will + be created. + + + **Note**: `view` and `keys` are also available to control the serialization + of the dataset.' + operationId: converted_ext_api_datasets__dataset_id__converted__ext__get + parameters: + - description: The ID of the History Dataset. + in: path + name: dataset_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: File extension of the new format to convert this dataset to. + in: path + name: ext + required: true + schema: + description: File extension of the new format to convert this dataset to. + title: Ext + type: string + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/HDADetailed' + - $ref: '#/components/schemas/HDASummary' + title: Response Converted Ext Api Datasets Dataset Id Converted Ext Get + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return information about datasets made by converting this dataset to + a new format. + tags: + - datasets + - datasets + /api/datasets/{dataset_id}/extra_files: + get: + operationId: extra_files_api_datasets__dataset_id__extra_files_get + parameters: + - description: The encoded database identifier of the dataset. + in: path + name: dataset_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DatasetExtraFiles' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get the list of extra files/directories associated with a dataset. + tags: + - datasets + - datasets + /api/datasets/{dataset_id}/get_content_as_text: + get: + operationId: get_content_as_text_api_datasets__dataset_id__get_content_as_text_get + parameters: + - description: The ID of the History Dataset. + in: path + name: dataset_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DatasetTextContentDetails' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns dataset content as Text. + tags: + - datasets + - datasets + /api/datasets/{dataset_id}/hash: + put: + operationId: compute_hash_api_datasets__dataset_id__hash_put + parameters: + - description: The ID of the History Dataset. + in: path + name: dataset_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: Whether this dataset belongs to a history (HDA) or a library + (LDDA). + in: query + name: hda_ldda + required: false + schema: + allOf: + - $ref: '#/components/schemas/DatasetSourceType' + default: hda + description: Whether this dataset belongs to a history (HDA) or a library + (LDDA). + title: Hda Ldda + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/ComputeDatasetHashPayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/AsyncTaskResultSummary' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Compute dataset hash for dataset and update model + tags: + - datasets + - datasets + /api/datasets/{dataset_id}/inheritance_chain: + get: + operationId: show_inheritance_chain_api_datasets__dataset_id__inheritance_chain_get + parameters: + - description: The ID of the History Dataset. + in: path + name: dataset_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: Whether this dataset belongs to a history (HDA) or a library + (LDDA). + in: query + name: hda_ldda + required: false + schema: + allOf: + - $ref: '#/components/schemas/DatasetSourceType' + default: hda + description: Whether this dataset belongs to a history (HDA) or a library + (LDDA). + title: Hda Ldda + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DatasetInheritanceChain' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: For internal use, this endpoint may change without warning. + tags: + - datasets + - datasets + /api/datasets/{dataset_id}/metrics: + get: + deprecated: true + operationId: get_metrics_api_datasets__dataset_id__metrics_get + parameters: + - description: The ID of the dataset + in: path + name: dataset_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: Whether this dataset belongs to a history (HDA) or a library + (LDDA). + in: query + name: hda_ldda + required: false + schema: + allOf: + - $ref: '#/components/schemas/DatasetSourceType' + default: hda + description: Whether this dataset belongs to a history (HDA) or a library + (LDDA). + title: HDA or LDDA + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + anyOf: + - $ref: '#/components/schemas/JobMetric' + - type: 'null' + title: Response Get Metrics Api Datasets Dataset Id Metrics Get + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return job metrics for specified job. + tags: + - jobs + - jobs + /api/datasets/{dataset_id}/object_store_id: + put: + operationId: datasets__update_object_store_id + parameters: + - description: The ID of the History Dataset. + in: path + name: dataset_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/UpdateObjectStoreIdPayload' + required: true + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Update an object store ID for a dataset you own. + tags: + - datasets + - datasets + /api/datasets/{dataset_id}/parameters_display: + get: + deprecated: true + description: 'Resolve parameters as a list for nested display. + + This API endpoint is unstable and tied heavily to Galaxy''s JS client code, + + this endpoint will change frequently.' + operationId: resolve_parameters_display_api_datasets__dataset_id__parameters_display_get + parameters: + - description: The ID of the dataset + in: path + name: dataset_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: Whether this dataset belongs to a history (HDA) or a library + (LDDA). + in: query + name: hda_ldda + required: false + schema: + allOf: + - $ref: '#/components/schemas/DatasetSourceType' + default: hda + description: Whether this dataset belongs to a history (HDA) or a library + (LDDA). + title: HDA or LDDA + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/JobDisplayParametersSummary' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Resolve parameters as a list for nested display. + tags: + - jobs + - jobs + /api/datasets/{dataset_id}/permissions: + put: + description: Set permissions of the given history dataset to the given role + ids. + operationId: update_permissions_api_datasets__dataset_id__permissions_put + parameters: + - description: The ID of the History Dataset. + in: path + name: dataset_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + examples: + - access_ids[]: [] + action: set_permissions + manage_ids[]: [] + modify_ids[]: [] + title: Payload + type: object + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DatasetAssociationRoles' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Set permissions of the given history dataset to the given role ids. + tags: + - datasets + - datasets + /api/datasets/{dataset_id}/storage: + get: + operationId: show_storage_api_datasets__dataset_id__storage_get + parameters: + - description: The ID of the History Dataset. + in: path + name: dataset_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: Whether this dataset belongs to a history (HDA) or a library + (LDDA). + in: query + name: hda_ldda + required: false + schema: + allOf: + - $ref: '#/components/schemas/DatasetSourceType' + default: hda + description: Whether this dataset belongs to a history (HDA) or a library + (LDDA). + title: Hda Ldda + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DatasetStorageDetails' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Display user-facing storage details related to the objectstore a dataset + resides in. + tags: + - datasets + - datasets + /api/datasets/{history_content_id}/display: + get: + description: Streams the dataset for download or the contents preview to be + displayed in a browser. + operationId: display_api_datasets__history_content_id__display_get + parameters: + - description: The ID of the History Dataset. + in: path + name: history_content_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: Whether to get preview contents to be directly displayed on the + web. If preview is False (default) the contents will be downloaded instead. + in: query + name: preview + required: false + schema: + default: false + description: Whether to get preview contents to be directly displayed on + the web. If preview is False (default) the contents will be downloaded + instead. + title: Preview + type: boolean + - description: If non-null, get the specified filename from the extra files + for this dataset. + in: query + name: filename + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: If non-null, get the specified filename from the extra files + for this dataset. + title: Filename + - description: The file extension when downloading the display data. Use the + value `data` to let the server infer it from the data type. + in: query + name: to_ext + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: The file extension when downloading the display data. Use the + value `data` to let the server infer it from the data type. + title: To Ext + - description: The query parameter 'raw' should be considered experimental and + may be dropped at some point in the future without warning. Generally, data + should be processed by its datatype prior to display. + in: query + name: raw + required: false + schema: + default: false + description: The query parameter 'raw' should be considered experimental + and may be dropped at some point in the future without warning. Generally, + data should be processed by its datatype prior to display. + title: Raw + type: boolean + - description: Set this for datatypes that allow chunked display through the + display_data method to enable chunking. This specifies a byte offset into + the target dataset's display. + in: query + name: offset + required: false + schema: + anyOf: + - type: integer + - type: 'null' + description: Set this for datatypes that allow chunked display through the + display_data method to enable chunking. This specifies a byte offset into + the target dataset's display. + title: Offset + - description: 'If offset is set, this recommends ''how large'' the next chunk + should be. This is not respected or interpreted uniformly and should be + interpreted as a very loose recommendation. Different datatypes interpret + ''largeness'' differently - for bam datasets this is a number of lines whereas + for tabular datatypes this is interpreted as a number of bytes. ' + in: query + name: ck_size + required: false + schema: + anyOf: + - type: integer + - type: 'null' + description: 'If offset is set, this recommends ''how large'' the next chunk + should be. This is not respected or interpreted uniformly and should be + interpreted as a very loose recommendation. Different datatypes interpret + ''largeness'' differently - for bam datasets this is a number of lines + whereas for tabular datatypes this is interpreted as a number of bytes. ' + title: Ck Size + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Displays (preview) or downloads dataset content. + tags: + - datasets + - datasets + head: + description: Streams the dataset for download or the contents preview to be + displayed in a browser. + operationId: display_api_datasets__history_content_id__display_head + parameters: + - description: The ID of the History Dataset. + in: path + name: history_content_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: Whether to get preview contents to be directly displayed on the + web. If preview is False (default) the contents will be downloaded instead. + in: query + name: preview + required: false + schema: + default: false + description: Whether to get preview contents to be directly displayed on + the web. If preview is False (default) the contents will be downloaded + instead. + title: Preview + type: boolean + - description: If non-null, get the specified filename from the extra files + for this dataset. + in: query + name: filename + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: If non-null, get the specified filename from the extra files + for this dataset. + title: Filename + - description: The file extension when downloading the display data. Use the + value `data` to let the server infer it from the data type. + in: query + name: to_ext + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: The file extension when downloading the display data. Use the + value `data` to let the server infer it from the data type. + title: To Ext + - description: The query parameter 'raw' should be considered experimental and + may be dropped at some point in the future without warning. Generally, data + should be processed by its datatype prior to display. + in: query + name: raw + required: false + schema: + default: false + description: The query parameter 'raw' should be considered experimental + and may be dropped at some point in the future without warning. Generally, + data should be processed by its datatype prior to display. + title: Raw + type: boolean + - description: Set this for datatypes that allow chunked display through the + display_data method to enable chunking. This specifies a byte offset into + the target dataset's display. + in: query + name: offset + required: false + schema: + anyOf: + - type: integer + - type: 'null' + description: Set this for datatypes that allow chunked display through the + display_data method to enable chunking. This specifies a byte offset into + the target dataset's display. + title: Offset + - description: 'If offset is set, this recommends ''how large'' the next chunk + should be. This is not respected or interpreted uniformly and should be + interpreted as a very loose recommendation. Different datatypes interpret + ''largeness'' differently - for bam datasets this is a number of lines whereas + for tabular datatypes this is interpreted as a number of bytes. ' + in: query + name: ck_size + required: false + schema: + anyOf: + - type: integer + - type: 'null' + description: 'If offset is set, this recommends ''how large'' the next chunk + should be. This is not respected or interpreted uniformly and should be + interpreted as a very loose recommendation. Different datatypes interpret + ''largeness'' differently - for bam datasets this is a number of lines + whereas for tabular datatypes this is interpreted as a number of bytes. ' + title: Ck Size + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Check if dataset content can be previewed or downloaded. + tags: + - datasets + - datasets + /api/datasets/{history_content_id}/metadata_file: + get: + operationId: datasets__get_metadata_file + parameters: + - description: The ID of the History Dataset. + in: path + name: history_content_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The name of the metadata file to retrieve. + in: query + name: metadata_file + required: true + schema: + description: The name of the metadata file to retrieve. + title: Metadata File + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns the metadata file associated with this history item. + tags: + - datasets + - datasets + head: + operationId: get_metadata_file_datasets_api_datasets__history_content_id__metadata_file_head + parameters: + - description: The ID of the History Dataset. + in: path + name: history_content_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The name of the metadata file to retrieve. + in: query + name: metadata_file + required: true + schema: + description: The name of the metadata file to retrieve. + title: Metadata File + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Check if metadata file can be downloaded. + tags: + - datasets + - datasets + /api/datatypes: + get: + description: Gets the list of all available data types. + operationId: index_api_datatypes_get + parameters: + - description: Whether to return only the datatype's extension rather than the + datatype's details + in: query + name: extension_only + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: true + description: Whether to return only the datatype's extension rather than + the datatype's details + title: Extension only + - description: Whether to return only datatypes which can be uploaded + in: query + name: upload_only + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: true + description: Whether to return only datatypes which can be uploaded + title: Upload only + responses: + '200': + content: + application/json: + schema: + anyOf: + - items: + $ref: '#/components/schemas/DatatypeDetails' + type: array + - items: + type: string + type: array + title: Response Index Api Datatypes Get + description: List of data types + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: [] + summary: Lists all available data types + tags: + - datatypes + - datatypes + /api/datatypes/converters: + get: + description: Gets the list of all installed converters. + operationId: converters_api_datatypes_converters_get + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DatatypeConverterList' + description: List of all datatype converters + security: [] + summary: Returns the list of all installed converters + tags: + - datatypes + - datatypes + /api/datatypes/edam_data: + get: + description: Gets a map of datatypes and their corresponding EDAM data. + operationId: edam_data_api_datatypes_edam_data_get + responses: + '200': + content: + application/json: + schema: + additionalProperties: + type: string + title: Response Edam Data Api Datatypes Edam Data Get + type: object + description: Dictionary/map of datatypes and EDAM data + security: [] + summary: Returns a dictionary/map of datatypes and EDAM data + tags: + - datatypes + - datatypes + /api/datatypes/edam_data/detailed: + get: + description: 'Gets a map of datatypes and their corresponding EDAM data. + + EDAM data contains the EDAM iri, label, and definition.' + operationId: edam_data_detailed_api_datatypes_edam_data_detailed_get + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DatatypesEDAMDetailsDict' + description: Dictionary of EDAM data details containing the EDAM iri, label, + and definition + security: [] + summary: Returns a dictionary of datatypes and EDAM data details + tags: + - datatypes + - datatypes + /api/datatypes/edam_formats: + get: + description: Gets a map of datatypes and their corresponding EDAM formats. + operationId: edam_formats_api_datatypes_edam_formats_get + responses: + '200': + content: + application/json: + schema: + additionalProperties: + type: string + title: Response Edam Formats Api Datatypes Edam Formats Get + type: object + description: Dictionary/map of datatypes and EDAM formats + security: [] + summary: Returns a dictionary/map of datatypes and EDAM formats + tags: + - datatypes + - datatypes + /api/datatypes/edam_formats/detailed: + get: + description: 'Gets a map of datatypes and their corresponding EDAM formats. + + EDAM formats contain the EDAM iri, label, and definition.' + operationId: edam_formats_detailed_api_datatypes_edam_formats_detailed_get + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DatatypesEDAMDetailsDict' + description: Dictionary of EDAM format details containing the EDAM iri, + label, and definition + security: [] + summary: Returns a dictionary of datatypes and EDAM format details + tags: + - datatypes + - datatypes + /api/datatypes/mapping: + get: + description: Gets mappings for data types. + operationId: mapping_api_datatypes_mapping_get + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DatatypesMap' + description: Dictionary to map data types with their classes + security: [] + summary: Returns mappings for data types and their implementing classes + tags: + - datatypes + - datatypes + /api/datatypes/sniffers: + get: + description: Gets the list of all installed data type sniffers. + operationId: sniffers_api_datatypes_sniffers_get + responses: + '200': + content: + application/json: + schema: + items: + type: string + title: Response Sniffers Api Datatypes Sniffers Get + type: array + description: List of datatype sniffers + security: [] + summary: Returns the list of all installed sniffers + tags: + - datatypes + - datatypes + /api/datatypes/types_and_mapping: + get: + description: 'Combines the datatype information from (/api/datatypes) and the + + mapping information from (/api/datatypes/mapping) into a single + + response.' + operationId: types_and_mapping_api_datatypes_types_and_mapping_get + parameters: + - description: Whether to return only the datatype's extension rather than the + datatype's details + in: query + name: extension_only + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: true + description: Whether to return only the datatype's extension rather than + the datatype's details + title: Extension only + - description: Whether to return only datatypes which can be uploaded + in: query + name: upload_only + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: true + description: Whether to return only datatypes which can be uploaded + title: Upload only + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DatatypesCombinedMap' + description: Dictionary to map data types with their classes + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: [] + summary: Returns all the data types extensions and their mappings + tags: + - datatypes + - datatypes + /api/display_applications: + get: + description: Returns the list of display applications. + operationId: display_applications_index_api_display_applications_get + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/DisplayApplication' + title: Response Display Applications Index Api Display Applications + Get + type: array + description: Successful Response + security: [] + summary: Returns the list of display applications. + tags: + - display_applications + - display_applications + /api/display_applications/reload: + post: + description: Reloads the list of display applications. + operationId: display_applications_reload_api_display_applications_reload_post + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + anyOf: + - additionalProperties: + items: + type: string + type: array + type: object + - type: 'null' + title: Payload + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ReloadFeedback' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Reloads the list of display applications. + tags: + - display_applications + - display_applications + /api/drs_download/{object_id}: + get: + operationId: download_api_drs_download__object_id__get + parameters: + - description: The ID of the group + in: path + name: object_id + required: true + schema: + description: The ID of the group + title: Object ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Download + tags: + - drs + - drs + /api/folders/{folder_id}/contents: + get: + description: 'Returns a list of a folder''s contents (files and sub-folders). + + + Additional metadata for the folder is provided in the response as a separate + object containing data + + for breadcrumb path building, permissions and other folder''s details. + + + *Note*: When sorting, folders always have priority (they show-up before any + dataset regardless of the sorting). + + + **Security note**: + + - Accessing a library folder or sub-folder requires only access to the parent + library. + + - Deleted folders can only be accessed by admins or users with `MODIFY` permission. + + - Datasets may be public, private or restricted (to a group of users). Listing + deleted datasets has the same requirements as folders.' + operationId: index_api_folders__folder_id__contents_get + parameters: + - description: The encoded identifier of the library folder. + in: path + name: folder_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Folder ID + type: string + - description: Maximum number of contents to return. + in: query + name: limit + required: false + schema: + default: 10 + description: Maximum number of contents to return. + title: Limit + type: integer + - description: Return contents from this specified position. For example, if + ``limit`` is set to 100 and ``offset`` to 200, contents between position + 200-299 will be returned. + in: query + name: offset + required: false + schema: + default: 0 + description: Return contents from this specified position. For example, + if ``limit`` is set to 100 and ``offset`` to 200, contents between position + 200-299 will be returned. + title: Offset + type: integer + - description: Used to filter the contents. Only the folders and files which + name contains this text will be returned. + in: query + name: search_text + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Used to filter the contents. Only the folders and files which + name contains this text will be returned. + title: Search Text + - description: Returns also deleted contents. Deleted contents can only be retrieved + by Administrators or users with + in: query + name: include_deleted + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: false + description: Returns also deleted contents. Deleted contents can only be + retrieved by Administrators or users with + title: Include Deleted + - description: Sort results by specified field. + in: query + name: order_by + required: false + schema: + default: name + description: Sort results by specified field. + enum: + - name + - description + - type + - size + - update_time + title: Sort By + type: string + - description: Sort results in descending order. + in: query + name: sort_desc + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: false + description: Sort results in descending order. + title: Sort Descending + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/LibraryFolderContentsIndexResult' + description: The contents of the folder that match the query parameters. + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns a list of a folder's contents (files and sub-folders) with + additional metadata about the folder. + tags: + - data libraries folders + - data libraries folders + post: + operationId: add_history_datasets_to_library_api_folders__folder_id__contents_post + parameters: + - description: The encoded identifier of the library folder. + in: path + name: folder_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Folder ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/CreateLibraryFilePayload' + required: true + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Creates a new library file from an existing HDA/HDCA. + tags: + - data libraries folders + - data libraries folders + /api/folders/{id}: + delete: + description: Marks the specified library folder as deleted (or undeleted). + operationId: delete_api_folders__id__delete + parameters: + - description: The encoded identifier of the library folder. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Folder ID + type: string + - description: Whether to restore a deleted library folder. + in: query + name: undelete + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + description: Whether to restore a deleted library folder. + title: Undelete + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/LibraryFolderDetails' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Marks the specified library folder as deleted (or undeleted). + tags: + - data libraries folders + - data libraries folders + get: + description: Returns detailed information about the library folder with the + given ID. + operationId: show_api_folders__id__get + parameters: + - description: The encoded identifier of the library folder. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Folder ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/LibraryFolderDetails' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Displays information about a particular library folder. + tags: + - data libraries folders + - data libraries folders + patch: + description: Updates the information of an existing library folder. + operationId: update_api_folders__id__patch + parameters: + - description: The encoded identifier of the library folder. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Folder ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/UpdateLibraryFolderPayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/LibraryFolderDetails' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Update + tags: + - data libraries folders + - data libraries folders + post: + description: Returns detailed information about the newly created library folder. + operationId: create_api_folders__id__post + parameters: + - description: The encoded identifier of the library folder. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Folder ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/CreateLibraryFolderPayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/LibraryFolderDetails' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Create a new library folder underneath the one specified by the ID. + tags: + - data libraries folders + - data libraries folders + put: + description: Updates the information of an existing library folder. + operationId: update_api_folders__id__put + parameters: + - description: The encoded identifier of the library folder. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Folder ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/UpdateLibraryFolderPayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/LibraryFolderDetails' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Updates the information of an existing library folder. + tags: + - data libraries folders + - data libraries folders + /api/folders/{id}/permissions: + get: + description: 'Gets the current or available permissions of a particular library. + + The results can be paginated and additionally filtered by a query.' + operationId: get_permissions_api_folders__id__permissions_get + parameters: + - description: The encoded identifier of the library folder. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Folder ID + type: string + - description: The scope of the permissions to retrieve. Either the `current` + permissions or the `available`. + in: query + name: scope + required: false + schema: + anyOf: + - $ref: '#/components/schemas/LibraryPermissionScope' + - type: 'null' + description: The scope of the permissions to retrieve. Either the `current` + permissions or the `available`. + title: Scope + - description: The page number to retrieve when paginating the available roles. + in: query + name: page + required: false + schema: + default: 1 + description: The page number to retrieve when paginating the available roles. + title: Page + type: integer + - description: The maximum number of permissions per page when paginating. + in: query + name: page_limit + required: false + schema: + default: 10 + description: The maximum number of permissions per page when paginating. + title: Page Limit + type: integer + - description: Optional search text to retrieve only the roles matching this + query. + in: query + name: q + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Optional search text to retrieve only the roles matching this + query. + title: Query + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/LibraryFolderCurrentPermissions' + - $ref: '#/components/schemas/LibraryAvailablePermissions' + title: Response Get Permissions Api Folders Id Permissions Get + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Gets the current or available permissions of a particular library folder. + tags: + - data libraries folders + - data libraries folders + post: + description: Sets the permissions to manage a library folder. + operationId: set_permissions_api_folders__id__permissions_post + parameters: + - description: The encoded identifier of the library folder. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Folder ID + type: string + - description: Indicates what action should be performed on the Library. Currently + only `set_permissions` is supported. + in: query + name: action + required: false + schema: + anyOf: + - $ref: '#/components/schemas/LibraryFolderPermissionAction' + - type: 'null' + description: Indicates what action should be performed on the Library. Currently + only `set_permissions` is supported. + title: Action + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/LibraryFolderPermissionsPayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/LibraryFolderCurrentPermissions' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Sets the permissions to manage a library folder. + tags: + - data libraries folders + - data libraries folders + /api/forms/{id}: + delete: + operationId: delete_api_forms__id__delete + parameters: + - in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Delete + tags: + - forms + - forms + /api/forms/{id}/undelete: + post: + operationId: undelete_api_forms__id__undelete_post + parameters: + - in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Undelete + tags: + - forms + - forms + /api/ftp_files: + get: + deprecated: true + description: Lists all remote files available to the user from different sources. + operationId: index_api_ftp_files_get + parameters: + - description: 'The source to load datasets from. Possible values: ftpdir, userdir, + importdir' + in: query + name: target + required: false + schema: + default: ftpdir + description: 'The source to load datasets from. Possible values: ftpdir, + userdir, importdir' + title: Target source + type: string + - description: The requested format of returned data. Either `flat` to simply + list all the files, `jstree` to get a tree representation of the files, + or the default `uri` to list files and directories by their URI. + in: query + name: format + required: false + schema: + anyOf: + - $ref: '#/components/schemas/RemoteFilesFormat' + - type: 'null' + default: uri + description: The requested format of returned data. Either `flat` to simply + list all the files, `jstree` to get a tree representation of the files, + or the default `uri` to list files and directories by their URI. + title: Response format + - description: Whether to recursively lists all sub-directories. This will be + `True` by default depending on the `target`. + in: query + name: recursive + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + description: Whether to recursively lists all sub-directories. This will + be `True` by default depending on the `target`. + title: Recursive + - description: (This only applies when `format` is `jstree`) The value can be + either `folders` or `files` and it will disable the corresponding nodes + of the tree. + in: query + name: disable + required: false + schema: + anyOf: + - $ref: '#/components/schemas/RemoteFilesDisableMode' + - type: 'null' + description: (This only applies when `format` is `jstree`) The value can + be either `folders` or `files` and it will disable the corresponding nodes + of the tree. + title: Disable mode + - description: Whether the query is made with the intention of writing to the + source. If set to True, only entries that can be written to will be returned. + in: query + name: writeable + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + description: Whether the query is made with the intention of writing to + the source. If set to True, only entries that can be written to will be + returned. + title: Writeable + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/ListUriResponse' + - $ref: '#/components/schemas/ListJstreeResponse' + title: Response Index Api Ftp Files Get + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Displays remote files available to the user. Please use /api/remote_files + instead. + tags: + - remote files + - remote files + /api/genomes: + get: + operationId: index_api_genomes_get + parameters: + - description: If true, return genome keys with chromosome lengths + in: query + name: chrom_info + required: false + schema: + description: If true, return genome keys with chromosome lengths + title: ChromInfo + type: boolean + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + items: + type: string + type: array + title: Response Index Api Genomes Get + type: array + description: Installed genomes + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return a list of installed genomes + tags: + - genomes + - genomes + /api/genomes/{id}: + get: + operationId: show_api_genomes__id__get + parameters: + - description: Genome ID + in: path + name: id + required: true + schema: + description: Genome ID + title: Genome ID + type: string + - description: If true, return reference data + in: query + name: reference + required: false + schema: + description: If true, return reference data + title: Reference + type: boolean + - description: Limits size of returned data + in: query + name: num + required: false + schema: + description: Limits size of returned data + title: Number + type: integer + - description: Limits size of returned data + in: query + name: chrom + required: false + schema: + description: Limits size of returned data + title: Chrom + type: string + - description: Limits size of returned data + in: query + name: low + required: false + schema: + description: Limits size of returned data + title: Low + type: integer + - description: Limits size of returned data + in: query + name: high + required: false + schema: + description: Limits size of returned data + title: High + type: integer + - description: Format + in: query + name: format + required: false + schema: + description: Format + title: Format + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + title: Response Show Api Genomes Id Get + description: Information about genome build + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return information about build + tags: + - genomes + - genomes + /api/genomes/{id}/indexes: + get: + operationId: indexes_api_genomes__id__indexes_get + parameters: + - description: Genome ID + in: path + name: id + required: true + schema: + description: Genome ID + title: Genome ID + type: string + - description: Index type + in: query + name: type + required: false + schema: + default: fasta_indexes + description: Index type + title: Index type + type: string + - description: Format + in: query + name: format + required: false + schema: + description: Format + title: Format + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + title: Response Indexes Api Genomes Id Indexes Get + description: Indexes for a genome id for provided type + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return all available indexes for a genome id for provided type + tags: + - genomes + - genomes + /api/genomes/{id}/sequences: + get: + operationId: sequences_api_genomes__id__sequences_get + parameters: + - description: Genome ID + in: path + name: id + required: true + schema: + description: Genome ID + title: Genome ID + type: string + - description: If true, return reference data + in: query + name: reference + required: false + schema: + description: If true, return reference data + title: Reference + type: boolean + - description: Limits size of returned data + in: query + name: chrom + required: false + schema: + description: Limits size of returned data + title: Chrom + type: string + - description: Limits size of returned data + in: query + name: low + required: false + schema: + description: Limits size of returned data + title: Low + type: integer + - description: Limits size of returned data + in: query + name: high + required: false + schema: + description: Limits size of returned data + title: High + type: integer + - description: Format + in: query + name: format + required: false + schema: + description: Format + title: Format + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + title: Response Sequences Api Genomes Id Sequences Get + description: Raw sequence data + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return raw sequence data + tags: + - genomes + - genomes + /api/groups: + get: + operationId: index_api_groups_get + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/GroupListResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Displays a collection (list) of groups. + tags: + - groups + - groups + post: + operationId: create_api_groups_post + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/GroupCreatePayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/GroupListResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Creates a new group. + tags: + - groups + - groups + /api/groups/{group_id}: + delete: + operationId: delete_api_groups__group_id__delete + parameters: + - in: path + name: group_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Delete + tags: + - groups + - groups + get: + operationId: show_group_api_groups__group_id__get + parameters: + - in: path + name: group_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/GroupResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Displays information about a group. + tags: + - groups + - groups + put: + operationId: update_api_groups__group_id__put + parameters: + - in: path + name: group_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/GroupCreatePayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/GroupResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Modifies a group. + tags: + - groups + - groups + /api/groups/{group_id}/purge: + post: + operationId: purge_api_groups__group_id__purge_post + parameters: + - in: path + name: group_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Purge + tags: + - groups + - groups + /api/groups/{group_id}/roles: + get: + operationId: group_roles_api_groups__group_id__roles_get + parameters: + - description: The ID of the group. + in: path + name: group_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/GroupRoleListResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Displays a collection (list) of groups. + tags: + - group_roles + - group_roles + /api/groups/{group_id}/roles/{role_id}: + delete: + operationId: delete_api_groups__group_id__roles__role_id__delete + parameters: + - description: The ID of the group. + in: path + name: group_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The ID of the role. + in: path + name: role_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/GroupRoleResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Removes a role from a group + tags: + - group_roles + - group_roles + get: + operationId: group_role_api_groups__group_id__roles__role_id__get + parameters: + - description: The ID of the group. + in: path + name: group_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The ID of the role. + in: path + name: role_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/GroupRoleResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Displays information about a group role. + tags: + - group_roles + - group_roles + put: + operationId: update_api_groups__group_id__roles__role_id__put + parameters: + - description: The ID of the group. + in: path + name: group_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The ID of the role. + in: path + name: role_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/GroupRoleResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Adds a role to a group + tags: + - group_roles + - group_roles + /api/groups/{group_id}/undelete: + post: + operationId: undelete_api_groups__group_id__undelete_post + parameters: + - in: path + name: group_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Undelete + tags: + - groups + - groups + /api/groups/{group_id}/user/{user_id}: + delete: + description: 'DELETE /api/groups/{encoded_group_id}/users/{encoded_user_id} + + Removes a user from a group' + operationId: delete_api_groups__group_id__user__user_id__delete + parameters: + - description: The ID of the group. + in: path + name: group_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The ID of the user. + in: path + name: user_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/GroupUserResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Removes a user from a group + tags: + - group_users + - group_users + get: + description: Displays information about a group user. + operationId: group_user_api_groups__group_id__user__user_id__get + parameters: + - description: The ID of the group. + in: path + name: group_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The ID of the user. + in: path + name: user_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/GroupUserResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Displays information about a group user. + tags: + - group_users + - group_users + put: + description: 'PUT /api/groups/{encoded_group_id}/users/{encoded_user_id} + + Adds a user to a group' + operationId: update_api_groups__group_id__user__user_id__put + parameters: + - description: The ID of the group. + in: path + name: group_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The ID of the user. + in: path + name: user_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/GroupUserResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Adds a user to a group + tags: + - group_users + - group_users + /api/groups/{group_id}/users: + get: + description: 'GET /api/groups/{encoded_group_id}/users + + Displays a collection (list) of groups.' + operationId: group_users_api_groups__group_id__users_get + parameters: + - description: The ID of the group. + in: path + name: group_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/GroupUserListResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Displays a collection (list) of groups. + tags: + - group_users + - group_users + /api/groups/{group_id}/users/{user_id}: + delete: + description: 'DELETE /api/groups/{encoded_group_id}/users/{encoded_user_id} + + Removes a user from a group' + operationId: delete_api_groups__group_id__users__user_id__delete + parameters: + - description: The ID of the group. + in: path + name: group_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The ID of the user. + in: path + name: user_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/GroupUserResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Removes a user from a group + tags: + - group_users + - group_users + get: + description: Displays information about a group user. + operationId: group_user_api_groups__group_id__users__user_id__get + parameters: + - description: The ID of the group. + in: path + name: group_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The ID of the user. + in: path + name: user_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/GroupUserResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Displays information about a group user. + tags: + - group_users + - group_users + put: + description: 'PUT /api/groups/{encoded_group_id}/users/{encoded_user_id} + + Adds a user to a group' + operationId: update_api_groups__group_id__users__user_id__put + parameters: + - description: The ID of the group. + in: path + name: group_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The ID of the user. + in: path + name: user_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/GroupUserResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Adds a user to a group + tags: + - group_users + - group_users + /api/help/forum/search: + get: + description: 'Search the Galaxy Help forum using the Discourse API. + + + **Note**: This endpoint is for **INTERNAL USE ONLY** and is not part of the + public Galaxy API.' + operationId: search_forum_api_help_forum_search_get + parameters: + - description: Search query to use for searching the Galaxy Help forum. + in: query + name: query + required: true + schema: + description: Search query to use for searching the Galaxy Help forum. + title: Query + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/HelpForumSearchResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Search the Galaxy Help forum. + tags: + - help + - help + /api/histories: + get: + operationId: index_api_histories_get + parameters: + - description: The maximum number of items to return. + in: query + name: limit + required: false + schema: + anyOf: + - minimum: 1 + type: integer + - type: 'null' + description: The maximum number of items to return. + title: Limit + - description: Starts at the beginning skip the first ( offset - 1 ) items and + begin returning at the Nth item + in: query + name: offset + required: false + schema: + anyOf: + - minimum: 0 + type: integer + - type: 'null' + default: 0 + description: Starts at the beginning skip the first ( offset - 1 ) items + and begin returning at the Nth item + title: Offset + - in: query + name: show_own + required: false + schema: + default: true + title: Show histories owned by user. + type: boolean + - in: query + name: show_published + required: false + schema: + default: true + title: Include published histories. + type: boolean + - in: query + name: show_shared + required: false + schema: + default: false + title: Include histories shared with authenticated user. + type: boolean + - description: Sort index by this specified attribute + in: query + name: sort_by + required: false + schema: + default: update_time + description: Sort index by this specified attribute + enum: + - create_time + - name + - update_time + - username + title: Sort attribute + type: string + - description: Sort in descending order? + in: query + name: sort_desc + required: false + schema: + default: true + description: Sort in descending order? + title: Sort Descending + type: boolean + - description: 'A mix of free text and GitHub-style tags used to filter the + index operation. + + + ## Query Structure + + + GitHub-style filter tags (not be confused with Galaxy tags) are tags of + the form + + `:` or `:''''`. + The tag name + + *generally* (but not exclusively) corresponds to the name of an attribute + on the model + + being indexed (i.e. a column in the database). + + + If the tag is quoted, the attribute will be filtered exactly. If the tag + is unquoted, + + generally a partial match will be used to filter the query (i.e. in terms + of the implementation + + this means the database operation `ILIKE` will typically be used). + + + Once the tagged filters are extracted from the search query, the remaining + text is just + + used to search various documented attributes of the object. + + + ## GitHub-style Tags Available + + + `name` + + : The history''s name. + + + `annotation` + + : The history''s annotation. (The tag `a` can be used a short hand alias + for this tag to filter on this attribute.) + + + `tag` + + : The history''s tags. (The tag `t` can be used a short hand alias for this + tag to filter on this attribute.) + + + ## Free Text + + + Free text search terms will be searched against the following attributes + of the + + Historys: `title`, `description`, `slug`, `tag`. + + + ' + in: query + name: search + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: 'A mix of free text and GitHub-style tags used to filter the + index operation. + + + ## Query Structure + + + GitHub-style filter tags (not be confused with Galaxy tags) are tags of + the form + + `:` or `:''''`. + The tag name + + *generally* (but not exclusively) corresponds to the name of an attribute + on the model + + being indexed (i.e. a column in the database). + + + If the tag is quoted, the attribute will be filtered exactly. If the tag + is unquoted, + + generally a partial match will be used to filter the query (i.e. in terms + of the implementation + + this means the database operation `ILIKE` will typically be used). + + + Once the tagged filters are extracted from the search query, the remaining + text is just + + used to search various documented attributes of the object. + + + ## GitHub-style Tags Available + + + `name` + + : The history''s name. + + + `annotation` + + : The history''s annotation. (The tag `a` can be used a short hand alias + for this tag to filter on this attribute.) + + + `tag` + + : The history''s tags. (The tag `t` can be used a short hand alias for + this tag to filter on this attribute.) + + + ## Free Text + + + Free text search terms will be searched against the following attributes + of the + + Historys: `title`, `description`, `slug`, `tag`. + + + ' + title: Search query. + - description: Whether all histories from other users in this Galaxy should + be included. Only admins are allowed to query all histories. + in: query + name: all + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: false + description: Whether all histories from other users in this Galaxy should + be included. Only admins are allowed to query all histories. + title: All Histories + - deprecated: true + description: Whether to return only deleted items. + in: query + name: deleted + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: false + description: Whether to return only deleted items. + title: Deleted Only + - description: Generally a property name to filter by followed by an (often + optional) hyphen and operator string. + in: query + name: q + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: Generally a property name to filter by followed by an (often + optional) hyphen and operator string. + examples: + - create_time-gt + title: Filter Query + - description: The value to filter by. + in: query + name: qv + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: The value to filter by. + examples: + - '2015-01-29' + title: Filter Value + - description: String containing one of the valid ordering attributes followed + (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. + Orders can be stacked as a comma-separated list of values. + in: query + name: order + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: String containing one of the valid ordering attributes followed + (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. + Orders can be stacked as a comma-separated list of values. + title: Order + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + anyOf: + - $ref: '#/components/schemas/HistoryDetailed' + - $ref: '#/components/schemas/HistorySummary' + - $ref: '#/components/schemas/HistoryMinimal' + title: Response Index Api Histories Get + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns histories available to the current user. + tags: + - histories + - histories + post: + description: The new history can also be copied form a existing history or imported + from an archive or URL. + operationId: create_api_histories_post + parameters: + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/x-www-form-urlencoded: + schema: + allOf: + - $ref: '#/components/schemas/Body_create_api_histories_post' + title: Body + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/JobImportHistoryResponse' + - $ref: '#/components/schemas/HistoryDetailed' + - $ref: '#/components/schemas/HistorySummary' + - $ref: '#/components/schemas/HistoryMinimal' + title: Response Create Api Histories Post + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Creates a new history. + tags: + - histories + - histories + /api/histories/archived: + get: + description: 'Get a list of all archived histories for the current user. + + + Archived histories are histories are not part of the active histories of the + user but they can be accessed using this endpoint.' + operationId: get_archived_histories_api_histories_archived_get + parameters: + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: Generally a property name to filter by followed by an (often + optional) hyphen and operator string. + in: query + name: q + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: Generally a property name to filter by followed by an (often + optional) hyphen and operator string. + examples: + - create_time-gt + title: Filter Query + - description: The value to filter by. + in: query + name: qv + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: The value to filter by. + examples: + - '2015-01-29' + title: Filter Value + - description: Starts at the beginning skip the first ( offset - 1 ) items and + begin returning at the Nth item + in: query + name: offset + required: false + schema: + anyOf: + - minimum: 0 + type: integer + - type: 'null' + default: 0 + description: Starts at the beginning skip the first ( offset - 1 ) items + and begin returning at the Nth item + title: Offset + - description: The maximum number of items to return. + in: query + name: limit + required: false + schema: + anyOf: + - minimum: 1 + type: integer + - type: 'null' + description: The maximum number of items to return. + title: Limit + - description: String containing one of the valid ordering attributes followed + (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. + Orders can be stacked as a comma-separated list of values. + in: query + name: order + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: String containing one of the valid ordering attributes followed + (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. + Orders can be stacked as a comma-separated list of values. + title: Order + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + anyOf: + - $ref: '#/components/schemas/ArchivedHistorySummary' + - $ref: '#/components/schemas/ArchivedHistoryDetailed' + - {} + title: Response Get Archived Histories Api Histories Archived Get + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get a list of all archived histories for the current user. + tags: + - histories + - histories + /api/histories/batch/delete: + put: + operationId: batch_delete_api_histories_batch_delete_put + parameters: + - in: query + name: purge + required: false + schema: + default: false + title: Purge + type: boolean + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/DeleteHistoriesPayload' + required: true + responses: + '200': + content: + application/json: + schema: + items: + anyOf: + - $ref: '#/components/schemas/HistoryDetailed' + - $ref: '#/components/schemas/HistorySummary' + - $ref: '#/components/schemas/HistoryMinimal' + title: Response Batch Delete Api Histories Batch Delete Put + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Marks several histories with the given IDs as deleted. + tags: + - histories + - histories + /api/histories/batch/undelete: + put: + operationId: batch_undelete_api_histories_batch_undelete_put + parameters: + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/UndeleteHistoriesPayload' + required: true + responses: + '200': + content: + application/json: + schema: + items: + anyOf: + - $ref: '#/components/schemas/HistoryDetailed' + - $ref: '#/components/schemas/HistorySummary' + - $ref: '#/components/schemas/HistoryMinimal' + title: Response Batch Undelete Api Histories Batch Undelete Put + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Marks several histories with the given IDs as undeleted. + tags: + - histories + - histories + /api/histories/count: + get: + operationId: count_api_histories_count_get + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + title: Response Count Api Histories Count Get + type: integer + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns number of histories for the current user. + tags: + - histories + - histories + /api/histories/deleted: + get: + operationId: index_deleted_api_histories_deleted_get + parameters: + - description: Whether all histories from other users in this Galaxy should + be included. Only admins are allowed to query all histories. + in: query + name: all + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: false + description: Whether all histories from other users in this Galaxy should + be included. Only admins are allowed to query all histories. + title: All Histories + - description: Generally a property name to filter by followed by an (often + optional) hyphen and operator string. + in: query + name: q + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: Generally a property name to filter by followed by an (often + optional) hyphen and operator string. + examples: + - create_time-gt + title: Filter Query + - description: The value to filter by. + in: query + name: qv + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: The value to filter by. + examples: + - '2015-01-29' + title: Filter Value + - description: Starts at the beginning skip the first ( offset - 1 ) items and + begin returning at the Nth item + in: query + name: offset + required: false + schema: + anyOf: + - minimum: 0 + type: integer + - type: 'null' + default: 0 + description: Starts at the beginning skip the first ( offset - 1 ) items + and begin returning at the Nth item + title: Offset + - description: The maximum number of items to return. + in: query + name: limit + required: false + schema: + anyOf: + - minimum: 1 + type: integer + - type: 'null' + description: The maximum number of items to return. + title: Limit + - description: String containing one of the valid ordering attributes followed + (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. + Orders can be stacked as a comma-separated list of values. + in: query + name: order + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: String containing one of the valid ordering attributes followed + (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. + Orders can be stacked as a comma-separated list of values. + title: Order + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + anyOf: + - $ref: '#/components/schemas/HistoryDetailed' + - $ref: '#/components/schemas/HistorySummary' + - $ref: '#/components/schemas/HistoryMinimal' + title: Response Index Deleted Api Histories Deleted Get + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns deleted histories for the current user. + tags: + - histories + - histories + /api/histories/deleted/{history_id}/undelete: + post: + operationId: undelete_api_histories_deleted__history_id__undelete_post + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/HistoryDetailed' + - $ref: '#/components/schemas/HistorySummary' + - $ref: '#/components/schemas/HistoryMinimal' + title: Response Undelete Api Histories Deleted History Id Undelete + Post + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Restores a deleted history with the given ID (that hasn't been purged). + tags: + - histories + - histories + /api/histories/from_store: + post: + operationId: create_from_store_api_histories_from_store_post + parameters: + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/CreateHistoryFromStore' + required: true + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/HistoryDetailed' + - $ref: '#/components/schemas/HistorySummary' + - $ref: '#/components/schemas/HistoryMinimal' + title: Response Create From Store Api Histories From Store Post + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Create histories from a model store. + tags: + - histories + - histories + /api/histories/from_store_async: + post: + operationId: create_from_store_async_api_histories_from_store_async_post + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/CreateHistoryFromStore' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/AsyncTaskResultSummary' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Launch a task to create histories from a model store. + tags: + - histories + - histories + /api/histories/most_recently_used: + get: + operationId: show_recent_api_histories_most_recently_used_get + parameters: + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/HistoryDetailed' + - $ref: '#/components/schemas/HistorySummary' + - $ref: '#/components/schemas/HistoryMinimal' + title: Response Show Recent Api Histories Most Recently Used Get + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns the most recently used history of the user. + tags: + - histories + - histories + /api/histories/published: + get: + operationId: published_api_histories_published_get + parameters: + - description: Generally a property name to filter by followed by an (often + optional) hyphen and operator string. + in: query + name: q + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: Generally a property name to filter by followed by an (often + optional) hyphen and operator string. + examples: + - create_time-gt + title: Filter Query + - description: The value to filter by. + in: query + name: qv + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: The value to filter by. + examples: + - '2015-01-29' + title: Filter Value + - description: Starts at the beginning skip the first ( offset - 1 ) items and + begin returning at the Nth item + in: query + name: offset + required: false + schema: + anyOf: + - minimum: 0 + type: integer + - type: 'null' + default: 0 + description: Starts at the beginning skip the first ( offset - 1 ) items + and begin returning at the Nth item + title: Offset + - description: The maximum number of items to return. + in: query + name: limit + required: false + schema: + anyOf: + - minimum: 1 + type: integer + - type: 'null' + description: The maximum number of items to return. + title: Limit + - description: String containing one of the valid ordering attributes followed + (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. + Orders can be stacked as a comma-separated list of values. + in: query + name: order + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: String containing one of the valid ordering attributes followed + (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. + Orders can be stacked as a comma-separated list of values. + title: Order + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + anyOf: + - $ref: '#/components/schemas/HistoryDetailed' + - $ref: '#/components/schemas/HistorySummary' + - $ref: '#/components/schemas/HistoryMinimal' + title: Response Published Api Histories Published Get + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return all histories that are published. + tags: + - histories + - histories + /api/histories/shared_with_me: + get: + operationId: shared_with_me_api_histories_shared_with_me_get + parameters: + - description: Generally a property name to filter by followed by an (often + optional) hyphen and operator string. + in: query + name: q + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: Generally a property name to filter by followed by an (often + optional) hyphen and operator string. + examples: + - create_time-gt + title: Filter Query + - description: The value to filter by. + in: query + name: qv + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: The value to filter by. + examples: + - '2015-01-29' + title: Filter Value + - description: Starts at the beginning skip the first ( offset - 1 ) items and + begin returning at the Nth item + in: query + name: offset + required: false + schema: + anyOf: + - minimum: 0 + type: integer + - type: 'null' + default: 0 + description: Starts at the beginning skip the first ( offset - 1 ) items + and begin returning at the Nth item + title: Offset + - description: The maximum number of items to return. + in: query + name: limit + required: false + schema: + anyOf: + - minimum: 1 + type: integer + - type: 'null' + description: The maximum number of items to return. + title: Limit + - description: String containing one of the valid ordering attributes followed + (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. + Orders can be stacked as a comma-separated list of values. + in: query + name: order + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: String containing one of the valid ordering attributes followed + (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. + Orders can be stacked as a comma-separated list of values. + title: Order + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + anyOf: + - $ref: '#/components/schemas/HistoryDetailed' + - $ref: '#/components/schemas/HistorySummary' + - $ref: '#/components/schemas/HistoryMinimal' + title: Response Shared With Me Api Histories Shared With Me Get + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return all histories that are shared with the current user. + tags: + - histories + - histories + /api/histories/{history_id}: + delete: + operationId: delete_api_histories__history_id__delete + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - in: query + name: purge + required: false + schema: + default: false + title: Purge + type: boolean + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/DeleteHistoryPayload' + - type: 'null' + title: Payload + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/HistoryDetailed' + - $ref: '#/components/schemas/HistorySummary' + - $ref: '#/components/schemas/HistoryMinimal' + title: Response Delete Api Histories History Id Delete + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Marks the history with the given ID as deleted. + tags: + - histories + - histories + get: + operationId: history_api_histories__history_id__get + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/HistoryDetailed' + - $ref: '#/components/schemas/HistorySummary' + - $ref: '#/components/schemas/HistoryMinimal' + title: Response History Api Histories History Id Get + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns the history with the given ID. + tags: + - histories + - histories + put: + operationId: update_api_histories__history_id__put + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + description: Object containing any of the editable fields of the history. + title: Payload + required: true + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/HistoryDetailed' + - $ref: '#/components/schemas/HistorySummary' + - $ref: '#/components/schemas/HistoryMinimal' + title: Response Update Api Histories History Id Put + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Updates the values for the history with the given ID. + tags: + - histories + - histories + /api/histories/{history_id}/archive: + post: + description: 'Marks the given history as ''archived'' and returns the history. + + + Archiving a history will remove it from the list of active histories of the + user but it will still be + + accessible via the `/api/histories/{id}` or the `/api/histories/archived` + endpoints. + + + Associating an export record: + + + - Optionally, an export record (containing information about a recent snapshot + of the history) can be associated with the + + archived history by providing an `archive_export_id` in the payload. The export + record must belong to the history and + + must be in the ready state. + + - When associating an export record, the history can be purged after it has + been archived using the `purge_history` flag. + + + If the history is already archived, this endpoint will return a 409 Conflict + error, indicating that the history is already archived. + + If the history was not purged after it was archived, you can restore it using + the `/api/histories/{id}/archive/restore` endpoint.' + operationId: archive_history_api_histories__history_id__archive_post + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/ArchiveHistoryRequestPayload' + - type: 'null' + title: Payload + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/ArchivedHistorySummary' + - $ref: '#/components/schemas/ArchivedHistoryDetailed' + - {} + title: Response Archive History Api Histories History Id Archive + Post + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Archive a history. + tags: + - histories + - histories + /api/histories/{history_id}/archive/restore: + put: + description: 'Restores an archived history and returns it. + + + Restoring an archived history will add it back to the list of active histories + of the user (unless it was purged). + + + **Warning**: Please note that histories that are associated with an archive + export might be purged after export, so un-archiving them + + will not restore the datasets that were in the history before it was archived. + You will need to import back the archive export + + record to restore the history and its datasets as a new copy. See `/api/histories/from_store_async` + for more information.' + operationId: restore_archived_history_api_histories__history_id__archive_restore_put + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: If true, the history will be un-archived even if it has an associated + archive export record and was purged. + in: query + name: force + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + description: If true, the history will be un-archived even if it has an + associated archive export record and was purged. + title: Force + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/HistoryDetailed' + - $ref: '#/components/schemas/HistorySummary' + - $ref: '#/components/schemas/HistoryMinimal' + title: Response Restore Archived History Api Histories History Id Archive + Restore Put + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Restore an archived history. + tags: + - histories + - histories + /api/histories/{history_id}/citations: + get: + operationId: citations_api_histories__history_id__citations_get + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: {} + title: Response Citations Api Histories History Id Citations Get + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return all the citations for the tools used to produce the datasets + in the history. + tags: + - histories + - histories + /api/histories/{history_id}/contents: + get: + description: 'Return a list of `HDA`/`HDCA` data for the history with the given + ``ID``. + + + - The contents can be filtered and queried using the appropriate parameters. + + - The amount of information returned for each item can be customized. + + + **Note**: Anonymous users are allowed to get their current history contents.' + operationId: history_contents__index + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: Only `dev` value is allowed. Set it to use the latest version + of this endpoint. **All parameters marked as `deprecated` will be ignored + when this parameter is set.** + in: query + name: v + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Only `dev` value is allowed. Set it to use the latest version + of this endpoint. **All parameters marked as `deprecated` will be ignored + when this parameter is set.** + examples: + - dev + title: Version + - deprecated: true + description: Legacy name for the `dataset_details` parameter. + in: query + name: details + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Legacy name for the `dataset_details` parameter. + title: Details + - deprecated: true + description: A comma-separated list of encoded `HDA/HDCA` IDs. If this list + is provided, only information about the specific datasets will be returned. + Also, setting this value will return `all` details of the content item. + in: query + name: ids + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: A comma-separated list of encoded `HDA/HDCA` IDs. If this list + is provided, only information about the specific datasets will be returned. + Also, setting this value will return `all` details of the content item. + title: IDs + - deprecated: true + description: A list or comma-separated list of kinds of contents to return + (currently just `dataset` and `dataset_collection` are available). If unset, + all types will be returned. + in: query + name: types + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: A list or comma-separated list of kinds of contents to return + (currently just `dataset` and `dataset_collection` are available). If + unset, all types will be returned. + title: Types + - deprecated: true + description: Whether to return deleted or undeleted datasets only. Leave unset + for both. + in: query + name: deleted + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + description: Whether to return deleted or undeleted datasets only. Leave + unset for both. + title: Deleted + - deprecated: true + description: Whether to return visible or hidden datasets only. Leave unset + for both. + in: query + name: visible + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + description: Whether to return visible or hidden datasets only. Leave unset + for both. + title: Visible + - description: Whether to return only shareable or not shareable datasets. Leave + unset for both. + in: query + name: shareable + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + description: Whether to return only shareable or not shareable datasets. + Leave unset for both. + title: Shareable + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: Generally a property name to filter by followed by an (often + optional) hyphen and operator string. + in: query + name: q + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: Generally a property name to filter by followed by an (often + optional) hyphen and operator string. + examples: + - create_time-gt + title: Filter Query + - description: The value to filter by. + in: query + name: qv + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: The value to filter by. + examples: + - '2015-01-29' + title: Filter Value + - description: Starts at the beginning skip the first ( offset - 1 ) items and + begin returning at the Nth item + in: query + name: offset + required: false + schema: + anyOf: + - minimum: 0 + type: integer + - type: 'null' + default: 0 + description: Starts at the beginning skip the first ( offset - 1 ) items + and begin returning at the Nth item + title: Offset + - description: The maximum number of items to return. + in: query + name: limit + required: false + schema: + anyOf: + - minimum: 1 + type: integer + - type: 'null' + description: The maximum number of items to return. + title: Limit + - description: String containing one of the valid ordering attributes followed + (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. + Orders can be stacked as a comma-separated list of values. + in: query + name: order + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: String containing one of the valid ordering attributes followed + (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. + Orders can be stacked as a comma-separated list of values. + title: Order + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/HistoryContentsResult' + anyOf: + - $ref: '#/components/schemas/HistoryContentsResult' + - $ref: '#/components/schemas/HistoryContentsWithStatsResult' + title: Response History Contents Index + application/vnd.galaxy.history.contents.stats+json: + schema: + $ref: '#/components/schemas/HistoryContentsWithStatsResult' + description: The contents of the history that match the query. + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns the contents of the given history. + tags: + - histories + - histories + post: + deprecated: true + description: Create a new `HDA` or `HDCA` in the given History. + operationId: history_contents__create + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The type of the target history element. + in: query + name: type + required: false + schema: + anyOf: + - $ref: '#/components/schemas/HistoryContentType' + - type: 'null' + description: The type of the target history element. + examples: + - dataset + title: Content Type + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/CreateHistoryContentPayload' + required: true + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/HDADetailed' + - $ref: '#/components/schemas/HDASummary' + - $ref: '#/components/schemas/HDCADetailed' + - $ref: '#/components/schemas/HDCASummary' + - $ref: '#/components/schemas/CustomHistoryItem' + - items: + anyOf: + - $ref: '#/components/schemas/HDADetailed' + - $ref: '#/components/schemas/HDASummary' + - $ref: '#/components/schemas/HDCADetailed' + - $ref: '#/components/schemas/HDCASummary' + - $ref: '#/components/schemas/CustomHistoryItem' + type: array + title: Response History Contents Create + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Create a new `HDA` or `HDCA` in the given History. + tags: + - histories + - histories + put: + description: 'Batch update specific properties of a set items contained in the + given History. + + + If you provide an invalid/unknown property key the request will not fail, + but no changes + + will be made to the items.' + operationId: update_batch_api_histories__history_id__contents_put + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/UpdateHistoryContentsBatchPayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/HistoryContentsResult' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Batch update specific properties of a set items contained in the given + History. + tags: + - histories + - histories + /api/histories/{history_id}/contents/archive: + get: + description: 'Build and return a compressed archive of the selected history + contents. + + + **Note**: this is a volatile endpoint and settings and behavior may change.' + operationId: history_contents__archive + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The name that the Archive will have (defaults to history name). + in: query + name: filename + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: The name that the Archive will have (defaults to history name). + title: Filename + - description: Whether to return the archive and file paths only (as JSON) and + not an actual archive file. + in: query + name: dry_run + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: true + description: Whether to return the archive and file paths only (as JSON) + and not an actual archive file. + title: Dry Run + - description: Generally a property name to filter by followed by an (often + optional) hyphen and operator string. + in: query + name: q + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: Generally a property name to filter by followed by an (often + optional) hyphen and operator string. + examples: + - create_time-gt + title: Filter Query + - description: The value to filter by. + in: query + name: qv + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: The value to filter by. + examples: + - '2015-01-29' + title: Filter Value + - description: Starts at the beginning skip the first ( offset - 1 ) items and + begin returning at the Nth item + in: query + name: offset + required: false + schema: + anyOf: + - minimum: 0 + type: integer + - type: 'null' + default: 0 + description: Starts at the beginning skip the first ( offset - 1 ) items + and begin returning at the Nth item + title: Offset + - description: The maximum number of items to return. + in: query + name: limit + required: false + schema: + anyOf: + - minimum: 1 + type: integer + - type: 'null' + description: The maximum number of items to return. + title: Limit + - description: String containing one of the valid ordering attributes followed + (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. + Orders can be stacked as a comma-separated list of values. + in: query + name: order + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: String containing one of the valid ordering attributes followed + (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. + Orders can be stacked as a comma-separated list of values. + title: Order + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Build and return a compressed archive of the selected history contents. + tags: + - histories + - histories + /api/histories/{history_id}/contents/archive/{filename}.{format}: + get: + description: 'Build and return a compressed archive of the selected history + contents. + + + **Note**: this is a volatile endpoint and settings and behavior may change.' + operationId: history_contents__archive_named + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The name that the Archive will have (defaults to history name). + in: path + name: filename + required: true + schema: + description: The name that the Archive will have (defaults to history name). + title: Filename + type: string + - deprecated: true + description: Output format of the archive. + in: path + name: format + required: true + schema: + description: Output format of the archive. + title: Format + type: string + - description: Whether to return the archive and file paths only (as JSON) and + not an actual archive file. + in: query + name: dry_run + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: true + description: Whether to return the archive and file paths only (as JSON) + and not an actual archive file. + title: Dry Run + - description: Generally a property name to filter by followed by an (often + optional) hyphen and operator string. + in: query + name: q + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: Generally a property name to filter by followed by an (often + optional) hyphen and operator string. + examples: + - create_time-gt + title: Filter Query + - description: The value to filter by. + in: query + name: qv + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: The value to filter by. + examples: + - '2015-01-29' + title: Filter Value + - description: Starts at the beginning skip the first ( offset - 1 ) items and + begin returning at the Nth item + in: query + name: offset + required: false + schema: + anyOf: + - minimum: 0 + type: integer + - type: 'null' + default: 0 + description: Starts at the beginning skip the first ( offset - 1 ) items + and begin returning at the Nth item + title: Offset + - description: The maximum number of items to return. + in: query + name: limit + required: false + schema: + anyOf: + - minimum: 1 + type: integer + - type: 'null' + description: The maximum number of items to return. + title: Limit + - description: String containing one of the valid ordering attributes followed + (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. + Orders can be stacked as a comma-separated list of values. + in: query + name: order + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: String containing one of the valid ordering attributes followed + (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. + Orders can be stacked as a comma-separated list of values. + title: Order + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Build and return a compressed archive of the selected history contents. + tags: + - histories + - histories + /api/histories/{history_id}/contents/bulk: + put: + description: 'Executes an operation on a set of items contained in the given + History. + + + The items to be processed can be explicitly set or determined by a dynamic + query.' + operationId: bulk_operation_api_histories__history_id__contents_bulk_put + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: Generally a property name to filter by followed by an (often + optional) hyphen and operator string. + in: query + name: q + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: Generally a property name to filter by followed by an (often + optional) hyphen and operator string. + examples: + - create_time-gt + title: Filter Query + - description: The value to filter by. + in: query + name: qv + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: The value to filter by. + examples: + - '2015-01-29' + title: Filter Value + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/HistoryContentBulkOperationPayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/HistoryContentBulkOperationResult' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Executes an operation on a set of items contained in the given History. + tags: + - histories + - histories + /api/histories/{history_id}/contents/dataset_collections/{id}/download: + get: + description: 'Download the content of a history dataset collection as a `zip` + archive + + while maintaining approximate collection structure.' + operationId: history_contents__download_collection + parameters: + - description: The ID of the `HDCA`. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The encoded database identifier of the History. + title: History Id + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Download the content of a dataset collection as a `zip` archive. + tags: + - histories + - histories + /api/histories/{history_id}/contents/datasets/{id}/materialize: + post: + operationId: materialize_dataset_api_histories__history_id__contents_datasets__id__materialize_post + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The ID of the item (`HDA`/`HDCA`) + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/AsyncTaskResultSummary' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Materialize a deferred dataset into real, usable dataset. + tags: + - histories + - histories + /api/histories/{history_id}/contents/{dataset_id}/permissions: + put: + description: Set permissions of the given history dataset to the given role + ids. + operationId: update_permissions_api_histories__history_id__contents__dataset_id__permissions_put + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The ID of the item (`HDA`/`HDCA`) + in: path + name: dataset_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + examples: + - access_ids: [] + action: set_permissions + manage_ids: [] + modify_ids: [] + title: Payload + type: object + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DatasetAssociationRoles' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Set permissions of the given history dataset to the given role ids. + tags: + - histories + - histories + /api/histories/{history_id}/contents/{history_content_id}/display: + get: + description: Streams the dataset for download or the contents preview to be + displayed in a browser. + operationId: history_contents_display_api_histories__history_id__contents__history_content_id__display_get + parameters: + - description: The ID of the History Dataset. + in: path + name: history_content_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - in: path + name: history_id + required: true + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + title: History Id + - description: Whether to get preview contents to be directly displayed on the + web. If preview is False (default) the contents will be downloaded instead. + in: query + name: preview + required: false + schema: + default: false + description: Whether to get preview contents to be directly displayed on + the web. If preview is False (default) the contents will be downloaded + instead. + title: Preview + type: boolean + - description: If non-null, get the specified filename from the extra files + for this dataset. + in: query + name: filename + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: If non-null, get the specified filename from the extra files + for this dataset. + title: Filename + - description: The file extension when downloading the display data. Use the + value `data` to let the server infer it from the data type. + in: query + name: to_ext + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: The file extension when downloading the display data. Use the + value `data` to let the server infer it from the data type. + title: To Ext + - description: The query parameter 'raw' should be considered experimental and + may be dropped at some point in the future without warning. Generally, data + should be processed by its datatype prior to display. + in: query + name: raw + required: false + schema: + default: false + description: The query parameter 'raw' should be considered experimental + and may be dropped at some point in the future without warning. Generally, + data should be processed by its datatype prior to display. + title: Raw + type: boolean + - description: Set this for datatypes that allow chunked display through the + display_data method to enable chunking. This specifies a byte offset into + the target dataset's display. + in: query + name: offset + required: false + schema: + anyOf: + - type: integer + - type: 'null' + description: Set this for datatypes that allow chunked display through the + display_data method to enable chunking. This specifies a byte offset into + the target dataset's display. + title: Offset + - description: 'If offset is set, this recommends ''how large'' the next chunk + should be. This is not respected or interpreted uniformly and should be + interpreted as a very loose recommendation. Different datatypes interpret + ''largeness'' differently - for bam datasets this is a number of lines whereas + for tabular datatypes this is interpreted as a number of bytes. ' + in: query + name: ck_size + required: false + schema: + anyOf: + - type: integer + - type: 'null' + description: 'If offset is set, this recommends ''how large'' the next chunk + should be. This is not respected or interpreted uniformly and should be + interpreted as a very loose recommendation. Different datatypes interpret + ''largeness'' differently - for bam datasets this is a number of lines + whereas for tabular datatypes this is interpreted as a number of bytes. ' + title: Ck Size + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Displays (preview) or downloads dataset content. + tags: + - datasets + - datasets + - histories + head: + description: Streams the dataset for download or the contents preview to be + displayed in a browser. + operationId: history_contents_display_api_histories__history_id__contents__history_content_id__display_head + parameters: + - description: The ID of the History Dataset. + in: path + name: history_content_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - in: path + name: history_id + required: true + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + title: History Id + - description: Whether to get preview contents to be directly displayed on the + web. If preview is False (default) the contents will be downloaded instead. + in: query + name: preview + required: false + schema: + default: false + description: Whether to get preview contents to be directly displayed on + the web. If preview is False (default) the contents will be downloaded + instead. + title: Preview + type: boolean + - description: If non-null, get the specified filename from the extra files + for this dataset. + in: query + name: filename + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: If non-null, get the specified filename from the extra files + for this dataset. + title: Filename + - description: The file extension when downloading the display data. Use the + value `data` to let the server infer it from the data type. + in: query + name: to_ext + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: The file extension when downloading the display data. Use the + value `data` to let the server infer it from the data type. + title: To Ext + - description: The query parameter 'raw' should be considered experimental and + may be dropped at some point in the future without warning. Generally, data + should be processed by its datatype prior to display. + in: query + name: raw + required: false + schema: + default: false + description: The query parameter 'raw' should be considered experimental + and may be dropped at some point in the future without warning. Generally, + data should be processed by its datatype prior to display. + title: Raw + type: boolean + - description: Set this for datatypes that allow chunked display through the + display_data method to enable chunking. This specifies a byte offset into + the target dataset's display. + in: query + name: offset + required: false + schema: + anyOf: + - type: integer + - type: 'null' + description: Set this for datatypes that allow chunked display through the + display_data method to enable chunking. This specifies a byte offset into + the target dataset's display. + title: Offset + - description: 'If offset is set, this recommends ''how large'' the next chunk + should be. This is not respected or interpreted uniformly and should be + interpreted as a very loose recommendation. Different datatypes interpret + ''largeness'' differently - for bam datasets this is a number of lines whereas + for tabular datatypes this is interpreted as a number of bytes. ' + in: query + name: ck_size + required: false + schema: + anyOf: + - type: integer + - type: 'null' + description: 'If offset is set, this recommends ''how large'' the next chunk + should be. This is not respected or interpreted uniformly and should be + interpreted as a very loose recommendation. Different datatypes interpret + ''largeness'' differently - for bam datasets this is a number of lines + whereas for tabular datatypes this is interpreted as a number of bytes. ' + title: Ck Size + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Check if dataset content can be previewed or downloaded. + tags: + - datasets + - datasets + - histories + /api/histories/{history_id}/contents/{history_content_id}/extra_files: + get: + operationId: extra_files_history_api_histories__history_id__contents__history_content_id__extra_files_get + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The ID of the History Dataset. + in: path + name: history_content_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DatasetExtraFiles' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get the list of extra files/directories associated with a dataset. + tags: + - datasets + - datasets + - histories + /api/histories/{history_id}/contents/{history_content_id}/metadata_file: + get: + operationId: history_contents__get_metadata_file + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The ID of the History Dataset. + in: path + name: history_content_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The name of the metadata file to retrieve. + in: query + name: metadata_file + required: true + schema: + description: The name of the metadata file to retrieve. + title: Metadata File + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns the metadata file associated with this history item. + tags: + - datasets + - datasets + - histories + /api/histories/{history_id}/contents/{history_content_id}/tags: + get: + operationId: index_api_histories__history_id__contents__history_content_id__tags_get + parameters: + - in: path + name: history_content_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + - in: path + name: history_id + required: true + schema: + title: History ID + type: string + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ItemTagsListResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Show tags based on history_content_id + tags: + - histories + /api/histories/{history_id}/contents/{history_content_id}/tags/{tag_name}: + delete: + operationId: delete_api_histories__history_id__contents__history_content_id__tags__tag_name__delete + parameters: + - in: path + name: history_content_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - in: path + name: tag_name + required: true + schema: + title: Tag Name + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + - in: path + name: history_id + required: true + schema: + title: History ID + type: string + responses: + '200': + content: + application/json: + schema: + title: Response Delete Api Histories History Id Contents History + Content Id Tags Tag Name Delete + type: boolean + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Delete tag based on history_content_id + tags: + - histories + get: + operationId: show_api_histories__history_id__contents__history_content_id__tags__tag_name__get + parameters: + - in: path + name: history_content_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - in: path + name: tag_name + required: true + schema: + title: Tag Name + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + - in: path + name: history_id + required: true + schema: + title: History ID + type: string + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ItemTagsResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Show tag based on history_content_id + tags: + - histories + post: + operationId: create_api_histories__history_id__contents__history_content_id__tags__tag_name__post + parameters: + - in: path + name: history_content_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - in: path + name: tag_name + required: true + schema: + title: Tag Name + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + - in: path + name: history_id + required: true + schema: + title: History ID + type: string + requestBody: + content: + application/json: + schema: + allOf: + - $ref: '#/components/schemas/ItemTagsCreatePayload' + title: Payload + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ItemTagsResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Create tag based on history_content_id + tags: + - histories + put: + operationId: update_api_histories__history_id__contents__history_content_id__tags__tag_name__put + parameters: + - in: path + name: history_content_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - in: path + name: tag_name + required: true + schema: + title: Tag Name + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + - in: path + name: history_id + required: true + schema: + title: History ID + type: string + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/ItemTagsCreatePayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ItemTagsResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Update tag based on history_content_id + tags: + - histories + /api/histories/{history_id}/contents/{id}: + delete: + description: 'Delete the history content with the given ``ID`` and query specified + type (defaults to dataset). + + + **Note**: Currently does not stop any active jobs for which this dataset is + an output.' + operationId: history_contents__delete_legacy + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The ID of the item (`HDA`/`HDCA`) + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The type of the target history element. + in: query + name: type + required: false + schema: + allOf: + - $ref: '#/components/schemas/HistoryContentType' + default: dataset + description: The type of the target history element. + examples: + - dataset + title: Content Type + - deprecated: true + description: Whether to remove from disk the target HDA or child HDAs of the + target HDCA. + in: query + name: purge + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: false + description: Whether to remove from disk the target HDA or child HDAs of + the target HDCA. + title: Purge + - deprecated: true + description: When deleting a dataset collection, whether to also delete containing + datasets. + in: query + name: recursive + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: false + description: When deleting a dataset collection, whether to also delete + containing datasets. + title: Recursive + - deprecated: true + description: Whether to stop the creating job if all outputs of the job have + been deleted. + in: query + name: stop_job + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: false + description: Whether to stop the creating job if all outputs of the job + have been deleted. + title: Stop Job + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + allOf: + - $ref: '#/components/schemas/DeleteHistoryContentPayload' + title: Payload + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DeleteHistoryContentResult' + description: Request has been executed. + '202': + content: + application/json: + schema: + $ref: '#/components/schemas/DeleteHistoryContentResult' + description: Request accepted, processing will finish later. + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Delete the history dataset with the given ``ID``. + tags: + - histories + - histories + get: + deprecated: true + description: 'Return detailed information about an `HDA` or `HDCA` within a + history. + + + **Note**: Anonymous users are allowed to get their current history contents.' + operationId: history_contents__show_legacy + parameters: + - description: The ID of the item (`HDA`/`HDCA`) + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The type of the target history element. + in: query + name: type + required: false + schema: + allOf: + - $ref: '#/components/schemas/HistoryContentType' + default: dataset + description: The type of the target history element. + examples: + - dataset + title: Content Type + - description: This value can be used to broadly restrict the magnitude of the + number of elements returned via the API for large collections. The number + of actual elements returned may be "a bit" more than this number or "a lot" + less - varying on the depth of nesting, balance of nesting at each level, + and size of target collection. The consumer of this API should not expect + a stable number or pre-calculable number of elements to be produced given + this parameter - the only promise is that this API will not respond with + an order of magnitude more elements estimated with this value. The UI uses + this parameter to fetch a "balanced" concept of the "start" of large collections + at every depth of the collection. + in: query + name: fuzzy_count + required: false + schema: + anyOf: + - type: integer + - type: 'null' + description: This value can be used to broadly restrict the magnitude of + the number of elements returned via the API for large collections. The + number of actual elements returned may be "a bit" more than this number + or "a lot" less - varying on the depth of nesting, balance of nesting + at each level, and size of target collection. The consumer of this API + should not expect a stable number or pre-calculable number of elements + to be produced given this parameter - the only promise is that this API + will not respond with an order of magnitude more elements estimated with + this value. The UI uses this parameter to fetch a "balanced" concept of + the "start" of large collections at every depth of the collection. + title: Fuzzy Count + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/HDADetailed' + - $ref: '#/components/schemas/HDASummary' + - $ref: '#/components/schemas/HDCADetailed' + - $ref: '#/components/schemas/HDCASummary' + - $ref: '#/components/schemas/CustomHistoryItem' + title: Response History Contents Show Legacy + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return detailed information about an HDA within a history. ``/api/histories/{history_id}/contents/{type}s/{id}`` + should be used instead. + tags: + - histories + - histories + put: + deprecated: true + description: Updates the values for the history content item with the given + ``ID``. + operationId: history_contents__update_legacy + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The ID of the item (`HDA`/`HDCA`) + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The type of the target history element. + in: query + name: type + required: false + schema: + allOf: + - $ref: '#/components/schemas/HistoryContentType' + default: dataset + description: The type of the target history element. + examples: + - dataset + title: Content Type + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/UpdateHistoryContentsPayload' + required: true + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/HDADetailed' + - $ref: '#/components/schemas/HDASummary' + - $ref: '#/components/schemas/HDCADetailed' + - $ref: '#/components/schemas/HDCASummary' + - $ref: '#/components/schemas/CustomHistoryItem' + title: Response History Contents Update Legacy + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Updates the values for the history content item with the given ``ID`` + and query specified type. ``/api/histories/{history_id}/contents/{type}s/{id}`` + should be used instead. + tags: + - histories + - histories + /api/histories/{history_id}/contents/{id}/validate: + put: + description: Validates the metadata associated with a dataset within a History. + operationId: validate_api_histories__history_id__contents__id__validate_put + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The ID of the item (`HDA`/`HDCA`) + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + title: Response Validate Api Histories History Id Contents Id Validate + Put + type: object + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Validates the metadata associated with a dataset within a History. + tags: + - histories + - histories + /api/histories/{history_id}/contents/{type}s: + get: + description: 'Return a list of either `HDA`/`HDCA` data for the history with + the given ``ID``. + + + - The contents can be filtered and queried using the appropriate parameters. + + - The amount of information returned for each item can be customized. + + + **Note**: Anonymous users are allowed to get their current history contents.' + operationId: history_contents__index_typed + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The type of the target history element. + in: path + name: type + required: true + schema: + allOf: + - $ref: '#/components/schemas/HistoryContentType' + description: The type of the target history element. + examples: + - dataset + title: Content Type + - description: Only `dev` value is allowed. Set it to use the latest version + of this endpoint. **All parameters marked as `deprecated` will be ignored + when this parameter is set.** + in: query + name: v + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Only `dev` value is allowed. Set it to use the latest version + of this endpoint. **All parameters marked as `deprecated` will be ignored + when this parameter is set.** + examples: + - dev + title: Version + - deprecated: true + description: Legacy name for the `dataset_details` parameter. + in: query + name: details + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Legacy name for the `dataset_details` parameter. + title: Details + - deprecated: true + description: A comma-separated list of encoded `HDA/HDCA` IDs. If this list + is provided, only information about the specific datasets will be returned. + Also, setting this value will return `all` details of the content item. + in: query + name: ids + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: A comma-separated list of encoded `HDA/HDCA` IDs. If this list + is provided, only information about the specific datasets will be returned. + Also, setting this value will return `all` details of the content item. + title: IDs + - deprecated: true + description: A list or comma-separated list of kinds of contents to return + (currently just `dataset` and `dataset_collection` are available). If unset, + all types will be returned. + in: query + name: types + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: A list or comma-separated list of kinds of contents to return + (currently just `dataset` and `dataset_collection` are available). If + unset, all types will be returned. + title: Types + - deprecated: true + description: Whether to return deleted or undeleted datasets only. Leave unset + for both. + in: query + name: deleted + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + description: Whether to return deleted or undeleted datasets only. Leave + unset for both. + title: Deleted + - deprecated: true + description: Whether to return visible or hidden datasets only. Leave unset + for both. + in: query + name: visible + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + description: Whether to return visible or hidden datasets only. Leave unset + for both. + title: Visible + - description: Whether to return only shareable or not shareable datasets. Leave + unset for both. + in: query + name: shareable + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + description: Whether to return only shareable or not shareable datasets. + Leave unset for both. + title: Shareable + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: Generally a property name to filter by followed by an (often + optional) hyphen and operator string. + in: query + name: q + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: Generally a property name to filter by followed by an (often + optional) hyphen and operator string. + examples: + - create_time-gt + title: Filter Query + - description: The value to filter by. + in: query + name: qv + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: The value to filter by. + examples: + - '2015-01-29' + title: Filter Value + - description: Starts at the beginning skip the first ( offset - 1 ) items and + begin returning at the Nth item + in: query + name: offset + required: false + schema: + anyOf: + - minimum: 0 + type: integer + - type: 'null' + default: 0 + description: Starts at the beginning skip the first ( offset - 1 ) items + and begin returning at the Nth item + title: Offset + - description: The maximum number of items to return. + in: query + name: limit + required: false + schema: + anyOf: + - minimum: 1 + type: integer + - type: 'null' + description: The maximum number of items to return. + title: Limit + - description: String containing one of the valid ordering attributes followed + (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. + Orders can be stacked as a comma-separated list of values. + in: query + name: order + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: String containing one of the valid ordering attributes followed + (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. + Orders can be stacked as a comma-separated list of values. + title: Order + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/HistoryContentsResult' + - $ref: '#/components/schemas/HistoryContentsWithStatsResult' + title: Response History Contents Index Typed + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns the contents of the given history filtered by type. + tags: + - histories + - histories + post: + description: Create a new `HDA` or `HDCA` in the given History. + operationId: history_contents__create_typed + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The type of the target history element. + in: path + name: type + required: true + schema: + allOf: + - $ref: '#/components/schemas/HistoryContentType' + description: The type of the target history element. + examples: + - dataset + title: Content Type + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/CreateHistoryContentPayload' + required: true + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/HDADetailed' + - $ref: '#/components/schemas/HDASummary' + - $ref: '#/components/schemas/HDCADetailed' + - $ref: '#/components/schemas/HDCASummary' + - $ref: '#/components/schemas/CustomHistoryItem' + - items: + anyOf: + - $ref: '#/components/schemas/HDADetailed' + - $ref: '#/components/schemas/HDASummary' + - $ref: '#/components/schemas/HDCADetailed' + - $ref: '#/components/schemas/HDCASummary' + - $ref: '#/components/schemas/CustomHistoryItem' + type: array + title: Response History Contents Create Typed + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Create a new `HDA` or `HDCA` in the given History. + tags: + - histories + - histories + /api/histories/{history_id}/contents/{type}s/{id}: + delete: + description: 'Delete the history content with the given ``ID`` and path specified + type. + + + **Note**: Currently does not stop any active jobs for which this dataset is + an output.' + operationId: history_contents__delete_typed + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The ID of the item (`HDA`/`HDCA`) + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The type of the target history element. + in: path + name: type + required: true + schema: + allOf: + - $ref: '#/components/schemas/HistoryContentType' + description: The type of the target history element. + examples: + - dataset + title: Content Type + - deprecated: true + description: Whether to remove from disk the target HDA or child HDAs of the + target HDCA. + in: query + name: purge + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: false + description: Whether to remove from disk the target HDA or child HDAs of + the target HDCA. + title: Purge + - deprecated: true + description: When deleting a dataset collection, whether to also delete containing + datasets. + in: query + name: recursive + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: false + description: When deleting a dataset collection, whether to also delete + containing datasets. + title: Recursive + - deprecated: true + description: Whether to stop the creating job if all outputs of the job have + been deleted. + in: query + name: stop_job + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: false + description: Whether to stop the creating job if all outputs of the job + have been deleted. + title: Stop Job + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + allOf: + - $ref: '#/components/schemas/DeleteHistoryContentPayload' + title: Payload + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DeleteHistoryContentResult' + description: Request has been executed. + '202': + content: + application/json: + schema: + $ref: '#/components/schemas/DeleteHistoryContentResult' + description: Request accepted, processing will finish later. + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Delete the history content with the given ``ID`` and path specified + type. + tags: + - histories + - histories + get: + description: 'Return detailed information about an `HDA` or `HDCA` within a + history. + + + **Note**: Anonymous users are allowed to get their current history contents.' + operationId: history_contents__show + parameters: + - description: The ID of the item (`HDA`/`HDCA`) + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The type of the target history element. + in: path + name: type + required: true + schema: + allOf: + - $ref: '#/components/schemas/HistoryContentType' + description: The type of the target history element. + examples: + - dataset + title: Content Type + - description: This value can be used to broadly restrict the magnitude of the + number of elements returned via the API for large collections. The number + of actual elements returned may be "a bit" more than this number or "a lot" + less - varying on the depth of nesting, balance of nesting at each level, + and size of target collection. The consumer of this API should not expect + a stable number or pre-calculable number of elements to be produced given + this parameter - the only promise is that this API will not respond with + an order of magnitude more elements estimated with this value. The UI uses + this parameter to fetch a "balanced" concept of the "start" of large collections + at every depth of the collection. + in: query + name: fuzzy_count + required: false + schema: + anyOf: + - type: integer + - type: 'null' + description: This value can be used to broadly restrict the magnitude of + the number of elements returned via the API for large collections. The + number of actual elements returned may be "a bit" more than this number + or "a lot" less - varying on the depth of nesting, balance of nesting + at each level, and size of target collection. The consumer of this API + should not expect a stable number or pre-calculable number of elements + to be produced given this parameter - the only promise is that this API + will not respond with an order of magnitude more elements estimated with + this value. The UI uses this parameter to fetch a "balanced" concept of + the "start" of large collections at every depth of the collection. + title: Fuzzy Count + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/HDADetailed' + - $ref: '#/components/schemas/HDASummary' + - $ref: '#/components/schemas/HDCADetailed' + - $ref: '#/components/schemas/HDCASummary' + - $ref: '#/components/schemas/CustomHistoryItem' + title: Response History Contents Show + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return detailed information about a specific HDA or HDCA with the given + `ID` within a history. + tags: + - histories + - histories + put: + description: Updates the values for the history content item with the given + ``ID``. + operationId: history_contents__update_typed + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The ID of the item (`HDA`/`HDCA`) + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The type of the target history element. + in: path + name: type + required: true + schema: + allOf: + - $ref: '#/components/schemas/HistoryContentType' + description: The type of the target history element. + examples: + - dataset + title: Content Type + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/UpdateHistoryContentsPayload' + required: true + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/HDADetailed' + - $ref: '#/components/schemas/HDASummary' + - $ref: '#/components/schemas/HDCADetailed' + - $ref: '#/components/schemas/HDCASummary' + - $ref: '#/components/schemas/CustomHistoryItem' + title: Response History Contents Update Typed + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Updates the values for the history content item with the given ``ID`` + and path specified type. + tags: + - histories + - histories + /api/histories/{history_id}/contents/{type}s/{id}/jobs_summary: + get: + description: 'Return detailed information about an `HDA` or `HDCAs` jobs. + + + **Warning**: We allow anyone to fetch job state information about any object + they + + can guess an encoded ID for - it isn''t considered protected data. This keeps + + polling IDs as part of state calculation for large histories and collections + as + + efficient as possible.' + operationId: show_jobs_summary_api_histories__history_id__contents__type_s__id__jobs_summary_get + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The ID of the item (`HDA`/`HDCA`) + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The type of the target history element. + in: path + name: type + required: true + schema: + allOf: + - $ref: '#/components/schemas/HistoryContentType' + description: The type of the target history element. + examples: + - dataset + title: Content Type + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + discriminator: + mapping: + ImplicitCollectionJobs: '#/components/schemas/ImplicitCollectionJobsStateSummary' + Job: '#/components/schemas/JobStateSummary' + WorkflowInvocation: '#/components/schemas/WorkflowInvocationStateSummary' + propertyName: model + oneOf: + - $ref: '#/components/schemas/JobStateSummary' + - $ref: '#/components/schemas/ImplicitCollectionJobsStateSummary' + - $ref: '#/components/schemas/WorkflowInvocationStateSummary' + title: Response Show Jobs Summary Api Histories History Id Contents Type + S Id Jobs Summary Get + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return detailed information about an `HDA` or `HDCAs` jobs. + tags: + - histories + - histories + /api/histories/{history_id}/contents/{type}s/{id}/prepare_store_download: + post: + operationId: prepare_store_download_api_histories__history_id__contents__type_s__id__prepare_store_download_post + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The ID of the item (`HDA`/`HDCA`) + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The type of the target history element. + in: path + name: type + required: true + schema: + allOf: + - $ref: '#/components/schemas/HistoryContentType' + description: The type of the target history element. + examples: + - dataset + title: Content Type + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/StoreExportPayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/AsyncFile' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Prepare a dataset or dataset collection for export-style download. + tags: + - histories + - histories + /api/histories/{history_id}/contents/{type}s/{id}/write_store: + post: + operationId: write_store_api_histories__history_id__contents__type_s__id__write_store_post + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The ID of the item (`HDA`/`HDCA`) + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The type of the target history element. + in: path + name: type + required: true + schema: + allOf: + - $ref: '#/components/schemas/HistoryContentType' + description: The type of the target history element. + examples: + - dataset + title: Content Type + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/WriteStoreToPayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/AsyncTaskResultSummary' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Prepare a dataset or dataset collection for export-style download and + write to supplied URI. + tags: + - histories + - histories + /api/histories/{history_id}/contents_from_store: + post: + description: 'Create history contents from model store. + + Input can be a tarfile created with build_objects script distributed + + with galaxy-data, from an exported history with files stripped out, + + or hand-crafted JSON dictionary.' + operationId: create_from_store_api_histories__history_id__contents_from_store_post + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Comma-separated list of keys to be passed to the serializer + in: query + name: keys + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Comma-separated list of keys to be passed to the serializer + title: Keys + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/CreateHistoryContentFromStore' + required: true + responses: + '200': + content: + application/json: + schema: + items: + anyOf: + - $ref: '#/components/schemas/HDADetailed' + - $ref: '#/components/schemas/HDASummary' + - $ref: '#/components/schemas/HDCADetailed' + - $ref: '#/components/schemas/HDCASummary' + - $ref: '#/components/schemas/CustomHistoryItem' + title: Response Create From Store Api Histories History Id Contents + From Store Post + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Create contents from store. + tags: + - histories + - histories + /api/histories/{history_id}/custom_builds_metadata: + get: + operationId: get_custom_builds_metadata_api_histories__history_id__custom_builds_metadata_get + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/CustomBuildsMetadataResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns meta data for custom builds. + tags: + - histories + - histories + /api/histories/{history_id}/disable_link_access: + put: + description: Makes this item inaccessible by a URL link and return the current + sharing status. + operationId: disable_link_access_api_histories__history_id__disable_link_access_put + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/SharingStatus' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Makes this item inaccessible by a URL link. + tags: + - histories + - histories + /api/histories/{history_id}/enable_link_access: + put: + description: Makes this item accessible by a URL link and return the current + sharing status. + operationId: enable_link_access_api_histories__history_id__enable_link_access_put + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/SharingStatus' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Makes this item accessible by a URL link. + tags: + - histories + - histories + /api/histories/{history_id}/exports: + get: + description: 'By default the legacy job-based history exports (jeha) are returned. + + + Change the `accept` content type header to return the new task-based history + exports.' + operationId: get_history_exports_api_histories__history_id__exports_get + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The maximum number of items to return. + in: query + name: limit + required: false + schema: + anyOf: + - minimum: 1 + type: integer + - type: 'null' + description: The maximum number of items to return. + title: Limit + - description: Starts at the beginning skip the first ( offset - 1 ) items and + begin returning at the Nth item + in: query + name: offset + required: false + schema: + anyOf: + - minimum: 0 + type: integer + - type: 'null' + default: 0 + description: Starts at the beginning skip the first ( offset - 1 ) items + and begin returning at the Nth item + title: Offset + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/JobExportHistoryArchiveListResponse' + anyOf: + - $ref: '#/components/schemas/JobExportHistoryArchiveListResponse' + - $ref: '#/components/schemas/ExportTaskListResponse' + title: Response Get History Exports Api Histories History Id Exports + Get + application/vnd.galaxy.task.export+json: + schema: + $ref: '#/components/schemas/ExportTaskListResponse' + description: A list of history exports + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get previous history exports. + tags: + - histories + - histories + put: + deprecated: true + description: 'This will start a job to create a history export archive. + + + Calling this endpoint multiple times will return the 202 status code until + the archive + + has been completely generated and is ready to download. When ready, it will + return + + the 200 status code along with the download link information. + + + If the history will be exported to a `directory_uri`, instead of returning + the download + + link information, the Job ID will be returned so it can be queried to determine + when + + the file has been written. + + + **Deprecation notice**: Please use `/api/histories/{id}/prepare_store_download` + or + + `/api/histories/{id}/write_store` instead.' + operationId: archive_export_api_histories__history_id__exports_put + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/ExportHistoryArchivePayload' + - type: 'null' + title: Payload + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/JobExportHistoryArchiveModel' + - $ref: '#/components/schemas/JobIdResponse' + title: Response Archive Export Api Histories History Id Exports + Put + description: Object containing url to fetch export from. + '202': + description: The exported archive file is not ready yet. + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Start job (if needed) to create history export for corresponding history. + tags: + - histories + - histories + /api/histories/{history_id}/exports/{jeha_id}: + get: + deprecated: true + description: 'See ``PUT /api/histories/{id}/exports`` to initiate the creation + + of the history export - when ready, that route will return 200 status + + code (instead of 202) and this route can be used to download the archive. + + + **Deprecation notice**: Please use `/api/histories/{id}/prepare_store_download` + or + + `/api/histories/{id}/write_store` instead.' + operationId: history_archive_download_api_histories__history_id__exports__jeha_id__get + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The ID of the specific Job Export History Association or `latest` + (default) to download the last generated archive. + in: path + name: jeha_id + required: true + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - const: latest + description: The ID of the specific Job Export History Association or `latest` + (default) to download the last generated archive. + examples: + - latest + title: Job Export History ID + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + description: The archive file containing the History. + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: If ready and available, return raw contents of exported history as + a downloadable archive. + tags: + - histories + - histories + /api/histories/{history_id}/jobs_summary: + get: + description: 'Return job state summary info for jobs, implicit groups jobs for + collections or workflow invocations. + + + **Warning**: We allow anyone to fetch job state information about any object + they + + can guess an encoded ID for - it isn''t considered protected data. This keeps + + polling IDs as part of state calculation for large histories and collections + as + + efficient as possible.' + operationId: index_jobs_summary_api_histories__history_id__jobs_summary_get + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: A comma-separated list of encoded ids of job summary objects + to return - if `ids` is specified types must also be specified and have + same length. + in: query + name: ids + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: A comma-separated list of encoded ids of job summary objects + to return - if `ids` is specified types must also be specified and have + same length. + title: IDs + - description: A comma-separated list of type of object represented by elements + in the `ids` array - any of `Job`, `ImplicitCollectionJob`, or `WorkflowInvocation`. + in: query + name: types + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: A comma-separated list of type of object represented by elements + in the `ids` array - any of `Job`, `ImplicitCollectionJob`, or `WorkflowInvocation`. + title: Types + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + discriminator: + mapping: + ImplicitCollectionJobs: '#/components/schemas/ImplicitCollectionJobsStateSummary' + Job: '#/components/schemas/JobStateSummary' + WorkflowInvocation: '#/components/schemas/WorkflowInvocationStateSummary' + propertyName: model + oneOf: + - $ref: '#/components/schemas/JobStateSummary' + - $ref: '#/components/schemas/ImplicitCollectionJobsStateSummary' + - $ref: '#/components/schemas/WorkflowInvocationStateSummary' + title: Response Index Jobs Summary Api Histories History Id Jobs + Summary Get + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return job state summary info for jobs, implicit groups jobs for collections + or workflow invocations. + tags: + - histories + - histories + /api/histories/{history_id}/materialize: + post: + operationId: materialize_to_history_api_histories__history_id__materialize_post + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/MaterializeDatasetInstanceAPIRequest' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/AsyncTaskResultSummary' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Materialize a deferred library or HDA dataset into real, usable dataset + in specified history. + tags: + - histories + - histories + /api/histories/{history_id}/prepare_store_download: + post: + operationId: prepare_store_download_api_histories__history_id__prepare_store_download_post + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/StoreExportPayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/AsyncFile' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return a short term storage token to monitor download of the history. + tags: + - histories + - histories + /api/histories/{history_id}/publish: + put: + description: Makes this item publicly available by a URL link and return the + current sharing status. + operationId: publish_api_histories__history_id__publish_put + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/SharingStatus' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Makes this item public and accessible by a URL link. + tags: + - histories + - histories + /api/histories/{history_id}/share_with_users: + put: + description: Shares this item with specific users and return the current sharing + status. + operationId: share_with_users_api_histories__history_id__share_with_users_put + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/ShareWithPayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ShareHistoryWithStatus' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Share this item with specific users. + tags: + - histories + - histories + /api/histories/{history_id}/sharing: + get: + description: Return the sharing status of the item. + operationId: sharing_api_histories__history_id__sharing_get + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/SharingStatus' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get the current sharing status of the given item. + tags: + - histories + - histories + /api/histories/{history_id}/slug: + put: + description: Sets a new slug to access this item by URL. The new slug must be + unique. + operationId: set_slug_api_histories__history_id__slug_put + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/SetSlugPayload' + required: true + responses: + '204': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Set a new slug for this shared item. + tags: + - histories + - histories + /api/histories/{history_id}/tags: + get: + operationId: index_api_histories__history_id__tags_get + parameters: + - in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ItemTagsListResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Show tags based on history_id + tags: + - histories + /api/histories/{history_id}/tags/{tag_name}: + delete: + operationId: delete_api_histories__history_id__tags__tag_name__delete + parameters: + - in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - in: path + name: tag_name + required: true + schema: + title: Tag Name + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + title: Response Delete Api Histories History Id Tags Tag Name Delete + type: boolean + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Delete tag based on history_id + tags: + - histories + get: + operationId: show_api_histories__history_id__tags__tag_name__get + parameters: + - in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - in: path + name: tag_name + required: true + schema: + title: Tag Name + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ItemTagsResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Show tag based on history_id + tags: + - histories + post: + operationId: create_api_histories__history_id__tags__tag_name__post + parameters: + - in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - in: path + name: tag_name + required: true + schema: + title: Tag Name + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + allOf: + - $ref: '#/components/schemas/ItemTagsCreatePayload' + title: Payload + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ItemTagsResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Create tag based on history_id + tags: + - histories + put: + operationId: update_api_histories__history_id__tags__tag_name__put + parameters: + - in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - in: path + name: tag_name + required: true + schema: + title: Tag Name + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/ItemTagsCreatePayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ItemTagsResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Update tag based on history_id + tags: + - histories + /api/histories/{history_id}/unpublish: + put: + description: Removes this item from the published list and return the current + sharing status. + operationId: unpublish_api_histories__history_id__unpublish_put + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/SharingStatus' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Removes this item from the published list. + tags: + - histories + - histories + /api/histories/{history_id}/write_store: + post: + operationId: write_store_api_histories__history_id__write_store_post + parameters: + - description: The encoded database identifier of the History. + in: path + name: history_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/WriteStoreToPayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/AsyncTaskResultSummary' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Prepare history for export-style download and write to supplied URI. + tags: + - histories + - histories + /api/invocations: + get: + operationId: index_invocations_api_invocations_get + parameters: + - description: Return only invocations for this Workflow ID + in: query + name: workflow_id + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: Return only invocations for this Workflow ID + title: Workflow ID + - description: Return only invocations for this History ID + in: query + name: history_id + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: Return only invocations for this History ID + title: History ID + - description: Return only invocations for this Job ID + in: query + name: job_id + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: Return only invocations for this Job ID + title: Job ID + - description: Return invocations for this User ID. + in: query + name: user_id + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: Return invocations for this User ID. + title: User ID + - description: Sort Workflow Invocations by this attribute + in: query + name: sort_by + required: false + schema: + anyOf: + - $ref: '#/components/schemas/InvocationSortByEnum' + - type: 'null' + description: Sort Workflow Invocations by this attribute + title: Sort By + - description: Sort in descending order? + in: query + name: sort_desc + required: false + schema: + default: false + description: Sort in descending order? + title: Sort Descending + type: boolean + - description: Set to false to only include terminal Invocations. + in: query + name: include_terminal + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: true + description: Set to false to only include terminal Invocations. + title: Include Terminal + - description: Limit the number of invocations to return. + in: query + name: limit + required: false + schema: + anyOf: + - type: integer + - type: 'null' + description: Limit the number of invocations to return. + title: Limit + - description: Number of invocations to skip. + in: query + name: offset + required: false + schema: + anyOf: + - type: integer + - type: 'null' + description: Number of invocations to skip. + title: Offset + - description: Is provided workflow id for Workflow instead of StoredWorkflow? + in: query + name: instance + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: false + description: Is provided workflow id for Workflow instead of StoredWorkflow? + title: Instance + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Include details for individual invocation steps and populate + a steps attribute in the resulting dictionary. + in: query + name: step_details + required: false + schema: + default: false + description: Include details for individual invocation steps and populate + a steps attribute in the resulting dictionary. + title: Include step details + type: boolean + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/WorkflowInvocationResponse' + title: Response Index Invocations Api Invocations Get + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get the list of a user's workflow invocations. + tags: + - workflows + - workflows + /api/invocations/from_store: + post: + description: Create invocation(s) from a supplied model store. + operationId: create_invocations_from_store_api_invocations_from_store_post + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + allOf: + - $ref: '#/components/schemas/CreateInvocationsFromStorePayload' + description: The values and serialization parameters for creating invocations + from a supplied model store. + title: Create invocations from store + required: true + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/WorkflowInvocationResponse' + title: Response Create Invocations From Store Api Invocations From + Store Post + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Create Invocations From Store + tags: + - workflows + - workflows + /api/invocations/steps/{step_id}: + get: + operationId: step_api_invocations_steps__step_id__get + parameters: + - description: The encoded database identifier of the WorkflowInvocationStep. + in: path + name: step_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/InvocationStep' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Show details of workflow invocation step. + tags: + - workflows + - workflows + /api/invocations/{invocation_id}: + delete: + operationId: cancel_invocation_api_invocations__invocation_id__delete + parameters: + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: Include details for individual invocation steps and populate + a steps attribute in the resulting dictionary. + in: query + name: step_details + required: false + schema: + default: false + description: Include details for individual invocation steps and populate + a steps attribute in the resulting dictionary. + title: Include step details + type: boolean + - description: "Populate the invocation step state with the job state instead\ + \ of the invocation step state.\n This will also produce one step\ + \ per job in mapping jobs to mimic the older behavior with respect to collections.\n\ + \ Partially scheduled steps may provide incomplete information and\ + \ the listed steps outputs\n are not the mapped over step outputs\ + \ but the individual job outputs." + in: query + name: legacy_job_state + required: false + schema: + default: false + description: "Populate the invocation step state with the job state instead\ + \ of the invocation step state.\n This will also produce one step\ + \ per job in mapping jobs to mimic the older behavior with respect to\ + \ collections.\n Partially scheduled steps may provide incomplete\ + \ information and the listed steps outputs\n are not the mapped\ + \ over step outputs but the individual job outputs." + title: Replace with job state + type: boolean + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/WorkflowInvocationResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Cancel the specified workflow invocation. + tags: + - workflows + - workflows + get: + operationId: show_invocation_api_invocations__invocation_id__get + parameters: + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: Include details for individual invocation steps and populate + a steps attribute in the resulting dictionary. + in: query + name: step_details + required: false + schema: + default: false + description: Include details for individual invocation steps and populate + a steps attribute in the resulting dictionary. + title: Include step details + type: boolean + - description: "Populate the invocation step state with the job state instead\ + \ of the invocation step state.\n This will also produce one step\ + \ per job in mapping jobs to mimic the older behavior with respect to collections.\n\ + \ Partially scheduled steps may provide incomplete information and\ + \ the listed steps outputs\n are not the mapped over step outputs\ + \ but the individual job outputs." + in: query + name: legacy_job_state + required: false + schema: + default: false + description: "Populate the invocation step state with the job state instead\ + \ of the invocation step state.\n This will also produce one step\ + \ per job in mapping jobs to mimic the older behavior with respect to\ + \ collections.\n Partially scheduled steps may provide incomplete\ + \ information and the listed steps outputs\n are not the mapped\ + \ over step outputs but the individual job outputs." + title: Replace with job state + type: boolean + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/WorkflowInvocationResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get detailed description of a workflow invocation. + tags: + - workflows + - workflows + /api/invocations/{invocation_id}/biocompute: + get: + deprecated: true + description: "The BioCompute Object endpoints are in beta - important details\ + \ such\nas how inputs and outputs are represented, how the workflow is encoded,\n\ + and how author and version information is encoded, and how URLs are\ngenerated\ + \ will very likely change in important ways over time.\n\n**Deprecation Notice**:\ + \ please use the asynchronous short_term_storage export system instead.\n\n\ + 1. call POST `api/invocations/{id}/prepare_store_download` with payload:\n\ + \ ```\n {\n model_store_format: bco.json\n }\n ```\n2.\ + \ Get `storageRequestId` from response and poll GET `api/short_term_storage/${storageRequestId}/ready`\ + \ until `SUCCESS`\n\n3. Get the resulting file with `api/short_term_storage/${storageRequestId}`" + operationId: export_invocation_bco_api_invocations__invocation_id__biocompute_get + parameters: + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - in: query + name: merge_history_metadata + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: false + title: Merge History Metadata + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return a BioCompute Object for the workflow invocation. + tags: + - workflows + - workflows + /api/invocations/{invocation_id}/biocompute/download: + get: + deprecated: true + description: "The BioCompute Object endpoints are in beta - important details\ + \ such\nas how inputs and outputs are represented, how the workflow is encoded,\n\ + and how author and version information is encoded, and how URLs are\ngenerated\ + \ will very likely change in important ways over time.\n\n**Deprecation Notice**:\ + \ please use the asynchronous short_term_storage export system instead.\n\n\ + 1. call POST `api/invocations/{id}/prepare_store_download` with payload:\n\ + \ ```\n {\n model_store_format: bco.json\n }\n ```\n2.\ + \ Get `storageRequestId` from response and poll GET `api/short_term_storage/${storageRequestId}/ready`\ + \ until `SUCCESS`\n\n3. Get the resulting file with `api/short_term_storage/${storageRequestId}`" + operationId: download_invocation_bco_api_invocations__invocation_id__biocompute_download_get + parameters: + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - in: query + name: merge_history_metadata + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: false + title: Merge History Metadata + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return a BioCompute Object for the workflow invocation as a file for + download. + tags: + - workflows + - workflows + /api/invocations/{invocation_id}/jobs_summary: + get: + description: 'Warning: We allow anyone to fetch job state information about + any object they + + can guess an encoded ID for - it isn''t considered protected data. This keeps + + polling IDs as part of state calculation for large histories and collections + as + + efficient as possible.' + operationId: invocation_jobs_summary_api_invocations__invocation_id__jobs_summary_get + parameters: + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/InvocationJobsResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get job state summary info aggregated across all current jobs of the + workflow invocation. + tags: + - workflows + - workflows + /api/invocations/{invocation_id}/prepare_store_download: + post: + operationId: prepare_store_download_api_invocations__invocation_id__prepare_store_download_post + parameters: + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/PrepareStoreDownloadPayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/AsyncFile' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Prepare a workflow invocation export-style download. + tags: + - workflows + - workflows + /api/invocations/{invocation_id}/report: + get: + operationId: show_invocation_report_api_invocations__invocation_id__report_get + parameters: + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/InvocationReport' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get JSON summarizing invocation for reporting. + tags: + - workflows + - workflows + /api/invocations/{invocation_id}/report.pdf: + get: + operationId: show_invocation_report_pdf_api_invocations__invocation_id__report_pdf_get + parameters: + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get PDF summarizing invocation for reporting. + tags: + - workflows + - workflows + /api/invocations/{invocation_id}/step_jobs_summary: + get: + description: 'Warning: We allow anyone to fetch job state information about + any object they + + can guess an encoded ID for - it isn''t considered protected data. This keeps + + polling IDs as part of state calculation for large histories and collections + as + + efficient as possible.' + operationId: invocation_step_jobs_summary_api_invocations__invocation_id__step_jobs_summary_get + parameters: + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + anyOf: + - $ref: '#/components/schemas/InvocationStepJobsResponseStepModel' + - $ref: '#/components/schemas/InvocationStepJobsResponseJobModel' + - $ref: '#/components/schemas/InvocationStepJobsResponseCollectionJobsModel' + title: Response Invocation Step Jobs Summary Api Invocations Invocation + Id Step Jobs Summary Get + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get job state summary info aggregated per step of the workflow invocation. + tags: + - workflows + - workflows + /api/invocations/{invocation_id}/steps/{step_id}: + get: + description: An alias for `GET /api/invocations/steps/{step_id}`. `invocation_id` + is ignored. + operationId: invocation_step_api_invocations__invocation_id__steps__step_id__get + parameters: + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The encoded database identifier of the WorkflowInvocationStep. + in: path + name: step_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/InvocationStep' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Show details of workflow invocation step. + tags: + - workflows + - workflows + put: + operationId: update_invocation_step_api_invocations__invocation_id__steps__step_id__put + parameters: + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The encoded database identifier of the WorkflowInvocationStep. + in: path + name: step_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/InvocationUpdatePayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/InvocationStep' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Update state of running workflow step invocation - still very nebulous + but this would be for stuff like confirming paused steps can proceed etc. + tags: + - workflows + - workflows + /api/invocations/{invocation_id}/write_store: + post: + operationId: write_store_api_invocations__invocation_id__write_store_post + parameters: + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/WriteInvocationStoreToPayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/AsyncTaskResultSummary' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Prepare a workflow invocation export-style download and write to supplied + URI. + tags: + - workflows + - workflows + /api/job_lock: + get: + description: Get job lock status. + operationId: job_lock_status_api_job_lock_get + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/JobLock' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Job Lock Status + tags: + - job_lock + put: + description: Set job lock status. + operationId: update_job_lock_api_job_lock_put + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/JobLock' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/JobLock' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Update Job Lock + tags: + - job_lock + /api/jobs: + get: + operationId: index_api_jobs_get + parameters: + - description: If true, and requester is an admin, will return external job + id and user email. This is only available to admins. + in: query + name: user_details + required: false + schema: + default: false + description: If true, and requester is an admin, will return external job + id and user email. This is only available to admins. + title: Include user details + type: boolean + - description: an encoded user id to restrict query to, must be own id if not + admin user + in: query + name: user_id + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: an encoded user id to restrict query to, must be own id if + not admin user + title: User ID + - description: Determines columns to return. Defaults to 'collection'. + in: query + name: view + required: false + schema: + allOf: + - $ref: '#/components/schemas/JobIndexViewEnum' + default: collection + description: Determines columns to return. Defaults to 'collection'. + title: View + - description: Limit listing of jobs to those that are updated after specified + date (e.g. '2014-01-01') + in: query + name: date_range_min + required: false + schema: + anyOf: + - format: date-time + type: string + - format: date + type: string + - type: 'null' + description: Limit listing of jobs to those that are updated after specified + date (e.g. '2014-01-01') + title: Date Range Minimum + - description: Limit listing of jobs to those that are updated before specified + date (e.g. '2014-01-01') + in: query + name: date_range_max + required: false + schema: + anyOf: + - format: date-time + type: string + - format: date + type: string + - type: 'null' + description: Limit listing of jobs to those that are updated before specified + date (e.g. '2014-01-01') + title: Date Range Maximum + - description: Limit listing of jobs to those that match the history_id. If + none, jobs from any history may be returned. + in: query + name: history_id + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: Limit listing of jobs to those that match the history_id. If + none, jobs from any history may be returned. + title: History ID + - description: Limit listing of jobs to those that match the specified workflow + ID. If none, jobs from any workflow (or from no workflows) may be returned. + in: query + name: workflow_id + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: Limit listing of jobs to those that match the specified workflow + ID. If none, jobs from any workflow (or from no workflows) may be returned. + title: Workflow ID + - description: Limit listing of jobs to those that match the specified workflow + invocation ID. If none, jobs from any workflow invocation (or from no workflows) + may be returned. + in: query + name: invocation_id + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: Limit listing of jobs to those that match the specified workflow + invocation ID. If none, jobs from any workflow invocation (or from no + workflows) may be returned. + title: Invocation ID + - description: Limit listing of jobs to those that match the specified implicit + collection job ID. If none, jobs from any implicit collection execution + (or from no implicit collection execution) may be returned. + in: query + name: implicit_collection_jobs_id + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: Limit listing of jobs to those that match the specified implicit + collection job ID. If none, jobs from any implicit collection execution + (or from no implicit collection execution) may be returned. + title: Implicit Collection Jobs ID + - description: Sort results by specified field. + in: query + name: order_by + required: false + schema: + allOf: + - $ref: '#/components/schemas/JobIndexSortByEnum' + default: update_time + description: Sort results by specified field. + title: Sort By + - description: 'A mix of free text and GitHub-style tags used to filter the + index operation. + + + ## Query Structure + + + GitHub-style filter tags (not be confused with Galaxy tags) are tags of + the form + + `:` or `:''''`. + The tag name + + *generally* (but not exclusively) corresponds to the name of an attribute + on the model + + being indexed (i.e. a column in the database). + + + If the tag is quoted, the attribute will be filtered exactly. If the tag + is unquoted, + + generally a partial match will be used to filter the query (i.e. in terms + of the implementation + + this means the database operation `ILIKE` will typically be used). + + + Once the tagged filters are extracted from the search query, the remaining + text is just + + used to search various documented attributes of the object. + + + ## GitHub-style Tags Available + + + `user` + + : The user email of the user that executed the Job. (The tag `u` can be + used a short hand alias for this tag to filter on this attribute.) + + + `tool_id` + + : The tool ID corresponding to the job. (The tag `t` can be used a short + hand alias for this tag to filter on this attribute.) + + + `runner` + + : The job runner name used to execute the job. (The tag `r` can be used + a short hand alias for this tag to filter on this attribute.) This tag is + only available for requests using admin keys and/or sessions. + + + `handler` + + : The job handler name used to execute the job. (The tag `h` can be used + a short hand alias for this tag to filter on this attribute.) This tag is + only available for requests using admin keys and/or sessions. + + + ## Free Text + + + Free text search terms will be searched against the following attributes + of the + + Jobs: `user`, `tool`, `handler`, `runner`. + + + ' + in: query + name: search + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: 'A mix of free text and GitHub-style tags used to filter the + index operation. + + + ## Query Structure + + + GitHub-style filter tags (not be confused with Galaxy tags) are tags of + the form + + `:` or `:''''`. + The tag name + + *generally* (but not exclusively) corresponds to the name of an attribute + on the model + + being indexed (i.e. a column in the database). + + + If the tag is quoted, the attribute will be filtered exactly. If the tag + is unquoted, + + generally a partial match will be used to filter the query (i.e. in terms + of the implementation + + this means the database operation `ILIKE` will typically be used). + + + Once the tagged filters are extracted from the search query, the remaining + text is just + + used to search various documented attributes of the object. + + + ## GitHub-style Tags Available + + + `user` + + : The user email of the user that executed the Job. (The tag `u` can be + used a short hand alias for this tag to filter on this attribute.) + + + `tool_id` + + : The tool ID corresponding to the job. (The tag `t` can be used a short + hand alias for this tag to filter on this attribute.) + + + `runner` + + : The job runner name used to execute the job. (The tag `r` can be used + a short hand alias for this tag to filter on this attribute.) This tag + is only available for requests using admin keys and/or sessions. + + + `handler` + + : The job handler name used to execute the job. (The tag `h` can be used + a short hand alias for this tag to filter on this attribute.) This tag + is only available for requests using admin keys and/or sessions. + + + ## Free Text + + + Free text search terms will be searched against the following attributes + of the + + Jobs: `user`, `tool`, `handler`, `runner`. + + + ' + title: Search query. + - description: Maximum number of jobs to return. + in: query + name: limit + required: false + schema: + default: 500 + description: Maximum number of jobs to return. + title: Limit + type: integer + - description: Return jobs starting from this specified position. For example, + if ``limit`` is set to 100 and ``offset`` to 200, jobs 200-299 will be returned. + in: query + name: offset + required: false + schema: + default: 0 + description: Return jobs starting from this specified position. For example, + if ``limit`` is set to 100 and ``offset`` to 200, jobs 200-299 will be + returned. + title: Offset + type: integer + - description: A list or comma-separated list of states to filter job query + on. If unspecified, jobs of any state may be returned. + in: query + name: state + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: A list or comma-separated list of states to filter job query + on. If unspecified, jobs of any state may be returned. + title: States + - description: Limit listing of jobs to those that match one of the included + tool_ids. If none, all are returned + in: query + name: tool_id + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: Limit listing of jobs to those that match one of the included + tool_ids. If none, all are returned + title: Tool ID(s) + - description: Limit listing of jobs to those that match one of the included + tool ID sql-like patterns. If none, all are returned + in: query + name: tool_id_like + required: false + schema: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: Limit listing of jobs to those that match one of the included + tool ID sql-like patterns. If none, all are returned + title: Tool ID Pattern(s) + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + anyOf: + - $ref: '#/components/schemas/ShowFullJobResponse' + - $ref: '#/components/schemas/EncodedJobDetails' + - $ref: '#/components/schemas/JobSummary' + title: Response Index Api Jobs Get + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Index + tags: + - jobs + - jobs + /api/jobs/search: + post: + description: 'This method is designed to scan the list of previously run jobs + and find records of jobs that had + + the exact some input parameters and datasets. This can be used to minimize + the amount of repeated work, and simply + + recycle the old results.' + operationId: search_jobs_api_jobs_search_post + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + allOf: + - $ref: '#/components/schemas/SearchJobsPayload' + description: The values to search an Job + title: Search job + required: true + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/EncodedJobDetails' + title: Response Search Jobs Api Jobs Search Post + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return jobs for current user + tags: + - jobs + - jobs + /api/jobs/{job_id}: + delete: + operationId: cancel_job_api_jobs__job_id__delete + parameters: + - description: The ID of the job + in: path + name: job_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/DeleteJobPayload' + - type: 'null' + description: The values to delete/cancel a job + title: Delete/cancel job + responses: + '200': + content: + application/json: + schema: + title: Response Cancel Job Api Jobs Job Id Delete + type: boolean + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Cancels specified job + tags: + - jobs + - jobs + get: + operationId: show_job_api_jobs__job_id__get + parameters: + - description: The ID of the job + in: path + name: job_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: Show extra information. + in: query + name: full + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: false + description: Show extra information. + title: Full show + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/ShowFullJobResponse' + - $ref: '#/components/schemas/EncodedJobDetails' + title: Response Show Job Api Jobs Job Id Get + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return dictionary containing description of job data. + tags: + - jobs + - jobs + /api/jobs/{job_id}/common_problems: + get: + operationId: check_common_problems_api_jobs__job_id__common_problems_get + parameters: + - description: The ID of the job + in: path + name: job_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/JobInputSummary' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Check inputs and job for common potential problems to aid in error + reporting + tags: + - jobs + - jobs + /api/jobs/{job_id}/destination_params: + get: + operationId: destination_params_job_api_jobs__job_id__destination_params_get + parameters: + - description: The ID of the job + in: path + name: job_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/JobDestinationParams' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return destination parameters for specified job. + tags: + - jobs + - jobs + /api/jobs/{job_id}/error: + post: + operationId: report_error_api_jobs__job_id__error_post + parameters: + - description: The ID of the job + in: path + name: job_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + allOf: + - $ref: '#/components/schemas/ReportJobErrorPayload' + description: The values to report an Error + title: Report error + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/JobErrorSummary' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Submits a bug report via the API. + tags: + - jobs + - jobs + /api/jobs/{job_id}/inputs: + get: + operationId: get_inputs_api_jobs__job_id__inputs_get + parameters: + - description: The ID of the job + in: path + name: job_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/JobInputAssociation' + title: Response Get Inputs Api Jobs Job Id Inputs Get + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns input datasets created by a job. + tags: + - jobs + - jobs + /api/jobs/{job_id}/metrics: + get: + operationId: get_metrics_api_jobs__job_id__metrics_get + parameters: + - description: The ID of the job + in: path + name: job_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - deprecated: true + description: Whether this dataset belongs to a history (HDA) or a library + (LDDA). + in: query + name: hda_ldda + required: false + schema: + anyOf: + - $ref: '#/components/schemas/DatasetSourceType' + - type: 'null' + default: hda + description: Whether this dataset belongs to a history (HDA) or a library + (LDDA). + title: HDA or LDDA + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + anyOf: + - $ref: '#/components/schemas/JobMetric' + - type: 'null' + title: Response Get Metrics Api Jobs Job Id Metrics Get + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return job metrics for specified job. + tags: + - jobs + - jobs + /api/jobs/{job_id}/oidc-tokens: + get: + description: Allows remote job running mechanisms to get a fresh OIDC token + that can be used on remote side to authorize user. It is not meant to represent + part of Galaxy's stable, user facing API + operationId: get_token_api_jobs__job_id__oidc_tokens_get + parameters: + - in: path + name: job_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Job Id + type: string + - description: A key used to authenticate this request as acting onbehalf or + a job runner for the specified job + in: query + name: job_key + required: true + schema: + description: A key used to authenticate this request as acting onbehalf + or a job runner for the specified job + title: Job Key + type: string + - description: OIDC provider name + in: query + name: provider + required: true + schema: + description: OIDC provider name + title: Provider + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + text/plain: + schema: + type: string + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get a fresh OIDC token + tags: + - remote files + - remote files + - oidc_tokens + /api/jobs/{job_id}/outputs: + get: + operationId: get_outputs_api_jobs__job_id__outputs_get + parameters: + - description: The ID of the job + in: path + name: job_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/JobOutputAssociation' + title: Response Get Outputs Api Jobs Job Id Outputs Get + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns output datasets created by a job. + tags: + - jobs + - jobs + /api/jobs/{job_id}/parameters_display: + get: + description: 'Resolve parameters as a list for nested display. + + This API endpoint is unstable and tied heavily to Galaxy''s JS client code, + + this endpoint will change frequently.' + operationId: resolve_parameters_display_api_jobs__job_id__parameters_display_get + parameters: + - description: The ID of the job + in: path + name: job_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - deprecated: true + description: Whether this dataset belongs to a history (HDA) or a library + (LDDA). + in: query + name: hda_ldda + required: false + schema: + anyOf: + - $ref: '#/components/schemas/DatasetSourceType' + - type: 'null' + default: hda + description: Whether this dataset belongs to a history (HDA) or a library + (LDDA). + title: HDA or LDDA + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/JobDisplayParametersSummary' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Resolve parameters as a list for nested display. + tags: + - jobs + - jobs + /api/jobs/{job_id}/resume: + put: + operationId: resume_paused_job_api_jobs__job_id__resume_put + parameters: + - description: The ID of the job + in: path + name: job_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/JobOutputAssociation' + title: Response Resume Paused Job Api Jobs Job Id Resume Put + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Resumes a paused job. + tags: + - jobs + - jobs + /api/libraries: + get: + description: Returns a list of summary data for all libraries. + operationId: index_api_libraries_get + parameters: + - description: Whether to include deleted libraries in the result. + in: query + name: deleted + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + description: Whether to include deleted libraries in the result. + title: Display deleted + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/LibrarySummaryList' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns a list of summary data for all libraries. + tags: + - libraries + - libraries + post: + description: Creates a new library and returns its summary information. Currently, + only admin users can create libraries. + operationId: create_api_libraries_post + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/CreateLibraryPayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/LibrarySummary' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Creates a new library and returns its summary information. + tags: + - libraries + - libraries + /api/libraries/deleted: + get: + description: Returns a list of summary data for all libraries marked as deleted. + operationId: index_deleted_api_libraries_deleted_get + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/LibrarySummaryList' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns a list of summary data for all libraries marked as deleted. + tags: + - libraries + - libraries + /api/libraries/from_store: + post: + operationId: create_from_store_api_libraries_from_store_post + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/CreateLibrariesFromStore' + required: true + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/LibrarySummary' + title: Response Create From Store Api Libraries From Store Post + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Create libraries from a model store. + tags: + - libraries + - libraries + /api/libraries/{id}: + delete: + description: 'Marks the specified library as deleted (or undeleted). + + Currently, only admin users can delete or restore libraries.' + operationId: delete_api_libraries__id__delete + parameters: + - description: The ID of the Library. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: Whether to restore a deleted library. + in: query + name: undelete + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + description: Whether to restore a deleted library. + title: Undelete + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/DeleteLibraryPayload' + - type: 'null' + title: Payload + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/LibrarySummary' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Marks the specified library as deleted (or undeleted). + tags: + - libraries + - libraries + get: + description: Returns summary information about a particular library. + operationId: show_api_libraries__id__get + parameters: + - description: The ID of the Library. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/LibrarySummary' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns summary information about a particular library. + tags: + - libraries + - libraries + patch: + description: Updates the information of an existing library. + operationId: update_api_libraries__id__patch + parameters: + - description: The ID of the Library. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/UpdateLibraryPayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/LibrarySummary' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Updates the information of an existing library. + tags: + - libraries + - libraries + /api/libraries/{id}/permissions: + get: + description: 'Gets the current or available permissions of a particular library. + + The results can be paginated and additionally filtered by a query.' + operationId: get_permissions_api_libraries__id__permissions_get + parameters: + - description: The ID of the Library. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The scope of the permissions to retrieve. Either the `current` + permissions or the `available`. + in: query + name: scope + required: false + schema: + anyOf: + - $ref: '#/components/schemas/LibraryPermissionScope' + - type: 'null' + description: The scope of the permissions to retrieve. Either the `current` + permissions or the `available`. + title: Scope + - description: Indicates whether the roles available for the library access + are requested. + in: query + name: is_library_access + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + description: Indicates whether the roles available for the library access + are requested. + title: Is Library Access + - description: The page number to retrieve when paginating the available roles. + in: query + name: page + required: false + schema: + default: 1 + description: The page number to retrieve when paginating the available roles. + title: Page + type: integer + - description: The maximum number of permissions per page when paginating. + in: query + name: page_limit + required: false + schema: + default: 10 + description: The maximum number of permissions per page when paginating. + title: Page Limit + type: integer + - description: Optional search text to retrieve only the roles matching this + query. + in: query + name: q + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Optional search text to retrieve only the roles matching this + query. + title: Query + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/LibraryCurrentPermissions' + - $ref: '#/components/schemas/LibraryAvailablePermissions' + title: Response Get Permissions Api Libraries Id Permissions Get + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Gets the current or available permissions of a particular library. + tags: + - libraries + - libraries + post: + description: Sets the permissions to access and manipulate a library. + operationId: set_permissions_api_libraries__id__permissions_post + parameters: + - description: The ID of the Library. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: Indicates what action should be performed on the Library. + in: query + name: action + required: false + schema: + anyOf: + - $ref: '#/components/schemas/LibraryPermissionAction' + - type: 'null' + description: Indicates what action should be performed on the Library. + title: Action + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/LibraryPermissionsPayload' + - $ref: '#/components/schemas/LegacyLibraryPermissionsPayload' + title: Payload + required: true + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/LibraryLegacySummary' + - $ref: '#/components/schemas/LibraryCurrentPermissions' + title: Response Set Permissions Api Libraries Id Permissions Post + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Sets the permissions to access and manipulate a library. + tags: + - libraries + - libraries + /api/licenses: + get: + description: Returns an index with all the available [SPDX licenses](https://spdx.org/licenses/). + operationId: index_api_licenses_get + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/LicenseMetadataModel' + title: Response Index Api Licenses Get + type: array + description: List of SPDX licenses + security: [] + summary: Lists all available SPDX licenses + tags: + - licenses + - licenses + /api/licenses/{id}: + get: + description: 'Returns the license metadata associated with the given + + [SPDX license short ID](https://spdx.github.io/spdx-spec/appendix-I-SPDX-license-list/).' + operationId: get_api_licenses__id__get + parameters: + - description: The [SPDX license short identifier](https://spdx.github.io/spdx-spec/appendix-I-SPDX-license-list/) + in: path + name: id + required: true + schema: + description: The [SPDX license short identifier](https://spdx.github.io/spdx-spec/appendix-I-SPDX-license-list/) + examples: + - Apache-2.0 + title: SPDX license short ID + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/LicenseMetadataModel' + description: SPDX license metadata + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: [] + summary: Gets the SPDX license metadata associated with the short identifier + tags: + - licenses + - licenses + /api/metrics: + post: + description: Record any metrics sent and return some status object. + operationId: create_api_metrics_post + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/CreateMetricsPayload' + required: true + responses: + '200': + content: + application/json: + schema: + title: Response Create Api Metrics Post + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Records a collection of metrics. + tags: + - metrics + - metrics + /api/notifications: + delete: + operationId: delete_user_notifications_api_notifications_delete + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/NotificationsBatchRequest' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/NotificationsBatchUpdateResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Deletes a list of notifications received by the user in a single request. + tags: + - notifications + - notifications + get: + description: 'Anonymous users cannot receive personal notifications, only broadcasted + notifications. + + + You can use the `limit` and `offset` parameters to paginate through the notifications.' + operationId: get_user_notifications_api_notifications_get + parameters: + - in: query + name: limit + required: false + schema: + anyOf: + - type: integer + - type: 'null' + default: 20 + title: Limit + - in: query + name: offset + required: false + schema: + anyOf: + - type: integer + - type: 'null' + title: Offset + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/UserNotificationListResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns the list of notifications associated with the user. + tags: + - notifications + - notifications + post: + description: Sends a notification to a list of recipients (users, groups or + roles). + operationId: send_notification_api_notifications_post + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/NotificationCreateRequest' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/NotificationCreatedResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Sends a notification to a list of recipients (users, groups or roles). + tags: + - notifications + - notifications + put: + operationId: update_user_notifications_api_notifications_put + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/UserNotificationsBatchUpdateRequest' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/NotificationsBatchUpdateResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Updates a list of notifications with the requested values in a single + request. + tags: + - notifications + - notifications + /api/notifications/broadcast: + get: + description: Only Admin users can access inactive notifications (scheduled or + recently expired). + operationId: get_all_broadcasted_api_notifications_broadcast_get + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/BroadcastNotificationListResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns all currently active broadcasted notifications. + tags: + - notifications + - notifications + post: + description: 'Broadcasted notifications are a special kind of notification that + are always accessible to all users, including anonymous users. + + They are typically used to display important information such as maintenance + windows or new features. + + These notifications are displayed differently from regular notifications, + usually in a banner at the top or bottom of the page. + + + Broadcasted notifications can include action links that are displayed as buttons. + + This allows users to easily perform tasks such as filling out surveys, accepting + legal agreements, or accessing new tutorials. + + + Some key features of broadcasted notifications include: + + - They are not associated with a specific user, so they cannot be deleted + or marked as read. + + - They can be scheduled to be displayed in the future or to expire after a + certain time. + + - By default, broadcasted notifications are published immediately and expire + six months after publication. + + - Only admins can create, edit, reschedule, or expire broadcasted notifications + as needed.' + operationId: broadcast_notification_api_notifications_broadcast_post + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/BroadcastNotificationCreateRequest' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/NotificationCreatedResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Broadcasts a notification to every user in the system. + tags: + - notifications + - notifications + /api/notifications/broadcast/{notification_id}: + get: + description: Only Admin users can access inactive notifications (scheduled or + recently expired). + operationId: get_broadcasted_api_notifications_broadcast__notification_id__get + parameters: + - description: The ID of the Notification. + in: path + name: notification_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/BroadcastNotificationResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns the information of a specific broadcasted notification. + tags: + - notifications + - notifications + put: + description: Only Admins can update broadcasted notifications. This is useful + to reschedule, edit or expire broadcasted notifications. + operationId: update_broadcasted_notification_api_notifications_broadcast__notification_id__put + parameters: + - description: The ID of the Notification. + in: path + name: notification_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/NotificationBroadcastUpdateRequest' + required: true + responses: + '204': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Updates the state of a broadcasted notification. + tags: + - notifications + - notifications + /api/notifications/preferences: + get: + description: Anonymous users cannot have notification preferences. They will + receive only broadcasted notifications. + operationId: get_notification_preferences_api_notifications_preferences_get + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/UserNotificationPreferences' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns the current user's preferences for notifications. + tags: + - notifications + - notifications + put: + description: 'Anonymous users cannot have notification preferences. They will + receive only broadcasted notifications. + + + - Can be used to completely enable/disable notifications for a particular + type (category) + + or to enable/disable a particular channel on each category.' + operationId: update_notification_preferences_api_notifications_preferences_put + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/UpdateUserNotificationPreferencesRequest' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/UserNotificationPreferences' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Updates the user's preferences for notifications. + tags: + - notifications + - notifications + /api/notifications/status: + get: + description: Anonymous users cannot receive personal notifications, only broadcasted + notifications. + operationId: get_notifications_status_api_notifications_status_get + parameters: + - in: query + name: since + required: true + schema: + format: date-time + title: Since + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/NotificationStatusSummary' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns the current status summary of the user's notifications since + a particular date. + tags: + - notifications + - notifications + /api/notifications/{notification_id}: + delete: + description: 'When a notification is deleted, it is not immediately removed + from the database, but marked as deleted. + + + - It will not be returned in the list of notifications, but admins can still + access it as long as it is not expired. + + - It will be eventually removed from the database by a background task after + the expiration time. + + - Deleted notifications will be permanently deleted when the expiration time + is reached.' + operationId: delete_user_notification_api_notifications__notification_id__delete + parameters: + - description: The ID of the Notification. + in: path + name: notification_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '204': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Deletes a notification received by the user. + tags: + - notifications + - notifications + get: + operationId: show_notification_api_notifications__notification_id__get + parameters: + - description: The ID of the Notification. + in: path + name: notification_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/UserNotificationResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Displays information about a notification received by the user. + tags: + - notifications + - notifications + put: + operationId: update_user_notification_api_notifications__notification_id__put + parameters: + - description: The ID of the Notification. + in: path + name: notification_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/UserNotificationUpdateRequest' + required: true + responses: + '204': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Updates the state of a notification received by the user. + tags: + - notifications + - notifications + /api/object_stores: + get: + operationId: index_api_object_stores_get + parameters: + - description: Restrict index query to user selectable object stores, the current + implementation requires this to be true. + in: query + name: selectable + required: false + schema: + default: false + description: Restrict index query to user selectable object stores, the + current implementation requires this to be true. + title: Selectable + type: boolean + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/ConcreteObjectStoreModel' + title: Response Index Api Object Stores Get + type: array + description: A list of the configured object stores. + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get a list of (currently only concrete) object stores configured with + this Galaxy instance. + tags: + - object sstore + - object sstore + /api/object_stores/{object_store_id}: + get: + operationId: show_info_api_object_stores__object_store_id__get + parameters: + - description: The concrete object store ID. + in: path + name: object_store_id + required: true + schema: + description: The concrete object store ID. + title: Concrete Object Store ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ConcreteObjectStoreModel' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get information about a concrete object store configured with Galaxy. + tags: + - object sstore + - object sstore + /api/pages: + get: + description: Get a list with summary information of all Pages available to the + user. + operationId: index_api_pages_get + parameters: + - description: Whether to include deleted pages in the result. + in: query + name: deleted + required: false + schema: + default: false + description: Whether to include deleted pages in the result. + title: Display deleted + type: boolean + - in: query + name: user_id + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + title: Encoded user ID to restrict query to, must be own id if not an admin + user + - in: query + name: show_published + required: false + schema: + default: true + title: Include published pages. + type: boolean + - in: query + name: show_shared + required: false + schema: + default: false + title: Include pages shared with authenticated user. + type: boolean + - description: Sort page index by this specified attribute on the page model + in: query + name: sort_by + required: false + schema: + default: update_time + description: Sort page index by this specified attribute on the page model + enum: + - update_time + - title + - username + title: Sort attribute + type: string + - description: Sort in descending order? + in: query + name: sort_desc + required: false + schema: + default: false + description: Sort in descending order? + title: Sort Descending + type: boolean + - in: query + name: limit + required: false + schema: + default: 100 + exclusiveMaximum: 1000 + title: Limit number of queries. + type: integer + - in: query + name: offset + required: false + schema: + default: 0 + title: Number of pages to skip in sorted query (to enable pagination). + type: integer + - description: 'A mix of free text and GitHub-style tags used to filter the + index operation. + + + ## Query Structure + + + GitHub-style filter tags (not be confused with Galaxy tags) are tags of + the form + + `:` or `:''''`. + The tag name + + *generally* (but not exclusively) corresponds to the name of an attribute + on the model + + being indexed (i.e. a column in the database). + + + If the tag is quoted, the attribute will be filtered exactly. If the tag + is unquoted, + + generally a partial match will be used to filter the query (i.e. in terms + of the implementation + + this means the database operation `ILIKE` will typically be used). + + + Once the tagged filters are extracted from the search query, the remaining + text is just + + used to search various documented attributes of the object. + + + ## GitHub-style Tags Available + + + `title` + + : The page''s title. + + + `slug` + + : The page''s slug. (The tag `s` can be used a short hand alias for this + tag to filter on this attribute.) + + + `tag` + + : The page''s tags. (The tag `t` can be used a short hand alias for this + tag to filter on this attribute.) + + + `user` + + : The page''s owner''s username. (The tag `u` can be used a short hand alias + for this tag to filter on this attribute.) + + + ## Free Text + + + Free text search terms will be searched against the following attributes + of the + + Pages: `title`, `slug`, `tag`, `user`. + + + ' + in: query + name: search + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: 'A mix of free text and GitHub-style tags used to filter the + index operation. + + + ## Query Structure + + + GitHub-style filter tags (not be confused with Galaxy tags) are tags of + the form + + `:` or `:''''`. + The tag name + + *generally* (but not exclusively) corresponds to the name of an attribute + on the model + + being indexed (i.e. a column in the database). + + + If the tag is quoted, the attribute will be filtered exactly. If the tag + is unquoted, + + generally a partial match will be used to filter the query (i.e. in terms + of the implementation + + this means the database operation `ILIKE` will typically be used). + + + Once the tagged filters are extracted from the search query, the remaining + text is just + + used to search various documented attributes of the object. + + + ## GitHub-style Tags Available + + + `title` + + : The page''s title. + + + `slug` + + : The page''s slug. (The tag `s` can be used a short hand alias for this + tag to filter on this attribute.) + + + `tag` + + : The page''s tags. (The tag `t` can be used a short hand alias for this + tag to filter on this attribute.) + + + `user` + + : The page''s owner''s username. (The tag `u` can be used a short hand + alias for this tag to filter on this attribute.) + + + ## Free Text + + + Free text search terms will be searched against the following attributes + of the + + Pages: `title`, `slug`, `tag`, `user`. + + + ' + title: Search query. + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/PageSummaryList' + description: A list with summary page information. + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Lists all Pages viewable by the user. + tags: + - pages + - pages + post: + description: Get a list with details of all Pages available to the user. + operationId: create_api_pages_post + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/CreatePagePayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/PageSummary' + description: The page summary information. + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Create a page and return summary information. + tags: + - pages + - pages + /api/pages/{id}: + delete: + description: Marks the Page with the given ID as deleted. + operationId: delete_api_pages__id__delete + parameters: + - description: The ID of the Page. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '204': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Marks the specific Page as deleted. + tags: + - pages + - pages + get: + description: Return summary information about a specific Page and the content + of the last revision. + operationId: show_api_pages__id__get + parameters: + - description: The ID of the Page. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/PageDetails' + description: The page summary information. + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return a page summary and the content of the last revision. + tags: + - pages + - pages + /api/pages/{id}.pdf: + get: + description: 'Return a PDF document of the last revision of the Page. + + + This feature may not be available in this Galaxy.' + operationId: show_pdf_api_pages__id__pdf_get + parameters: + - description: The ID of the Page. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/pdf: {} + description: PDF document with the last revision of the page. + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + '501': + description: PDF conversion service not available. + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return a PDF document of the last revision of the Page. + tags: + - pages + - pages + /api/pages/{id}/disable_link_access: + put: + description: Makes this item inaccessible by a URL link and return the current + sharing status. + operationId: disable_link_access_api_pages__id__disable_link_access_put + parameters: + - description: The ID of the Page. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/SharingStatus' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Makes this item inaccessible by a URL link. + tags: + - pages + - pages + /api/pages/{id}/enable_link_access: + put: + description: Makes this item accessible by a URL link and return the current + sharing status. + operationId: enable_link_access_api_pages__id__enable_link_access_put + parameters: + - description: The ID of the Page. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/SharingStatus' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Makes this item accessible by a URL link. + tags: + - pages + - pages + /api/pages/{id}/prepare_download: + post: + description: 'Return a STS download link for this page to be downloaded as a + PDF. + + + This feature may not be available in this Galaxy.' + operationId: prepare_pdf_api_pages__id__prepare_download_post + parameters: + - description: The ID of the Page. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/AsyncFile' + description: Short term storage reference for async monitoring of this download. + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + '501': + description: PDF conversion service not available. + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return a PDF document of the last revision of the Page. + tags: + - pages + - pages + /api/pages/{id}/publish: + put: + description: Makes this item publicly available by a URL link and return the + current sharing status. + operationId: publish_api_pages__id__publish_put + parameters: + - description: The ID of the Page. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/SharingStatus' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Makes this item public and accessible by a URL link. + tags: + - pages + - pages + /api/pages/{id}/share_with_users: + put: + description: Shares this item with specific users and return the current sharing + status. + operationId: share_with_users_api_pages__id__share_with_users_put + parameters: + - description: The ID of the Page. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/ShareWithPayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ShareWithStatus' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Share this item with specific users. + tags: + - pages + - pages + /api/pages/{id}/sharing: + get: + description: Return the sharing status of the item. + operationId: sharing_api_pages__id__sharing_get + parameters: + - description: The ID of the Page. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/SharingStatus' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get the current sharing status of the given Page. + tags: + - pages + - pages + /api/pages/{id}/slug: + put: + description: Sets a new slug to access this item by URL. The new slug must be + unique. + operationId: set_slug_api_pages__id__slug_put + parameters: + - description: The ID of the Page. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/SetSlugPayload' + required: true + responses: + '204': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Set a new slug for this shared item. + tags: + - pages + - pages + /api/pages/{id}/unpublish: + put: + description: Removes this item from the published list and return the current + sharing status. + operationId: unpublish_api_pages__id__unpublish_put + parameters: + - description: The ID of the Page. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/SharingStatus' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Removes this item from the published list. + tags: + - pages + - pages + /api/quotas: + get: + description: Displays a list with information of quotas that are currently active. + operationId: index_api_quotas_get + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/QuotaSummaryList' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Displays a list with information of quotas that are currently active. + tags: + - quotas + - quotas + post: + description: Creates a new quota. + operationId: create_api_quotas_post + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/CreateQuotaParams' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/CreateQuotaResult' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Creates a new quota. + tags: + - quotas + - quotas + /api/quotas/deleted: + get: + description: Displays a list with information of quotas that have been deleted. + operationId: index_deleted_api_quotas_deleted_get + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/QuotaSummaryList' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Displays a list with information of quotas that have been deleted. + tags: + - quotas + - quotas + /api/quotas/deleted/{id}: + get: + description: Displays details on a particular quota that has been deleted. + operationId: deleted_quota_api_quotas_deleted__id__get + parameters: + - description: The ID of the Quota. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/QuotaDetails' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Displays details on a particular quota that has been deleted. + tags: + - quotas + - quotas + /api/quotas/deleted/{id}/undelete: + post: + description: Restores a previously deleted quota. + operationId: undelete_api_quotas_deleted__id__undelete_post + parameters: + - description: The ID of the Quota. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + title: Response Undelete Api Quotas Deleted Id Undelete Post + type: string + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Restores a previously deleted quota. + tags: + - quotas + - quotas + /api/quotas/{id}: + delete: + description: Deletes an existing quota. + operationId: delete_api_quotas__id__delete + parameters: + - description: The ID of the Quota. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + allOf: + - $ref: '#/components/schemas/DeleteQuotaPayload' + title: Payload + responses: + '200': + content: + application/json: + schema: + title: Response Delete Api Quotas Id Delete + type: string + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Deletes an existing quota. + tags: + - quotas + - quotas + get: + description: Displays details on a particular active quota. + operationId: quota_api_quotas__id__get + parameters: + - description: The ID of the Quota. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/QuotaDetails' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Displays details on a particular active quota. + tags: + - quotas + - quotas + put: + description: Updates an existing quota. + operationId: update_api_quotas__id__put + parameters: + - description: The ID of the Quota. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/UpdateQuotaParams' + required: true + responses: + '200': + content: + application/json: + schema: + title: Response Update Api Quotas Id Put + type: string + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Updates an existing quota. + tags: + - quotas + - quotas + /api/quotas/{id}/purge: + post: + operationId: purge_api_quotas__id__purge_post + parameters: + - description: The ID of the Quota. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + title: Response Purge Api Quotas Id Purge Post + type: string + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Purges a previously deleted quota. + tags: + - quotas + - quotas + /api/remote_files: + get: + description: Lists all remote files available to the user from different sources. + operationId: index_api_remote_files_get + parameters: + - description: 'The source to load datasets from. Possible values: ftpdir, userdir, + importdir' + in: query + name: target + required: false + schema: + default: ftpdir + description: 'The source to load datasets from. Possible values: ftpdir, + userdir, importdir' + title: Target source + type: string + - description: The requested format of returned data. Either `flat` to simply + list all the files, `jstree` to get a tree representation of the files, + or the default `uri` to list files and directories by their URI. + in: query + name: format + required: false + schema: + anyOf: + - $ref: '#/components/schemas/RemoteFilesFormat' + - type: 'null' + default: uri + description: The requested format of returned data. Either `flat` to simply + list all the files, `jstree` to get a tree representation of the files, + or the default `uri` to list files and directories by their URI. + title: Response format + - description: Whether to recursively lists all sub-directories. This will be + `True` by default depending on the `target`. + in: query + name: recursive + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + description: Whether to recursively lists all sub-directories. This will + be `True` by default depending on the `target`. + title: Recursive + - description: (This only applies when `format` is `jstree`) The value can be + either `folders` or `files` and it will disable the corresponding nodes + of the tree. + in: query + name: disable + required: false + schema: + anyOf: + - $ref: '#/components/schemas/RemoteFilesDisableMode' + - type: 'null' + description: (This only applies when `format` is `jstree`) The value can + be either `folders` or `files` and it will disable the corresponding nodes + of the tree. + title: Disable mode + - description: Whether the query is made with the intention of writing to the + source. If set to True, only entries that can be written to will be returned. + in: query + name: writeable + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + description: Whether the query is made with the intention of writing to + the source. If set to True, only entries that can be written to will be + returned. + title: Writeable + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/ListUriResponse' + - $ref: '#/components/schemas/ListJstreeResponse' + title: Response Index Api Remote Files Get + description: A list with details about the remote files available to the + user. + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Displays remote files available to the user. + tags: + - remote files + - remote files + post: + description: Creates a new entry on the remote files source. + operationId: create_entry_api_remote_files_post + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + allOf: + - $ref: '#/components/schemas/CreateEntryPayload' + description: Information about the entry to create. Depends on the target + file source. + title: Entry Data + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/CreatedEntryResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Creates a new entry (directory/record) on the remote files source. + tags: + - remote files + - remote files + /api/remote_files/plugins: + get: + description: Display plugin information for each of the gxfiles:// URI targets + available. + operationId: plugins_api_remote_files_plugins_get + parameters: + - description: Whether to return browsable filesources only. The default is + `True`, which will omit filesourceslike `http` and `base64` that do not + implement a list method. + in: query + name: browsable_only + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: true + description: Whether to return browsable filesources only. The default is + `True`, which will omit filesourceslike `http` and `base64` that do not + implement a list method. + title: Browsable filesources only + - description: Whether to return **only** filesources of the specified kind. + The default is `None`, which will return all filesources. Multiple values + can be specified by repeating the parameter. + in: query + name: include_kind + required: false + schema: + anyOf: + - items: + $ref: '#/components/schemas/PluginKind' + type: array + - type: 'null' + description: Whether to return **only** filesources of the specified kind. + The default is `None`, which will return all filesources. Multiple values + can be specified by repeating the parameter. + title: Include kind + - description: Whether to exclude filesources of the specified kind from the + list. The default is `None`, which will return all filesources. Multiple + values can be specified by repeating the parameter. + in: query + name: exclude_kind + required: false + schema: + anyOf: + - items: + $ref: '#/components/schemas/PluginKind' + type: array + - type: 'null' + description: Whether to exclude filesources of the specified kind from the + list. The default is `None`, which will return all filesources. Multiple + values can be specified by repeating the parameter. + title: Exclude kind + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/FilesSourcePluginList' + description: A list with details about each plugin. + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Display plugin information for each of the gxfiles:// URI targets available. + tags: + - remote files + - remote files + /api/roles: + get: + operationId: index_api_roles_get + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/RoleListResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Index + tags: + - roles + - roles + post: + operationId: create_api_roles_post + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/RoleDefinitionModel' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/RoleModelResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Create + tags: + - roles + - roles + /api/roles/{id}: + delete: + operationId: delete_api_roles__id__delete + parameters: + - in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/RoleModelResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Delete + tags: + - roles + - roles + get: + operationId: show_api_roles__id__get + parameters: + - in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/RoleModelResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Show + tags: + - roles + - roles + /api/roles/{id}/purge: + post: + operationId: purge_api_roles__id__purge_post + parameters: + - in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/RoleModelResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Purge + tags: + - roles + - roles + /api/roles/{id}/undelete: + post: + operationId: undelete_api_roles__id__undelete_post + parameters: + - in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/RoleModelResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Undelete + tags: + - roles + - roles + /api/short_term_storage/{storage_request_id}: + get: + operationId: serve_api_short_term_storage__storage_request_id__get + parameters: + - in: path + name: storage_request_id + required: true + schema: + format: uuid + title: Storage Request Id + type: string + responses: + '200': + description: The archive file containing the History. + '204': + description: Request was cancelled without an exception condition recorded. + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: [] + summary: Serve the staged download specified by request ID. + tags: + - short_term_storage + - short_term_storage + /api/short_term_storage/{storage_request_id}/ready: + get: + operationId: is_ready_api_short_term_storage__storage_request_id__ready_get + parameters: + - in: path + name: storage_request_id + required: true + schema: + format: uuid + title: Storage Request Id + type: string + responses: + '200': + content: + application/json: + schema: + title: Response Is Ready Api Short Term Storage Storage Request Id Ready + Get + type: boolean + description: Boolean indicating if the storage is ready. + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: [] + summary: Determine if specified storage request ID is ready for download. + tags: + - short_term_storage + - short_term_storage + /api/storage/datasets: + delete: + description: '**Warning**: This operation cannot be undone. All objects will + be deleted permanently from the disk.' + operationId: cleanup_datasets_api_storage_datasets_delete + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/CleanupStorageItemsRequest' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/StorageItemsCleanupResult' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Purges a set of datasets by ID from disk. The datasets must be owned + by the user. + tags: + - storage management + - storage management + /api/storage/datasets/discarded: + get: + operationId: discarded_datasets_api_storage_datasets_discarded_get + parameters: + - description: Starts at the beginning skip the first ( offset - 1 ) items and + begin returning at the Nth item + in: query + name: offset + required: false + schema: + anyOf: + - minimum: 0 + type: integer + - type: 'null' + default: 0 + description: Starts at the beginning skip the first ( offset - 1 ) items + and begin returning at the Nth item + title: Offset + - description: The maximum number of items to return. + in: query + name: limit + required: false + schema: + anyOf: + - minimum: 1 + type: integer + - type: 'null' + description: The maximum number of items to return. + title: Limit + - description: String containing one of the valid ordering attributes followed + by '-asc' or '-dsc' for ascending and descending order respectively. + in: query + name: order + required: false + schema: + anyOf: + - $ref: '#/components/schemas/StoredItemOrderBy' + - type: 'null' + description: String containing one of the valid ordering attributes followed + by '-asc' or '-dsc' for ascending and descending order respectively. + title: Order + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/StoredItem' + title: Response Discarded Datasets Api Storage Datasets Discarded + Get + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns discarded datasets owned by the given user. The results can + be paginated. + tags: + - storage management + - storage management + /api/storage/datasets/discarded/summary: + get: + operationId: discarded_datasets_summary_api_storage_datasets_discarded_summary_get + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/CleanableItemsSummary' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns information with the total storage space taken by discarded + datasets owned by the given user. + tags: + - storage management + - storage management + /api/storage/histories: + delete: + description: '**Warning**: This operation cannot be undone. All objects will + be deleted permanently from the disk.' + operationId: cleanup_histories_api_storage_histories_delete + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/CleanupStorageItemsRequest' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/StorageItemsCleanupResult' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Purges a set of histories by ID. The histories must be owned by the + user. + tags: + - storage management + - storage management + /api/storage/histories/archived: + get: + operationId: archived_histories_api_storage_histories_archived_get + parameters: + - description: Starts at the beginning skip the first ( offset - 1 ) items and + begin returning at the Nth item + in: query + name: offset + required: false + schema: + anyOf: + - minimum: 0 + type: integer + - type: 'null' + default: 0 + description: Starts at the beginning skip the first ( offset - 1 ) items + and begin returning at the Nth item + title: Offset + - description: The maximum number of items to return. + in: query + name: limit + required: false + schema: + anyOf: + - minimum: 1 + type: integer + - type: 'null' + description: The maximum number of items to return. + title: Limit + - description: String containing one of the valid ordering attributes followed + by '-asc' or '-dsc' for ascending and descending order respectively. + in: query + name: order + required: false + schema: + anyOf: + - $ref: '#/components/schemas/StoredItemOrderBy' + - type: 'null' + description: String containing one of the valid ordering attributes followed + by '-asc' or '-dsc' for ascending and descending order respectively. + title: Order + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/StoredItem' + title: Response Archived Histories Api Storage Histories Archived + Get + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns archived histories owned by the given user that are not purged. + The results can be paginated. + tags: + - storage management + - storage management + /api/storage/histories/archived/summary: + get: + operationId: archived_histories_summary_api_storage_histories_archived_summary_get + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/CleanableItemsSummary' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns information with the total storage space taken by non-purged + archived histories associated with the given user. + tags: + - storage management + - storage management + /api/storage/histories/discarded: + get: + operationId: discarded_histories_api_storage_histories_discarded_get + parameters: + - description: Starts at the beginning skip the first ( offset - 1 ) items and + begin returning at the Nth item + in: query + name: offset + required: false + schema: + anyOf: + - minimum: 0 + type: integer + - type: 'null' + default: 0 + description: Starts at the beginning skip the first ( offset - 1 ) items + and begin returning at the Nth item + title: Offset + - description: The maximum number of items to return. + in: query + name: limit + required: false + schema: + anyOf: + - minimum: 1 + type: integer + - type: 'null' + description: The maximum number of items to return. + title: Limit + - description: String containing one of the valid ordering attributes followed + by '-asc' or '-dsc' for ascending and descending order respectively. + in: query + name: order + required: false + schema: + anyOf: + - $ref: '#/components/schemas/StoredItemOrderBy' + - type: 'null' + description: String containing one of the valid ordering attributes followed + by '-asc' or '-dsc' for ascending and descending order respectively. + title: Order + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/StoredItem' + title: Response Discarded Histories Api Storage Histories Discarded + Get + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns all discarded histories associated with the given user. + tags: + - storage management + - storage management + /api/storage/histories/discarded/summary: + get: + operationId: discarded_histories_summary_api_storage_histories_discarded_summary_get + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/CleanableItemsSummary' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns information with the total storage space taken by discarded + histories associated with the given user. + tags: + - storage management + - storage management + /api/tags: + put: + description: 'Replaces the tags associated with an item with the new ones specified + in the payload. + + + - The previous tags will be __deleted__. + + - If no tags are provided in the request body, the currently associated tags + will also be __deleted__.' + operationId: update_api_tags_put + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + allOf: + - $ref: '#/components/schemas/ItemTagsPayload' + description: Request body containing the item and the tags to be assigned. + title: Payload + required: true + responses: + '204': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Apply a new set of tags to an item. + tags: + - tags + - tags + /api/tasks/{task_id}/state: + get: + operationId: state_api_tasks__task_id__state_get + parameters: + - in: path + name: task_id + required: true + schema: + format: uuid + title: Task Id + type: string + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/TaskState' + description: String indicating task state. + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: [] + summary: Determine state of task ID + tags: + - tasks + - tasks + /api/tool_data: + get: + description: Get the list of all available data tables. + operationId: index_api_tool_data_get + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ToolDataEntryList' + description: A list with details on individual data tables. + security: [] + summary: Lists all available data tables + tags: + - tool data tables + - tool data tables + post: + operationId: create_api_tool_data_post + parameters: + - in: query + name: tool_data_file_path + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Tool Data File Path + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/ImportToolDataBundle' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/AsyncTaskResultSummary' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Import a data manager bundle + tags: + - tool data tables + - tool data tables + /api/tool_data/{table_name}: + delete: + description: Removes an item from a data table and reloads it to return its + updated details. + operationId: delete_api_tool_data__table_name__delete + parameters: + - description: The name of the tool data table + in: path + name: table_name + required: true + schema: + description: The name of the tool data table + examples: + - all_fasta + title: Data table name + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/ToolDataItem' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ToolDataDetails' + description: A description of the affected data table and its content + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Removes an item from a data table + tags: + - tool data tables + - tool data tables + get: + description: Get details of a given tool data table. + operationId: show_api_tool_data__table_name__get + parameters: + - description: The name of the tool data table + in: path + name: table_name + required: true + schema: + description: The name of the tool data table + examples: + - all_fasta + title: Data table name + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ToolDataDetails' + description: A description of the given data table and its content + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get details of a given data table + tags: + - tool data tables + - tool data tables + /api/tool_data/{table_name}/fields/{field_name}: + get: + description: Reloads a data table and return its details. + operationId: show_field_api_tool_data__table_name__fields__field_name__get + parameters: + - description: The name of the tool data table + in: path + name: table_name + required: true + schema: + description: The name of the tool data table + examples: + - all_fasta + title: Data table name + type: string + - description: The name of the tool data table field + in: path + name: field_name + required: true + schema: + description: The name of the tool data table field + title: Field name + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ToolDataField' + description: Information about a data table field + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get information about a particular field in a tool data table + tags: + - tool data tables + - tool data tables + /api/tool_data/{table_name}/fields/{field_name}/files/{file_name}: + get: + description: Download a file associated with the data table field. + operationId: download_field_file_api_tool_data__table_name__fields__field_name__files__file_name__get + parameters: + - description: The name of the tool data table + in: path + name: table_name + required: true + schema: + description: The name of the tool data table + examples: + - all_fasta + title: Data table name + type: string + - description: The name of the tool data table field + in: path + name: field_name + required: true + schema: + description: The name of the tool data table field + title: Field name + type: string + - description: The name of a file associated with this data table field + in: path + name: file_name + required: true + schema: + description: The name of a file associated with this data table field + title: File name + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + description: Information about a data table field + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get information about a particular field in a tool data table + tags: + - tool data tables + - tool data tables + /api/tool_data/{table_name}/reload: + get: + description: Reloads a data table and return its details. + operationId: reload_api_tool_data__table_name__reload_get + parameters: + - description: The name of the tool data table + in: path + name: table_name + required: true + schema: + description: The name of the tool data table + examples: + - all_fasta + title: Data table name + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ToolDataDetails' + description: A description of the reloaded data table and its content + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Reloads a tool data table + tags: + - tool data tables + - tool data tables + /api/tool_shed_repositories: + get: + operationId: index_api_tool_shed_repositories_get + parameters: + - description: Filter by repository name. + in: query + name: name + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Filter by repository name. + title: Name + - description: Filter by repository owner. + in: query + name: owner + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Filter by repository owner. + title: Owner + - description: Filter by changeset revision. + in: query + name: changeset + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Filter by changeset revision. + title: Changeset + - description: Filter by whether the repository has been deleted. + in: query + name: deleted + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + description: Filter by whether the repository has been deleted. + title: Deleted? + - description: Filter by whether the repository has been uninstalled. + in: query + name: uninstalled + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + description: Filter by whether the repository has been uninstalled. + title: Uninstalled? + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/InstalledToolShedRepository' + title: Response Index Api Tool Shed Repositories Get + type: array + description: A list of installed tool shed repository objects. + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: [] + summary: Lists installed tool shed repositories. + tags: + - tool_shed_repositories + - tool_shed_repositories + /api/tool_shed_repositories/check_for_updates: + get: + operationId: check_for_updates_api_tool_shed_repositories_check_for_updates_get + parameters: + - in: query + name: id + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + title: Id + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/CheckForUpdatesResponse' + description: A description of the state and updates message. + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Check for updates to the specified repository, or all installed repositories. + tags: + - tool_shed_repositories + - tool_shed_repositories + /api/tool_shed_repositories/{id}: + get: + operationId: show_api_tool_shed_repositories__id__get + parameters: + - description: The encoded database identifier of the installed Tool Shed Repository. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/InstalledToolShedRepository' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: [] + summary: Show installed tool shed repository. + tags: + - tool_shed_repositories + - tool_shed_repositories + /api/tools/fetch: + post: + operationId: fetch_form_api_tools_fetch_post + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + multipart/form-data: + schema: + $ref: '#/components/schemas/Body_fetch_form_api_tools_fetch_post' + required: true + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Upload files to Galaxy + tags: + - tools + - tools + /api/tours: + get: + description: Return list of available tours. + operationId: index_api_tours_get + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/TourList' + description: Successful Response + security: [] + summary: Index + tags: + - tours + - tours + /api/tours/{tour_id}: + get: + description: Return a tour definition. + operationId: show_api_tours__tour_id__get + parameters: + - in: path + name: tour_id + required: true + schema: + title: Tour Id + type: string + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/TourDetails' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: [] + summary: Show + tags: + - tours + - tours + post: + description: Return a tour definition. + operationId: update_tour_api_tours__tour_id__post + parameters: + - in: path + name: tour_id + required: true + schema: + title: Tour Id + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/TourDetails' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Update Tour + tags: + - tours + - tours + /api/users: + get: + description: Return a collection of users. Filters will only work if enabled + in config or user is admin. + operationId: get_users_api_users_get + parameters: + - description: Indicates if the collection will be about deleted users + in: query + name: deleted + required: false + schema: + default: false + description: Indicates if the collection will be about deleted users + title: Deleted users + type: boolean + - description: An email address to filter on + in: query + name: f_email + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: An email address to filter on + title: Email filter + - description: An username address to filter on + in: query + name: f_name + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: An username address to filter on + title: Name filter + - description: Filter on username OR email + in: query + name: f_any + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Filter on username OR email + title: Any filter + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + anyOf: + - $ref: '#/components/schemas/UserModel' + - $ref: '#/components/schemas/LimitedUserModel' + title: Response Get Users Api Users Get + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get Users + tags: + - users + - users + post: + operationId: create_user_api_users_post + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/UserCreationPayload' + - $ref: '#/components/schemas/RemoteUserCreationPayload' + description: The values to add create a user. + title: Create User + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/CreatedUserModel' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Create a new Galaxy user. Only admins can create users for now. + tags: + - users + - users + /api/users/current/recalculate_disk_usage: + put: + description: 'This route will be removed in a future version. + + + Please use `/api/users/current/recalculate_disk_usage` instead.' + operationId: recalculate_disk_usage_api_users_current_recalculate_disk_usage_put + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/AsyncTaskResultSummary' + description: The asynchronous task summary to track the task state. + '204': + description: The background task was submitted but there is no status tracking + ID available. + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Triggers a recalculation of the current user disk usage. + tags: + - users + - users + /api/users/deleted: + get: + description: Return a collection of deleted users. Only admins can see deleted + users. + operationId: get_deleted_users_api_users_deleted_get + parameters: + - description: An email address to filter on + in: query + name: f_email + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: An email address to filter on + title: Email filter + - description: An username address to filter on + in: query + name: f_name + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: An username address to filter on + title: Name filter + - description: Filter on username OR email + in: query + name: f_any + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Filter on username OR email + title: Any filter + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + anyOf: + - $ref: '#/components/schemas/UserModel' + - $ref: '#/components/schemas/LimitedUserModel' + title: Response Get Deleted Users Api Users Deleted Get + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get Deleted Users + tags: + - users + - users + /api/users/deleted/{user_id}: + get: + operationId: get_deleted_user_api_users_deleted__user_id__get + parameters: + - description: The ID of the user. + in: path + name: user_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/DetailedUserModel' + - $ref: '#/components/schemas/AnonUserModel' + title: Response Get Deleted User Api Users Deleted User Id Get + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return information about a deleted user. Only admins can see deleted + users. + tags: + - users + - users + /api/users/deleted/{user_id}/undelete: + post: + operationId: undelete_user_api_users_deleted__user_id__undelete_post + parameters: + - description: The ID of the user. + in: path + name: user_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DetailedUserModel' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Restore a deleted user. Only admins can restore users. + tags: + - users + - users + /api/users/recalculate_disk_usage: + put: + deprecated: true + description: 'This route will be removed in a future version. + + + Please use `/api/users/current/recalculate_disk_usage` instead.' + operationId: recalculate_disk_usage_api_users_recalculate_disk_usage_put + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/AsyncTaskResultSummary' + description: The asynchronous task summary to track the task state. + '204': + description: The background task was submitted but there is no status tracking + ID available. + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Triggers a recalculation of the current user disk usage. + tags: + - users + - users + /api/users/{user_id}: + delete: + operationId: delete_user_api_users__user_id__delete + parameters: + - description: The ID of the user. + in: path + name: user_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/UserDeletionPayload' + - type: 'null' + description: Purge the user. + title: Purge user + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DetailedUserModel' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Delete a user. Only admins can delete others or purge users. + tags: + - users + - users + get: + operationId: get_user_api_users__user_id__get + parameters: + - description: The ID of the user to get or 'current'. + in: path + name: user_id + required: true + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - const: current + description: The ID of the user to get or 'current'. + title: User ID + - description: Indicates if the user is deleted + in: query + name: deleted + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + description: Indicates if the user is deleted + title: Deleted user + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/DetailedUserModel' + - $ref: '#/components/schemas/AnonUserModel' + title: Response Get User Api Users User Id Get + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return information about a specified or the current user. Only admin + can see deleted or other users + tags: + - users + - users + put: + operationId: update_user_api_users__user_id__put + parameters: + - description: The ID of the user to get or 'current'. + in: path + name: user_id + required: true + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - const: current + description: The ID of the user to get or 'current'. + title: User ID + - description: Indicates if the user is deleted + in: query + name: deleted + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + description: Indicates if the user is deleted + title: Deleted user + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + description: The user values to update. + title: Update user + type: object + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DetailedUserModel' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Update the values of a user. Only admin can update others. + tags: + - users + - users + /api/users/{user_id}/api_key: + delete: + operationId: delete_api_key_api_users__user_id__api_key_delete + parameters: + - description: The ID of the user. + in: path + name: user_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '204': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Delete the current API key of the user + tags: + - users + - users + get: + operationId: get_or_create_api_key_api_users__user_id__api_key_get + parameters: + - description: The ID of the user. + in: path + name: user_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + title: Response Get Or Create Api Key Api Users User Id Api Key + Get + type: string + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return the user's API key + tags: + - users + - users + post: + operationId: create_api_key_api_users__user_id__api_key_post + parameters: + - description: The ID of the user. + in: path + name: user_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + title: Response Create Api Key Api Users User Id Api Key Post + type: string + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Create a new API key for the user + tags: + - users + - users + /api/users/{user_id}/api_key/detailed: + get: + operationId: get_api_key_detailed_api_users__user_id__api_key_detailed_get + parameters: + - description: The ID of the user. + in: path + name: user_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/APIKeyModel' + description: The API key of the user. + '204': + description: The user doesn't have an API key. + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return the user's API key with extra information. + tags: + - users + - users + /api/users/{user_id}/beacon: + get: + description: '**Warning**: This endpoint is experimental and might change or + disappear in future versions.' + operationId: get_beacon_settings_api_users__user_id__beacon_get + parameters: + - description: The ID of the user. + in: path + name: user_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/UserBeaconSetting' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return information about beacon share settings + tags: + - users + - users + post: + description: '**Warning**: This endpoint is experimental and might change or + disappear in future versions.' + operationId: set_beacon_settings_api_users__user_id__beacon_post + parameters: + - description: The ID of the user. + in: path + name: user_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/UserBeaconSetting' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/UserBeaconSetting' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Change beacon setting + tags: + - users + - users + /api/users/{user_id}/custom_builds: + get: + operationId: get_custom_builds_api_users__user_id__custom_builds_get + parameters: + - description: The ID of the user. + in: path + name: user_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/CustomBuildsCollection' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: ' Returns collection of custom builds.' + tags: + - users + - users + /api/users/{user_id}/custom_builds/{key}: + delete: + operationId: delete_custom_build_api_users__user_id__custom_builds__key__delete + parameters: + - description: The ID of the user. + in: path + name: user_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The key of the custom build to be deleted. + in: path + name: key + required: true + schema: + description: The key of the custom build to be deleted. + title: Custom build key + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DeletedCustomBuild' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Delete a custom build + tags: + - users + - users + put: + operationId: add_custom_builds_api_users__user_id__custom_builds__key__put + parameters: + - description: The ID of the user. + in: path + name: user_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The key of the custom build to be deleted. + in: path + name: key + required: true + schema: + description: The key of the custom build to be deleted. + title: Custom build key + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + allOf: + - $ref: '#/components/schemas/CustomBuildCreationPayload' + description: The values to add a new custom build. + title: Add custom build + required: true + responses: + '200': + content: + application/json: + schema: + title: Response Add Custom Builds Api Users User Id Custom Builds Key Put + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Add new custom build. + tags: + - users + - users + /api/users/{user_id}/favorites/{object_type}: + put: + operationId: set_favorite_api_users__user_id__favorites__object_type__put + parameters: + - description: The ID of the user. + in: path + name: user_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The object type the user wants to favorite + in: path + name: object_type + required: true + schema: + allOf: + - $ref: '#/components/schemas/FavoriteObjectType' + description: The object type the user wants to favorite + title: Object type + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + allOf: + - $ref: '#/components/schemas/FavoriteObject' + description: The id of an object the user wants to favorite. + title: Set favorite + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/FavoriteObjectsSummary' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Add the object to user's favorites + tags: + - users + - users + /api/users/{user_id}/favorites/{object_type}/{object_id}: + delete: + operationId: remove_favorite_api_users__user_id__favorites__object_type___object_id__delete + parameters: + - description: The ID of the user. + in: path + name: user_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The object type the user wants to favorite + in: path + name: object_type + required: true + schema: + allOf: + - $ref: '#/components/schemas/FavoriteObjectType' + description: The object type the user wants to favorite + title: Object type + - description: The ID of an object the user wants to remove from favorites + in: path + name: object_id + required: true + schema: + description: The ID of an object the user wants to remove from favorites + title: Object ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/FavoriteObjectsSummary' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Remove the object from user's favorites + tags: + - users + - users + /api/users/{user_id}/recalculate_disk_usage: + put: + operationId: recalculate_disk_usage_by_user_id_api_users__user_id__recalculate_disk_usage_put + parameters: + - description: The ID of the user. + in: path + name: user_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/AsyncTaskResultSummary' + description: The asynchronous task summary to track the task state. + '204': + description: The background task was submitted but there is no status tracking + ID available. + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Triggers a recalculation of the current user disk usage. + tags: + - users + - users + /api/users/{user_id}/send_activation_email: + post: + operationId: send_activation_email_api_users__user_id__send_activation_email_post + parameters: + - description: The ID of the user. + in: path + name: user_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Sends activation email to user. + tags: + - users + - users + /api/users/{user_id}/theme/{theme}: + put: + operationId: set_theme_api_users__user_id__theme__theme__put + parameters: + - description: The ID of the user. + in: path + name: user_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The theme of the GUI + in: path + name: theme + required: true + schema: + description: The theme of the GUI + title: Theme + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + title: Response Set Theme Api Users User Id Theme Theme Put + type: string + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Set the user's theme choice + tags: + - users + - users + /api/users/{user_id}/usage: + get: + operationId: get_user_usage_api_users__user_id__usage_get + parameters: + - description: The ID of the user to get or 'current'. + in: path + name: user_id + required: true + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - const: current + description: The ID of the user to get or 'current'. + title: User ID + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/UserQuotaUsage' + title: Response Get User Usage Api Users User Id Usage Get + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return the user's quota usage summary broken down by quota source + tags: + - users + - users + /api/users/{user_id}/usage/{label}: + get: + operationId: get_user_usage_for_label_api_users__user_id__usage__label__get + parameters: + - description: The ID of the user to get or 'current'. + in: path + name: user_id + required: true + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - const: current + description: The ID of the user to get or 'current'. + title: User ID + - description: The label corresponding to the quota source to fetch usage information + about. + in: path + name: label + required: true + schema: + description: The label corresponding to the quota source to fetch usage + information about. + title: Quota Source Label + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/UserQuotaUsage' + - type: 'null' + title: Response Get User Usage For Label Api Users User Id Usage Label Get + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return the user's quota usage summary for a given quota source label + tags: + - users + - users + /api/version: + get: + description: 'Return Galaxy version information: major/minor version, optional + extra info.' + operationId: version_api_version_get + responses: + '200': + content: + application/json: + schema: + title: Response Version Api Version Get + type: object + description: 'Galaxy version information: major/minor version, optional + extra info' + security: [] + summary: 'Return Galaxy version information: major/minor version, optional extra + info' + tags: + - configuration + - configuration + /api/visualizations: + get: + operationId: index_api_visualizations_get + parameters: + - description: Whether to include deleted visualizations in the result. + in: query + name: deleted + required: false + schema: + default: false + description: Whether to include deleted visualizations in the result. + title: Display deleted + type: boolean + - description: The maximum number of items to return. + in: query + name: limit + required: false + schema: + anyOf: + - minimum: 1 + type: integer + - type: 'null' + description: The maximum number of items to return. + title: Limit + - description: Starts at the beginning skip the first ( offset - 1 ) items and + begin returning at the Nth item + in: query + name: offset + required: false + schema: + anyOf: + - minimum: 0 + type: integer + - type: 'null' + default: 0 + description: Starts at the beginning skip the first ( offset - 1 ) items + and begin returning at the Nth item + title: Offset + - in: query + name: user_id + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + title: Encoded user ID to restrict query to, must be own id if not an admin + user + - in: query + name: show_own + required: false + schema: + default: true + title: Show visualizations owned by user. + type: boolean + - in: query + name: show_published + required: false + schema: + default: true + title: Include published visualizations. + type: boolean + - in: query + name: show_shared + required: false + schema: + default: false + title: Include visualizations shared with authenticated user. + type: boolean + - description: Sort visualization index by this specified attribute on the visualization + model + in: query + name: sort_by + required: false + schema: + default: update_time + description: Sort visualization index by this specified attribute on the + visualization model + enum: + - create_time + - title + - update_time + - username + title: Sort attribute + type: string + - description: Sort in descending order? + in: query + name: sort_desc + required: false + schema: + default: true + description: Sort in descending order? + title: Sort Descending + type: boolean + - description: 'A mix of free text and GitHub-style tags used to filter the + index operation. + + + ## Query Structure + + + GitHub-style filter tags (not be confused with Galaxy tags) are tags of + the form + + `:` or `:''''`. + The tag name + + *generally* (but not exclusively) corresponds to the name of an attribute + on the model + + being indexed (i.e. a column in the database). + + + If the tag is quoted, the attribute will be filtered exactly. If the tag + is unquoted, + + generally a partial match will be used to filter the query (i.e. in terms + of the implementation + + this means the database operation `ILIKE` will typically be used). + + + Once the tagged filters are extracted from the search query, the remaining + text is just + + used to search various documented attributes of the object. + + + ## GitHub-style Tags Available + + + `title` + + : The visualization''s title. + + + `slug` + + : The visualization''s slug. (The tag `s` can be used a short hand alias + for this tag to filter on this attribute.) + + + `tag` + + : The visualization''s tags. (The tag `t` can be used a short hand alias + for this tag to filter on this attribute.) + + + `user` + + : The visualization''s owner''s username. (The tag `u` can be used a short + hand alias for this tag to filter on this attribute.) + + + ## Free Text + + + Free text search terms will be searched against the following attributes + of the + + Visualizations: `title`, `slug`, `tag`, `type`. + + + ' + in: query + name: search + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: 'A mix of free text and GitHub-style tags used to filter the + index operation. + + + ## Query Structure + + + GitHub-style filter tags (not be confused with Galaxy tags) are tags of + the form + + `:` or `:''''`. + The tag name + + *generally* (but not exclusively) corresponds to the name of an attribute + on the model + + being indexed (i.e. a column in the database). + + + If the tag is quoted, the attribute will be filtered exactly. If the tag + is unquoted, + + generally a partial match will be used to filter the query (i.e. in terms + of the implementation + + this means the database operation `ILIKE` will typically be used). + + + Once the tagged filters are extracted from the search query, the remaining + text is just + + used to search various documented attributes of the object. + + + ## GitHub-style Tags Available + + + `title` + + : The visualization''s title. + + + `slug` + + : The visualization''s slug. (The tag `s` can be used a short hand alias + for this tag to filter on this attribute.) + + + `tag` + + : The visualization''s tags. (The tag `t` can be used a short hand alias + for this tag to filter on this attribute.) + + + `user` + + : The visualization''s owner''s username. (The tag `u` can be used a short + hand alias for this tag to filter on this attribute.) + + + ## Free Text + + + Free text search terms will be searched against the following attributes + of the + + Visualizations: `title`, `slug`, `tag`, `type`. + + + ' + title: Search query. + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/VisualizationSummaryList' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Returns visualizations for the current user. + tags: + - visualizations + - visualizations + /api/visualizations/{id}/disable_link_access: + put: + description: Makes this item inaccessible by a URL link and return the current + sharing status. + operationId: disable_link_access_api_visualizations__id__disable_link_access_put + parameters: + - description: The encoded database identifier of the Visualization. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/SharingStatus' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Makes this item inaccessible by a URL link. + tags: + - visualizations + - visualizations + /api/visualizations/{id}/enable_link_access: + put: + description: Makes this item accessible by a URL link and return the current + sharing status. + operationId: enable_link_access_api_visualizations__id__enable_link_access_put + parameters: + - description: The encoded database identifier of the Visualization. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/SharingStatus' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Makes this item accessible by a URL link. + tags: + - visualizations + - visualizations + /api/visualizations/{id}/publish: + put: + description: Makes this item publicly available by a URL link and return the + current sharing status. + operationId: publish_api_visualizations__id__publish_put + parameters: + - description: The encoded database identifier of the Visualization. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/SharingStatus' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Makes this item public and accessible by a URL link. + tags: + - visualizations + - visualizations + /api/visualizations/{id}/share_with_users: + put: + description: Shares this item with specific users and return the current sharing + status. + operationId: share_with_users_api_visualizations__id__share_with_users_put + parameters: + - description: The encoded database identifier of the Visualization. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/ShareWithPayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ShareWithStatus' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Share this item with specific users. + tags: + - visualizations + - visualizations + /api/visualizations/{id}/sharing: + get: + description: Return the sharing status of the item. + operationId: sharing_api_visualizations__id__sharing_get + parameters: + - description: The encoded database identifier of the Visualization. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/SharingStatus' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get the current sharing status of the given Visualization. + tags: + - visualizations + - visualizations + /api/visualizations/{id}/slug: + put: + description: Sets a new slug to access this item by URL. The new slug must be + unique. + operationId: set_slug_api_visualizations__id__slug_put + parameters: + - description: The encoded database identifier of the Visualization. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/SetSlugPayload' + required: true + responses: + '204': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Set a new slug for this shared item. + tags: + - visualizations + - visualizations + /api/visualizations/{id}/unpublish: + put: + description: Removes this item from the published list and return the current + sharing status. + operationId: unpublish_api_visualizations__id__unpublish_put + parameters: + - description: The encoded database identifier of the Visualization. + in: path + name: id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/SharingStatus' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Removes this item from the published list. + tags: + - visualizations + - visualizations + /api/whoami: + get: + description: Return information about the current authenticated user. + operationId: whoami_api_whoami_get + parameters: + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/UserModel' + - type: 'null' + title: Response Whoami Api Whoami Get + description: Information about the current authenticated user + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Return information about the current authenticated user + tags: + - configuration + - configuration + /api/workflows: + get: + description: Lists stored workflows viewable by the user. + operationId: index_api_workflows_get + parameters: + - description: Whether to restrict result to deleted workflows. + in: query + name: show_deleted + required: false + schema: + default: false + description: Whether to restrict result to deleted workflows. + title: Display deleted + type: boolean + - description: Whether to restrict result to hidden workflows. + in: query + name: show_hidden + required: false + schema: + default: false + description: Whether to restrict result to hidden workflows. + title: Display hidden + type: boolean + - description: Whether to include a list of missing tools per workflow entry + in: query + name: missing_tools + required: false + schema: + default: false + description: Whether to include a list of missing tools per workflow entry + title: Display missing tools + type: boolean + - in: query + name: show_published + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + title: Include published workflows. + - in: query + name: show_shared + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + title: Include workflows shared with authenticated user. + - description: In unspecified, default ordering depends on other parameters + but generally the user's own workflows appear first based on update time + in: query + name: sort_by + required: false + schema: + anyOf: + - enum: + - create_time + - update_time + - name + type: string + - type: 'null' + description: In unspecified, default ordering depends on other parameters + but generally the user's own workflows appear first based on update time + title: Sort workflow index by this attribute + - description: Sort in descending order? + in: query + name: sort_desc + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + description: Sort in descending order? + title: Sort Descending + - in: query + name: limit + required: false + schema: + anyOf: + - type: integer + - type: 'null' + title: Limit number of queries. + - in: query + name: offset + required: false + schema: + anyOf: + - type: integer + - type: 'null' + default: 0 + title: Number of workflows to skip in sorted query (to enable pagination). + - description: 'A mix of free text and GitHub-style tags used to filter the + index operation. + + + ## Query Structure + + + GitHub-style filter tags (not be confused with Galaxy tags) are tags of + the form + + `:` or `:''''`. + The tag name + + *generally* (but not exclusively) corresponds to the name of an attribute + on the model + + being indexed (i.e. a column in the database). + + + If the tag is quoted, the attribute will be filtered exactly. If the tag + is unquoted, + + generally a partial match will be used to filter the query (i.e. in terms + of the implementation + + this means the database operation `ILIKE` will typically be used). + + + Once the tagged filters are extracted from the search query, the remaining + text is just + + used to search various documented attributes of the object. + + + ## GitHub-style Tags Available + + + `name` + + : The stored workflow''s name. (The tag `n` can be used a short hand alias + for this tag to filter on this attribute.) + + + `tag` + + : The workflow''s tag, if the tag contains a colon an approach will be made + to match the key and value of the tag separately. (The tag `t` can be used + a short hand alias for this tag to filter on this attribute.) + + + `user` + + : The stored workflow''s owner''s username. (The tag `u` can be used a short + hand alias for this tag to filter on this attribute.) + + + `is:published` + + : Include only published workflows in the final result. Be sure the query + parameter `show_published` is set to `true` if to include all published + workflows and not just the requesting user''s. + + + `is:share_with_me` + + : Include only workflows shared with the requesting user. Be sure the query + parameter `show_shared` is set to `true` if to include shared workflows. + + + ## Free Text + + + Free text search terms will be searched against the following attributes + of the + + Stored Workflows: `name`, `tag`, `user`. + + + ' + in: query + name: search + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: 'A mix of free text and GitHub-style tags used to filter the + index operation. + + + ## Query Structure + + + GitHub-style filter tags (not be confused with Galaxy tags) are tags of + the form + + `:` or `:''''`. + The tag name + + *generally* (but not exclusively) corresponds to the name of an attribute + on the model + + being indexed (i.e. a column in the database). + + + If the tag is quoted, the attribute will be filtered exactly. If the tag + is unquoted, + + generally a partial match will be used to filter the query (i.e. in terms + of the implementation + + this means the database operation `ILIKE` will typically be used). + + + Once the tagged filters are extracted from the search query, the remaining + text is just + + used to search various documented attributes of the object. + + + ## GitHub-style Tags Available + + + `name` + + : The stored workflow''s name. (The tag `n` can be used a short hand alias + for this tag to filter on this attribute.) + + + `tag` + + : The workflow''s tag, if the tag contains a colon an approach will be + made to match the key and value of the tag separately. (The tag `t` can + be used a short hand alias for this tag to filter on this attribute.) + + + `user` + + : The stored workflow''s owner''s username. (The tag `u` can be used a + short hand alias for this tag to filter on this attribute.) + + + `is:published` + + : Include only published workflows in the final result. Be sure the query + parameter `show_published` is set to `true` if to include all published + workflows and not just the requesting user''s. + + + `is:share_with_me` + + : Include only workflows shared with the requesting user. Be sure the + query parameter `show_shared` is set to `true` if to include shared workflows. + + + ## Free Text + + + Free text search terms will be searched against the following attributes + of the + + Stored Workflows: `name`, `tag`, `user`. + + + ' + title: Search query. + - description: Set this to true to skip joining workflow step counts and optimize + the resulting index query. Response objects will not contain step counts. + in: query + name: skip_step_counts + required: false + schema: + default: false + description: Set this to true to skip joining workflow step counts and optimize + the resulting index query. Response objects will not contain step counts. + title: Skip step counts. + type: boolean + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + type: object + title: Response Index Api Workflows Get + type: array + description: A list with summary stored workflow information per viewable + entry. + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Lists stored workflows viewable by the user. + tags: + - workflows + - workflows + /api/workflows/menu: + get: + operationId: get_workflow_menu_api_workflows_menu_get + parameters: + - description: Whether to restrict result to deleted workflows. + in: query + name: show_deleted + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: false + description: Whether to restrict result to deleted workflows. + title: Display deleted + - description: Whether to restrict result to hidden workflows. + in: query + name: show_hidden + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: false + description: Whether to restrict result to hidden workflows. + title: Display hidden + - description: Whether to include a list of missing tools per workflow entry + in: query + name: missing_tools + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: false + description: Whether to include a list of missing tools per workflow entry + title: Display missing tools + - in: query + name: show_published + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + title: Include published workflows. + - in: query + name: show_shared + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + title: Include workflows shared with authenticated user. + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get workflows present in the tools panel. + tags: + - workflows + - workflows + /api/workflows/{workflow_id}: + delete: + operationId: delete_workflow_api_workflows__workflow_id__delete + parameters: + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Add the deleted flag to a workflow. + tags: + - workflows + - workflows + /api/workflows/{workflow_id}/counts: + get: + operationId: workflows__invocation_counts + parameters: + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: Is provided workflow id for Workflow instead of StoredWorkflow? + in: query + name: instance + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: false + description: Is provided workflow id for Workflow instead of StoredWorkflow? + title: Instance + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/RootModel_Dict_str__int__' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get state counts for accessible workflow. + tags: + - workflows + - workflows + /api/workflows/{workflow_id}/disable_link_access: + put: + description: Makes this item inaccessible by a URL link and return the current + sharing status. + operationId: disable_link_access_api_workflows__workflow_id__disable_link_access_put + parameters: + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/SharingStatus' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Makes this item inaccessible by a URL link. + tags: + - workflows + - workflows + /api/workflows/{workflow_id}/enable_link_access: + put: + description: Makes this item accessible by a URL link and return the current + sharing status. + operationId: enable_link_access_api_workflows__workflow_id__enable_link_access_put + parameters: + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/SharingStatus' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Makes this item accessible by a URL link. + tags: + - workflows + - workflows + /api/workflows/{workflow_id}/invocations: + get: + operationId: index_invocations_api_workflows__workflow_id__invocations_get + parameters: + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: Return only invocations for this History ID + in: query + name: history_id + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: Return only invocations for this History ID + title: History ID + - description: Return only invocations for this Job ID + in: query + name: job_id + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: Return only invocations for this Job ID + title: Job ID + - description: Return invocations for this User ID. + in: query + name: user_id + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: Return invocations for this User ID. + title: User ID + - description: Sort Workflow Invocations by this attribute + in: query + name: sort_by + required: false + schema: + anyOf: + - $ref: '#/components/schemas/InvocationSortByEnum' + - type: 'null' + description: Sort Workflow Invocations by this attribute + title: Sort By + - description: Sort in descending order? + in: query + name: sort_desc + required: false + schema: + default: false + description: Sort in descending order? + title: Sort Descending + type: boolean + - description: Set to false to only include terminal Invocations. + in: query + name: include_terminal + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: true + description: Set to false to only include terminal Invocations. + title: Include Terminal + - description: Limit the number of invocations to return. + in: query + name: limit + required: false + schema: + anyOf: + - type: integer + - type: 'null' + description: Limit the number of invocations to return. + title: Limit + - description: Number of invocations to skip. + in: query + name: offset + required: false + schema: + anyOf: + - type: integer + - type: 'null' + description: Number of invocations to skip. + title: Offset + - description: Is provided workflow id for Workflow instead of StoredWorkflow? + in: query + name: instance + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: false + description: Is provided workflow id for Workflow instead of StoredWorkflow? + title: Instance + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Include details for individual invocation steps and populate + a steps attribute in the resulting dictionary. + in: query + name: step_details + required: false + schema: + default: false + description: Include details for individual invocation steps and populate + a steps attribute in the resulting dictionary. + title: Include step details + type: boolean + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/WorkflowInvocationResponse' + title: Response Index Invocations Api Workflows Workflow Id Invocations + Get + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get the list of a user's workflow invocations. + tags: + - workflows + - workflows + /api/workflows/{workflow_id}/invocations/{invocation_id}: + delete: + description: An alias for `DELETE /api/invocations/{invocation_id}`. `workflow_id` + is ignored. + operationId: cancel_workflow_invocation_api_workflows__workflow_id__invocations__invocation_id__delete + parameters: + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: Include details for individual invocation steps and populate + a steps attribute in the resulting dictionary. + in: query + name: step_details + required: false + schema: + default: false + description: Include details for individual invocation steps and populate + a steps attribute in the resulting dictionary. + title: Include step details + type: boolean + - description: "Populate the invocation step state with the job state instead\ + \ of the invocation step state.\n This will also produce one step\ + \ per job in mapping jobs to mimic the older behavior with respect to collections.\n\ + \ Partially scheduled steps may provide incomplete information and\ + \ the listed steps outputs\n are not the mapped over step outputs\ + \ but the individual job outputs." + in: query + name: legacy_job_state + required: false + schema: + default: false + description: "Populate the invocation step state with the job state instead\ + \ of the invocation step state.\n This will also produce one step\ + \ per job in mapping jobs to mimic the older behavior with respect to\ + \ collections.\n Partially scheduled steps may provide incomplete\ + \ information and the listed steps outputs\n are not the mapped\ + \ over step outputs but the individual job outputs." + title: Replace with job state + type: boolean + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/WorkflowInvocationResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Cancel the specified workflow invocation. + tags: + - workflows + - workflows + get: + description: An alias for `GET /api/invocations/{invocation_id}`. `workflow_id` + is ignored. + operationId: show_workflow_invocation_api_workflows__workflow_id__invocations__invocation_id__get + parameters: + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: Include details for individual invocation steps and populate + a steps attribute in the resulting dictionary. + in: query + name: step_details + required: false + schema: + default: false + description: Include details for individual invocation steps and populate + a steps attribute in the resulting dictionary. + title: Include step details + type: boolean + - description: "Populate the invocation step state with the job state instead\ + \ of the invocation step state.\n This will also produce one step\ + \ per job in mapping jobs to mimic the older behavior with respect to collections.\n\ + \ Partially scheduled steps may provide incomplete information and\ + \ the listed steps outputs\n are not the mapped over step outputs\ + \ but the individual job outputs." + in: query + name: legacy_job_state + required: false + schema: + default: false + description: "Populate the invocation step state with the job state instead\ + \ of the invocation step state.\n This will also produce one step\ + \ per job in mapping jobs to mimic the older behavior with respect to\ + \ collections.\n Partially scheduled steps may provide incomplete\ + \ information and the listed steps outputs\n are not the mapped\ + \ over step outputs but the individual job outputs." + title: Replace with job state + type: boolean + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/WorkflowInvocationResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get detailed description of a workflow invocation. + tags: + - workflows + - workflows + /api/workflows/{workflow_id}/invocations/{invocation_id}/jobs_summary: + get: + description: An alias for `GET /api/invocations/{invocation_id}/jobs_summary`. + `workflow_id` is ignored. + operationId: workflow_invocation_jobs_summary_api_workflows__workflow_id__invocations__invocation_id__jobs_summary_get + parameters: + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/InvocationJobsResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get job state summary info aggregated across all current jobs of the + workflow invocation. + tags: + - workflows + - workflows + /api/workflows/{workflow_id}/invocations/{invocation_id}/report: + get: + description: An alias for `GET /api/invocations/{invocation_id}/report`. `workflow_id` + is ignored. + operationId: show_workflow_invocation_report_api_workflows__workflow_id__invocations__invocation_id__report_get + parameters: + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/InvocationReport' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get JSON summarizing invocation for reporting. + tags: + - workflows + - workflows + /api/workflows/{workflow_id}/invocations/{invocation_id}/report.pdf: + get: + description: An alias for `GET /api/invocations/{invocation_id}/report.pdf`. + `workflow_id` is ignored. + operationId: show_workflow_invocation_report_pdf_api_workflows__workflow_id__invocations__invocation_id__report_pdf_get + parameters: + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get PDF summarizing invocation for reporting. + tags: + - workflows + - workflows + /api/workflows/{workflow_id}/invocations/{invocation_id}/step_jobs_summary: + get: + description: An alias for `GET /api/invocations/{invocation_id}/step_jobs_summary`. + `workflow_id` is ignored. + operationId: workflow_invocation_step_jobs_summary_api_workflows__workflow_id__invocations__invocation_id__step_jobs_summary_get + parameters: + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + anyOf: + - $ref: '#/components/schemas/InvocationStepJobsResponseStepModel' + - $ref: '#/components/schemas/InvocationStepJobsResponseJobModel' + - $ref: '#/components/schemas/InvocationStepJobsResponseCollectionJobsModel' + title: Response Workflow Invocation Step Jobs Summary Api Workflows Workflow + Id Invocations Invocation Id Step Jobs Summary Get + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get job state summary info aggregated per step of the workflow invocation. + tags: + - workflows + - workflows + /api/workflows/{workflow_id}/invocations/{invocation_id}/steps/{step_id}: + get: + description: An alias for `GET /api/invocations/{invocation_id}/steps/{step_id}`. + `workflow_id` and `invocation_id` are ignored. + operationId: workflow_invocation_step_api_workflows__workflow_id__invocations__invocation_id__steps__step_id__get + parameters: + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The encoded database identifier of the WorkflowInvocationStep. + in: path + name: step_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/InvocationStep' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Show details of workflow invocation step. + tags: + - workflows + - workflows + put: + description: An alias for `PUT /api/invocations/{invocation_id}/steps/{step_id}`. + `workflow_id` is ignored. + operationId: update_workflow_invocation_step_api_workflows__workflow_id__invocations__invocation_id__steps__step_id__put + parameters: + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The encoded database identifier of the WorkflowInvocationStep. + in: path + name: step_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/InvocationUpdatePayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/InvocationStep' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Update state of running workflow step invocation. + tags: + - workflows + - workflows + /api/workflows/{workflow_id}/publish: + put: + description: Makes this item publicly available by a URL link and return the + current sharing status. + operationId: publish_api_workflows__workflow_id__publish_put + parameters: + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/SharingStatus' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Makes this item public and accessible by a URL link. + tags: + - workflows + - workflows + /api/workflows/{workflow_id}/share_with_users: + put: + description: Shares this item with specific users and return the current sharing + status. + operationId: share_with_users_api_workflows__workflow_id__share_with_users_put + parameters: + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/ShareWithPayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ShareWithStatus' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Share this item with specific users. + tags: + - workflows + - workflows + /api/workflows/{workflow_id}/sharing: + get: + description: Return the sharing status of the item. + operationId: sharing_api_workflows__workflow_id__sharing_get + parameters: + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/SharingStatus' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get the current sharing status of the given item. + tags: + - workflows + - workflows + /api/workflows/{workflow_id}/slug: + put: + description: Sets a new slug to access this item by URL. The new slug must be + unique. + operationId: set_slug_api_workflows__workflow_id__slug_put + parameters: + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/SetSlugPayload' + required: true + responses: + '204': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Set a new slug for this shared item. + tags: + - workflows + - workflows + /api/workflows/{workflow_id}/tags: + get: + operationId: index_api_workflows__workflow_id__tags_get + parameters: + - in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ItemTagsListResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Show tags based on workflow_id + tags: + - workflows + /api/workflows/{workflow_id}/tags/{tag_name}: + delete: + operationId: delete_api_workflows__workflow_id__tags__tag_name__delete + parameters: + - in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - in: path + name: tag_name + required: true + schema: + title: Tag Name + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + title: Response Delete Api Workflows Workflow Id Tags Tag Name Delete + type: boolean + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Delete tag based on workflow_id + tags: + - workflows + get: + operationId: show_api_workflows__workflow_id__tags__tag_name__get + parameters: + - in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - in: path + name: tag_name + required: true + schema: + title: Tag Name + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ItemTagsResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Show tag based on workflow_id + tags: + - workflows + post: + operationId: create_api_workflows__workflow_id__tags__tag_name__post + parameters: + - in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - in: path + name: tag_name + required: true + schema: + title: Tag Name + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + allOf: + - $ref: '#/components/schemas/ItemTagsCreatePayload' + title: Payload + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ItemTagsResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Create tag based on workflow_id + tags: + - workflows + put: + operationId: update_api_workflows__workflow_id__tags__tag_name__put + parameters: + - in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - in: path + name: tag_name + required: true + schema: + title: Tag Name + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/ItemTagsCreatePayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ItemTagsResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Update tag based on workflow_id + tags: + - workflows + /api/workflows/{workflow_id}/undelete: + post: + operationId: undelete_workflow_api_workflows__workflow_id__undelete_post + parameters: + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Remove the deleted flag from a workflow. + tags: + - workflows + - workflows + /api/workflows/{workflow_id}/unpublish: + put: + description: Removes this item from the published list and return the current + sharing status. + operationId: unpublish_api_workflows__workflow_id__unpublish_put + parameters: + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/SharingStatus' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Removes this item from the published list. + tags: + - workflows + - workflows + /api/workflows/{workflow_id}/usage: + get: + deprecated: true + operationId: index_invocations_api_workflows__workflow_id__usage_get + parameters: + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: Return only invocations for this History ID + in: query + name: history_id + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: Return only invocations for this History ID + title: History ID + - description: Return only invocations for this Job ID + in: query + name: job_id + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: Return only invocations for this Job ID + title: Job ID + - description: Return invocations for this User ID. + in: query + name: user_id + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: Return invocations for this User ID. + title: User ID + - description: Sort Workflow Invocations by this attribute + in: query + name: sort_by + required: false + schema: + anyOf: + - $ref: '#/components/schemas/InvocationSortByEnum' + - type: 'null' + description: Sort Workflow Invocations by this attribute + title: Sort By + - description: Sort in descending order? + in: query + name: sort_desc + required: false + schema: + default: false + description: Sort in descending order? + title: Sort Descending + type: boolean + - description: Set to false to only include terminal Invocations. + in: query + name: include_terminal + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: true + description: Set to false to only include terminal Invocations. + title: Include Terminal + - description: Limit the number of invocations to return. + in: query + name: limit + required: false + schema: + anyOf: + - type: integer + - type: 'null' + description: Limit the number of invocations to return. + title: Limit + - description: Number of invocations to skip. + in: query + name: offset + required: false + schema: + anyOf: + - type: integer + - type: 'null' + description: Number of invocations to skip. + title: Offset + - description: Is provided workflow id for Workflow instead of StoredWorkflow? + in: query + name: instance + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: false + description: Is provided workflow id for Workflow instead of StoredWorkflow? + title: Instance + - description: View to be passed to the serializer + in: query + name: view + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: View to be passed to the serializer + title: View + - description: Include details for individual invocation steps and populate + a steps attribute in the resulting dictionary. + in: query + name: step_details + required: false + schema: + default: false + description: Include details for individual invocation steps and populate + a steps attribute in the resulting dictionary. + title: Include step details + type: boolean + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/WorkflowInvocationResponse' + title: Response Index Invocations Api Workflows Workflow Id Usage + Get + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get the list of a user's workflow invocations. + tags: + - workflows + - workflows + /api/workflows/{workflow_id}/usage/{invocation_id}: + delete: + deprecated: true + description: An alias for `DELETE /api/invocations/{invocation_id}`. `workflow_id` + is ignored. + operationId: cancel_workflow_invocation_api_workflows__workflow_id__usage__invocation_id__delete + parameters: + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: Include details for individual invocation steps and populate + a steps attribute in the resulting dictionary. + in: query + name: step_details + required: false + schema: + default: false + description: Include details for individual invocation steps and populate + a steps attribute in the resulting dictionary. + title: Include step details + type: boolean + - description: "Populate the invocation step state with the job state instead\ + \ of the invocation step state.\n This will also produce one step\ + \ per job in mapping jobs to mimic the older behavior with respect to collections.\n\ + \ Partially scheduled steps may provide incomplete information and\ + \ the listed steps outputs\n are not the mapped over step outputs\ + \ but the individual job outputs." + in: query + name: legacy_job_state + required: false + schema: + default: false + description: "Populate the invocation step state with the job state instead\ + \ of the invocation step state.\n This will also produce one step\ + \ per job in mapping jobs to mimic the older behavior with respect to\ + \ collections.\n Partially scheduled steps may provide incomplete\ + \ information and the listed steps outputs\n are not the mapped\ + \ over step outputs but the individual job outputs." + title: Replace with job state + type: boolean + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/WorkflowInvocationResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Cancel the specified workflow invocation. + tags: + - workflows + - workflows + get: + deprecated: true + description: An alias for `GET /api/invocations/{invocation_id}`. `workflow_id` + is ignored. + operationId: show_workflow_invocation_api_workflows__workflow_id__usage__invocation_id__get + parameters: + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: Include details for individual invocation steps and populate + a steps attribute in the resulting dictionary. + in: query + name: step_details + required: false + schema: + default: false + description: Include details for individual invocation steps and populate + a steps attribute in the resulting dictionary. + title: Include step details + type: boolean + - description: "Populate the invocation step state with the job state instead\ + \ of the invocation step state.\n This will also produce one step\ + \ per job in mapping jobs to mimic the older behavior with respect to collections.\n\ + \ Partially scheduled steps may provide incomplete information and\ + \ the listed steps outputs\n are not the mapped over step outputs\ + \ but the individual job outputs." + in: query + name: legacy_job_state + required: false + schema: + default: false + description: "Populate the invocation step state with the job state instead\ + \ of the invocation step state.\n This will also produce one step\ + \ per job in mapping jobs to mimic the older behavior with respect to\ + \ collections.\n Partially scheduled steps may provide incomplete\ + \ information and the listed steps outputs\n are not the mapped\ + \ over step outputs but the individual job outputs." + title: Replace with job state + type: boolean + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/WorkflowInvocationResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get detailed description of a workflow invocation. + tags: + - workflows + - workflows + /api/workflows/{workflow_id}/usage/{invocation_id}/jobs_summary: + get: + deprecated: true + description: An alias for `GET /api/invocations/{invocation_id}/jobs_summary`. + `workflow_id` is ignored. + operationId: workflow_invocation_jobs_summary_api_workflows__workflow_id__usage__invocation_id__jobs_summary_get + parameters: + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/InvocationJobsResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get job state summary info aggregated across all current jobs of the + workflow invocation. + tags: + - workflows + - workflows + /api/workflows/{workflow_id}/usage/{invocation_id}/report: + get: + deprecated: true + description: An alias for `GET /api/invocations/{invocation_id}/report`. `workflow_id` + is ignored. + operationId: show_workflow_invocation_report_api_workflows__workflow_id__usage__invocation_id__report_get + parameters: + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/InvocationReport' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get JSON summarizing invocation for reporting. + tags: + - workflows + - workflows + /api/workflows/{workflow_id}/usage/{invocation_id}/report.pdf: + get: + deprecated: true + description: An alias for `GET /api/invocations/{invocation_id}/report.pdf`. + `workflow_id` is ignored. + operationId: show_workflow_invocation_report_pdf_api_workflows__workflow_id__usage__invocation_id__report_pdf_get + parameters: + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get PDF summarizing invocation for reporting. + tags: + - workflows + - workflows + /api/workflows/{workflow_id}/usage/{invocation_id}/step_jobs_summary: + get: + deprecated: true + description: An alias for `GET /api/invocations/{invocation_id}/step_jobs_summary`. + `workflow_id` is ignored. + operationId: workflow_invocation_step_jobs_summary_api_workflows__workflow_id__usage__invocation_id__step_jobs_summary_get + parameters: + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + items: + anyOf: + - $ref: '#/components/schemas/InvocationStepJobsResponseStepModel' + - $ref: '#/components/schemas/InvocationStepJobsResponseJobModel' + - $ref: '#/components/schemas/InvocationStepJobsResponseCollectionJobsModel' + title: Response Workflow Invocation Step Jobs Summary Api Workflows Workflow + Id Usage Invocation Id Step Jobs Summary Get + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get job state summary info aggregated per step of the workflow invocation. + tags: + - workflows + - workflows + /api/workflows/{workflow_id}/usage/{invocation_id}/steps/{step_id}: + get: + deprecated: true + description: An alias for `GET /api/invocations/{invocation_id}/steps/{step_id}`. + `workflow_id` and `invocation_id` are ignored. + operationId: workflow_invocation_step_api_workflows__workflow_id__usage__invocation_id__steps__step_id__get + parameters: + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The encoded database identifier of the WorkflowInvocationStep. + in: path + name: step_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/InvocationStep' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Show details of workflow invocation step. + tags: + - workflows + - workflows + put: + deprecated: true + description: An alias for `PUT /api/invocations/{invocation_id}/steps/{step_id}`. + `workflow_id` is ignored. + operationId: update_workflow_invocation_step_api_workflows__workflow_id__usage__invocation_id__steps__step_id__put + parameters: + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The encoded database identifier of the Invocation. + in: path + name: invocation_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The encoded database identifier of the WorkflowInvocationStep. + in: path + name: step_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/InvocationUpdatePayload' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/InvocationStep' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Update state of running workflow step invocation. + tags: + - workflows + - workflows + /api/workflows/{workflow_id}/versions: + get: + operationId: show_versions_api_workflows__workflow_id__versions_get + parameters: + - description: The encoded database identifier of the Stored Workflow. + in: path + name: workflow_id + required: true + schema: + example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - in: query + name: instance + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: false + title: True when fetching by Workflow ID, False when fetching by StoredWorkflow + ID. + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: List all versions of a workflow. + tags: + - workflows + - workflows + /ga4gh/drs/v1/objects/{object_id}: + get: + operationId: get_object_ga4gh_drs_v1_objects__object_id__get + parameters: + - description: The ID of the group + in: path + name: object_id + required: true + schema: + description: The ID of the group + title: Object ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DrsObject' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get Object + tags: + - drs + - drs + post: + operationId: get_object_ga4gh_drs_v1_objects__object_id__post + parameters: + - description: The ID of the group + in: path + name: object_id + required: true + schema: + description: The ID of the group + title: Object ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DrsObject' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get Object + tags: + - drs + - drs + /ga4gh/drs/v1/objects/{object_id}/access/{access_id}: + get: + operationId: get_access_url_ga4gh_drs_v1_objects__object_id__access__access_id__get + parameters: + - description: The ID of the group + in: path + name: object_id + required: true + schema: + description: The ID of the group + title: Object ID + type: string + - description: The access ID of the access method for objects, unused in Galaxy. + in: path + name: access_id + required: true + schema: + description: The access ID of the access method for objects, unused in Galaxy. + title: Access ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get Access Url + tags: + - drs + - drs + post: + operationId: get_access_url_ga4gh_drs_v1_objects__object_id__access__access_id__post + parameters: + - description: The ID of the group + in: path + name: object_id + required: true + schema: + description: The ID of the group + title: Object ID + type: string + - description: The access ID of the access method for objects, unused in Galaxy. + in: path + name: access_id + required: true + schema: + description: The access ID of the access method for objects, unused in Galaxy. + title: Access ID + type: string + - description: The user ID that will be used to effectively make this API call. + Only admins and designated users can make API calls on behalf of other users. + in: header + name: run-as + required: false + schema: + anyOf: + - example: 0123456789ABCDEF + minLength: 16 + pattern: '[0-9a-fA-F]+' + title: Invocation ID + type: string + - type: 'null' + description: The user ID that will be used to effectively make this API + call. Only admins and designated users can make API calls on behalf of + other users. + title: Run as User + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + - HTTPBearer: [] + summary: Get Access Url + tags: + - drs + - drs + /ga4gh/drs/v1/service-info: + get: + operationId: service_info_ga4gh_drs_v1_service_info_get + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/Service' + description: Successful Response + security: [] + summary: Service Info + tags: + - drs + - drs diff --git a/_shed_schema.yaml b/_shed_schema.yaml new file mode 100644 index 000000000000..ae80d3c2b4e1 --- /dev/null +++ b/_shed_schema.yaml @@ -0,0 +1,3010 @@ +components: + schemas: + APIKeyResponse: + properties: + api_key: + title: Api Key + type: string + required: + - api_key + title: APIKeyResponse + type: object + Body_repositories__create_revision: + properties: + commit_message: + title: Commit Message + files: + anyOf: + - items: + format: binary + type: string + type: array + - type: 'null' + title: Files + title: Body_repositories__create_revision + type: object + BuildSearchIndexResponse: + properties: + repositories_indexed: + title: Repositories Indexed + type: integer + tools_indexed: + title: Tools Indexed + type: integer + required: + - repositories_indexed + - tools_indexed + title: BuildSearchIndexResponse + type: object + Category: + properties: + deleted: + title: Deleted + type: boolean + description: + title: Description + type: string + id: + title: Id + type: string + name: + title: Name + type: string + repositories: + title: Repositories + type: integer + required: + - id + - name + - description + - deleted + - repositories + title: Category + type: object + Checksum: + properties: + checksum: + description: 'The hex-string encoded checksum for the data. ' + title: Checksum + type: string + type: + description: 'The digest method used to create the checksum. + + The value (e.g. `sha-256`) SHOULD be listed as `Hash Name String` in the + https://github.com/ga4gh-discovery/ga4gh-checksum/blob/master/hash-alg.csv[GA4GH + Checksum Hash Algorithm Registry]. + + Other values MAY be used, as long as implementers are aware of the issues + discussed in https://tools.ietf.org/html/rfc6920#section-9.4[RFC6920]. + + GA4GH may provide more explicit guidance for use of non-IANA-registered + algorithms in the future.' + title: Type + type: string + required: + - checksum + - type + title: Checksum + type: object + CreateCategoryRequest: + properties: + description: + anyOf: + - type: string + - type: 'null' + title: Description + name: + title: Name + type: string + required: + - name + title: CreateCategoryRequest + type: object + CreateRepositoryRequest: + properties: + category_ids[]: + anyOf: + - items: + type: string + type: array + - type: string + - type: 'null' + title: Category IDs + description: + anyOf: + - type: string + - type: 'null' + title: Description + homepage_url: + anyOf: + - type: string + - type: 'null' + title: Homepage Url + name: + title: Name + type: string + remote_repository_url: + anyOf: + - type: string + - type: 'null' + title: Remote Repository Url + synopsis: + title: Synopsis + type: string + type: + default: unrestricted + enum: + - repository_suite_definition + - tool_dependency_definition + - unrestricted + title: Type + type: string + required: + - name + - synopsis + - category_ids[] + title: CreateRepositoryRequest + type: object + CreateUserRequest: + properties: + email: + title: Email + type: string + password: + title: Password + type: string + username: + title: Username + type: string + required: + - username + - email + - password + title: CreateUserRequest + type: object + DescriptorType: + enum: + - CWL + - WDL + - NFL + - GALAXY + - SMK + title: DescriptorType + type: string + DescriptorTypeVersion: + title: DescriptorTypeVersion + type: string + DetailedRepository: + properties: + create_time: + title: Create Time + type: string + deleted: + title: Deleted + type: boolean + deprecated: + title: Deprecated + type: boolean + description: + title: Description + type: string + homepage_url: + anyOf: + - type: string + - type: 'null' + title: Homepage Url + id: + title: Id + type: string + long_description: + anyOf: + - type: string + - type: 'null' + title: Long Description + name: + title: Name + type: string + owner: + title: Owner + type: string + private: + title: Private + type: boolean + remote_repository_url: + anyOf: + - type: string + - type: 'null' + title: Remote Repository Url + times_downloaded: + title: Times Downloaded + type: integer + type: + title: Type + type: string + update_time: + title: Update Time + type: string + user_id: + title: User Id + type: string + required: + - id + - name + - owner + - type + - description + - user_id + - private + - deleted + - times_downloaded + - deprecated + - create_time + - update_time + - long_description + title: DetailedRepository + type: object + FailedRepositoryUpdateMessage: + properties: + err_msg: + title: Err Msg + type: string + required: + - err_msg + title: FailedRepositoryUpdateMessage + type: object + HTTPValidationError: + properties: + detail: + items: + $ref: '#/components/schemas/ValidationError' + title: Detail + type: array + title: HTTPValidationError + type: object + ImageData: + properties: + checksum: + anyOf: + - items: + $ref: '#/components/schemas/Checksum' + type: array + - type: 'null' + description: A production (immutable) tool version is required to have a + hashcode. Not required otherwise, but might be useful to detect changes. This + exposes the hashcode for specific image versions to verify that the container + version pulled is actually the version that was indexed by the registry. + examples: + - checksum: 77af4d6b9913e693e8d0b4b294fa62ade6054e6b2f1ffb617ac955dd63fb0182 + type: sha256 + title: Checksum + image_name: + anyOf: + - type: string + - type: 'null' + description: Used in conjunction with a registry_url if provided to locate + images. + examples: + - quay.io/seqware/seqware_full/1.1 + - ubuntu:latest + title: Image Name + image_type: + anyOf: + - $ref: '#/components/schemas/ImageType' + - type: 'null' + registry_host: + anyOf: + - type: string + - type: 'null' + description: A docker registry or a URL to a Singularity registry. Used + along with image_name to locate a specific image. + examples: + - registry.hub.docker.com + title: Registry Host + size: + anyOf: + - type: integer + - type: 'null' + description: Size of the container in bytes. + title: Size + updated: + anyOf: + - type: string + - type: 'null' + description: Last time the container was updated. + title: Updated + title: ImageData + type: object + ImageType: + enum: + - Docker + - Singularity + - Conda + title: ImageType + type: string + InstallInfo: + properties: + metadata_info: + anyOf: + - $ref: '#/components/schemas/RepositoryMetadataInstallInfo' + - type: 'null' + repo_info: + anyOf: + - $ref: '#/components/schemas/RepositoryExtraInstallInfo' + - type: 'null' + title: InstallInfo + type: object + Organization: + properties: + name: + description: Name of the organization responsible for the service + examples: + - My organization + title: Name + type: string + url: + description: URL of the website of the organization (RFC 3986 format) + examples: + - https://example.com + format: uri + minLength: 1 + title: Url + type: string + required: + - name + - url + title: Organization + type: object + RepositoriesByCategory: + properties: + description: + title: Description + type: string + id: + title: Id + type: string + name: + title: Name + type: string + repositories: + items: + $ref: '#/components/schemas/Repository' + title: Repositories + type: array + repository_count: + title: Repository Count + type: integer + required: + - id + - name + - description + - repository_count + - repositories + title: RepositoriesByCategory + type: object + Repository: + properties: + create_time: + title: Create Time + type: string + deleted: + title: Deleted + type: boolean + deprecated: + title: Deprecated + type: boolean + description: + title: Description + type: string + homepage_url: + anyOf: + - type: string + - type: 'null' + title: Homepage Url + id: + title: Id + type: string + name: + title: Name + type: string + owner: + title: Owner + type: string + private: + title: Private + type: boolean + remote_repository_url: + anyOf: + - type: string + - type: 'null' + title: Remote Repository Url + times_downloaded: + title: Times Downloaded + type: integer + type: + title: Type + type: string + update_time: + title: Update Time + type: string + user_id: + title: User Id + type: string + required: + - id + - name + - owner + - type + - description + - user_id + - private + - deleted + - times_downloaded + - deprecated + - create_time + - update_time + title: Repository + type: object + RepositoryDependency: + properties: + changeset_revision: + title: Changeset Revision + type: string + downloadable: + title: Downloadable + type: boolean + has_repository_dependencies: + title: Has Repository Dependencies + type: boolean + id: + title: Id + type: string + includes_datatypes: + anyOf: + - type: boolean + - type: 'null' + title: Includes Datatypes + includes_tool_dependencies: + anyOf: + - type: boolean + - type: 'null' + title: Includes Tool Dependencies + includes_tools: + title: Includes Tools + type: boolean + includes_tools_for_display_in_tool_panel: + title: Includes Tools For Display In Tool Panel + type: boolean + includes_workflows: + anyOf: + - type: boolean + - type: 'null' + title: Includes Workflows + invalid_tools: + items: + type: string + title: Invalid Tools + type: array + malicious: + title: Malicious + type: boolean + missing_test_components: + title: Missing Test Components + type: boolean + numeric_revision: + title: Numeric Revision + type: integer + repository: + $ref: '#/components/schemas/Repository' + repository_dependencies: + items: + $ref: '#/components/schemas/RepositoryDependency' + title: Repository Dependencies + type: array + repository_id: + title: Repository Id + type: string + tools: + anyOf: + - items: + $ref: '#/components/schemas/RepositoryTool' + type: array + - type: 'null' + title: Tools + required: + - id + - repository + - repository_dependencies + - invalid_tools + - repository_id + - numeric_revision + - changeset_revision + - malicious + - downloadable + - missing_test_components + - has_repository_dependencies + - includes_tools + - includes_tools_for_display_in_tool_panel + title: RepositoryDependency + type: object + RepositoryExtraInstallInfo: + properties: + changeset_revision: + title: Changeset Revision + type: string + ctx_rev: + title: Ctx Rev + type: string + description: + title: Description + type: string + name: + title: Name + type: string + repository_clone_url: + title: Repository Clone Url + type: string + repository_dependencies: + anyOf: + - type: object + - type: 'null' + title: Repository Dependencies + repository_owner: + title: Repository Owner + type: string + required: + - name + - description + - repository_clone_url + - changeset_revision + - ctx_rev + - repository_owner + title: RepositoryExtraInstallInfo + type: object + RepositoryMetadata: + additionalProperties: + $ref: '#/components/schemas/RepositoryRevisionMetadata' + title: RepositoryMetadata + type: object + RepositoryMetadataInstallInfo: + properties: + changeset_revision: + title: Changeset Revision + type: string + downloadable: + title: Downloadable + type: boolean + has_repository_dependencies: + title: Has Repository Dependencies + type: boolean + id: + title: Id + type: string + includes_tools: + title: Includes Tools + type: boolean + includes_tools_for_display_in_tool_panel: + title: Includes Tools For Display In Tool Panel + type: boolean + malicious: + title: Malicious + type: boolean + repository_id: + title: Repository Id + type: string + url: + title: Url + type: string + valid_tools: + items: + $ref: '#/components/schemas/ValidTool' + title: Valid Tools + type: array + required: + - id + - changeset_revision + - downloadable + - has_repository_dependencies + - includes_tools + - includes_tools_for_display_in_tool_panel + - malicious + - repository_id + - url + - valid_tools + title: RepositoryMetadataInstallInfo + type: object + RepositoryPermissions: + properties: + allow_push: + items: + type: string + title: Allow Push + type: array + can_manage: + title: Can Manage + type: boolean + can_push: + title: Can Push + type: boolean + required: + - allow_push + - can_manage + - can_push + title: RepositoryPermissions + type: object + RepositoryRevisionMetadata: + properties: + changeset_revision: + title: Changeset Revision + type: string + downloadable: + title: Downloadable + type: boolean + has_repository_dependencies: + title: Has Repository Dependencies + type: boolean + id: + title: Id + type: string + includes_datatypes: + anyOf: + - type: boolean + - type: 'null' + title: Includes Datatypes + includes_tool_dependencies: + anyOf: + - type: boolean + - type: 'null' + title: Includes Tool Dependencies + includes_tools: + title: Includes Tools + type: boolean + includes_tools_for_display_in_tool_panel: + title: Includes Tools For Display In Tool Panel + type: boolean + includes_workflows: + anyOf: + - type: boolean + - type: 'null' + title: Includes Workflows + invalid_tools: + items: + type: string + title: Invalid Tools + type: array + malicious: + title: Malicious + type: boolean + missing_test_components: + title: Missing Test Components + type: boolean + numeric_revision: + title: Numeric Revision + type: integer + repository: + $ref: '#/components/schemas/Repository' + repository_dependencies: + items: + $ref: '#/components/schemas/RepositoryDependency' + title: Repository Dependencies + type: array + repository_id: + title: Repository Id + type: string + tools: + anyOf: + - items: + $ref: '#/components/schemas/RepositoryTool' + type: array + - type: 'null' + title: Tools + required: + - id + - repository + - repository_dependencies + - invalid_tools + - repository_id + - numeric_revision + - changeset_revision + - malicious + - downloadable + - missing_test_components + - has_repository_dependencies + - includes_tools + - includes_tools_for_display_in_tool_panel + title: RepositoryRevisionMetadata + type: object + RepositoryRevisionReadmes: + additionalProperties: + type: string + title: RepositoryRevisionReadmes + type: object + RepositorySearchHit: + properties: + repository: + $ref: '#/components/schemas/RepositorySearchResult' + score: + title: Score + type: number + required: + - score + - repository + title: RepositorySearchHit + type: object + RepositorySearchResult: + properties: + approved: + title: Approved + type: boolean + categories: + title: Categories + type: string + description: + title: Description + type: string + full_last_updated: + title: Full Last Updated + type: string + homepage_url: + anyOf: + - type: string + - type: 'null' + title: Homepage Url + id: + title: Id + type: string + last_update: + anyOf: + - type: string + - type: 'null' + title: Last Update + long_description: + anyOf: + - type: string + - type: 'null' + title: Long Description + name: + title: Name + type: string + remote_repository_url: + anyOf: + - type: string + - type: 'null' + title: Remote Repository Url + repo_lineage: + title: Repo Lineage + type: string + repo_owner_username: + title: Repo Owner Username + type: string + times_downloaded: + title: Times Downloaded + type: integer + required: + - id + - name + - repo_owner_username + - description + - full_last_updated + - repo_lineage + - approved + - times_downloaded + - categories + title: RepositorySearchResult + type: object + RepositorySearchResults: + properties: + hits: + items: + $ref: '#/components/schemas/RepositorySearchHit' + title: Hits + type: array + hostname: + title: Hostname + type: string + page: + title: Page + type: string + page_size: + title: Page Size + type: string + total_results: + title: Total Results + type: string + required: + - total_results + - page + - page_size + - hostname + - hits + title: RepositorySearchResults + type: object + RepositoryTool: + properties: + description: + title: Description + type: string + guid: + title: Guid + type: string + id: + title: Id + type: string + name: + title: Name + type: string + requirements: + items: {} + title: Requirements + type: array + tool_config: + title: Tool Config + type: string + tool_type: + title: Tool Type + type: string + version: + title: Version + type: string + required: + - description + - guid + - id + - name + - requirements + - tool_config + - tool_type + - version + title: RepositoryTool + type: object + RepositoryUpdate: + anyOf: + - $ref: '#/components/schemas/ValidRepostiroyUpdateMessage' + - $ref: '#/components/schemas/FailedRepositoryUpdateMessage' + title: RepositoryUpdate + ResetMetadataOnRepositoryResponse: + properties: + repository_status: + items: + type: string + title: Repository Status + type: array + start_time: + title: Start Time + type: string + status: + title: Status + type: string + stop_time: + title: Stop Time + type: string + required: + - status + - repository_status + - start_time + - stop_time + title: ResetMetadataOnRepositoryResponse + type: object + Service: + properties: + contactUrl: + anyOf: + - format: uri + minLength: 1 + type: string + - type: 'null' + description: URL of the contact for the provider of this service, e.g. a + link to a contact form (RFC 3986 format), or an email (RFC 2368 format). + examples: + - mailto:support@example.com + title: Contacturl + createdAt: + anyOf: + - format: date-time + type: string + - type: 'null' + description: Timestamp describing when the service was first deployed and + available (RFC 3339 format) + examples: + - '2019-06-04T12:58:19Z' + title: Createdat + description: + anyOf: + - type: string + - type: 'null' + description: Description of the service. Should be human readable and provide + information about the service. + examples: + - This service provides... + title: Description + documentationUrl: + anyOf: + - format: uri + minLength: 1 + type: string + - type: 'null' + description: URL of the documentation of this service (RFC 3986 format). + This should help someone learn how to use your service, including any + specifics required to access data, e.g. authentication. + examples: + - https://docs.myservice.example.com + title: Documentationurl + environment: + anyOf: + - type: string + - type: 'null' + description: Environment the service is running in. Use this to distinguish + between production, development and testing/staging deployments. Suggested + values are prod, test, dev, staging. However this is advised and not enforced. + examples: + - test + title: Environment + id: + description: Unique ID of this service. Reverse domain name notation is + recommended, though not required. The identifier should attempt to be + globally unique so it can be used in downstream aggregator services e.g. + Service Registry. + examples: + - org.ga4gh.myservice + title: Id + type: string + name: + description: Name of this service. Should be human readable. + examples: + - My project + title: Name + type: string + organization: + allOf: + - $ref: '#/components/schemas/Organization' + description: Organization providing the service + type: + $ref: '#/components/schemas/ServiceType' + updatedAt: + anyOf: + - format: date-time + type: string + - type: 'null' + description: Timestamp describing when the service was last updated (RFC + 3339 format) + examples: + - '2019-06-04T12:58:19Z' + title: Updatedat + version: + description: Version of the service being described. Semantic versioning + is recommended, but other identifiers, such as dates or commit hashes, + are also allowed. The version should be changed whenever the service is + updated. + examples: + - 1.0.0 + title: Version + type: string + required: + - id + - name + - type + - organization + - version + title: Service + type: object + ServiceType: + properties: + artifact: + description: Name of the API or GA4GH specification implemented. Official + GA4GH types should be assigned as part of standards approval process. + Custom artifacts are supported. + examples: + - beacon + title: Artifact + type: string + group: + description: Namespace in reverse domain name format. Use `org.ga4gh` for + implementations compliant with official GA4GH specifications. For services + with custom APIs not standardized by GA4GH, or implementations diverging + from official GA4GH specifications, use a different namespace (e.g. your + organization's reverse domain name). + examples: + - org.ga4gh + title: Group + type: string + version: + description: Version of the API or specification. GA4GH specifications use + semantic versioning. + examples: + - 1.0.0 + title: Version + type: string + required: + - group + - artifact + - version + title: ServiceType + type: object + Tool: + properties: + aliases: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: "Support for this parameter is optional for tool registries\ + \ that support aliases.\nA list of strings that can be used to identify\ + \ this tool which could be straight up URLs. \nThis can be used to expose\ + \ alternative ids (such as GUIDs) for a tool\nfor registries. Can be used\ + \ to match tools across registries." + title: Aliases + checker_url: + anyOf: + - type: string + - type: 'null' + description: Optional url to the checker tool that will exit successfully + if this tool produced the expected result given test data. + title: Checker Url + description: + anyOf: + - type: string + - type: 'null' + description: The description of the tool. + title: Description + has_checker: + anyOf: + - type: boolean + - type: 'null' + description: Whether this tool has a checker tool associated with it. + title: Has Checker + id: + description: A unique identifier of the tool, scoped to this registry. + examples: + - 123456 + title: Id + type: string + meta_version: + anyOf: + - type: string + - type: 'null' + description: The version of this tool in the registry. Iterates when fields + like the description, author, etc. are updated. + title: Meta Version + name: + anyOf: + - type: string + - type: 'null' + description: The name of the tool. + title: Name + organization: + description: The organization that published the image. + title: Organization + type: string + toolclass: + $ref: '#/components/schemas/ToolClass' + url: + description: The URL for this tool in this registry. + examples: + - http://agora.broadinstitute.org/tools/123456 + title: Url + type: string + versions: + description: A list of versions for this tool. + items: + $ref: '#/components/schemas/ToolVersion' + title: Versions + type: array + required: + - url + - id + - organization + - toolclass + - versions + title: Tool + type: object + ToolClass: + properties: + description: + anyOf: + - type: string + - type: 'null' + description: A longer explanation of what this class is and what it can + accomplish. + title: Description + id: + anyOf: + - type: string + - type: 'null' + description: The unique identifier for the class. + title: Id + name: + anyOf: + - type: string + - type: 'null' + description: A short friendly name for the class. + title: Name + title: ToolClass + type: object + ToolVersion: + properties: + author: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: Contact information for the author of this version of the tool + in the registry. (More complex authorship information is handled by the + descriptor). + title: Author + containerfile: + anyOf: + - type: boolean + - type: 'null' + description: Reports if this tool has a containerfile available. (For Docker-based + tools, this would indicate the presence of a Dockerfile) + title: Containerfile + descriptor_type: + anyOf: + - items: + $ref: '#/components/schemas/DescriptorType' + type: array + - type: 'null' + description: The type (or types) of descriptors available. + title: Descriptor Type + descriptor_type_version: + anyOf: + - additionalProperties: + items: + $ref: '#/components/schemas/DescriptorTypeVersion' + type: array + type: object + - type: 'null' + description: A map providing information about the language versions used + in this tool. The keys should be the same values used in the `descriptor_type` + field, and the value should be an array of all the language versions used + for the given `descriptor_type`. Depending on the `descriptor_type` (e.g. + CWL) multiple version values may be used in a single tool. + examples: + - "{\n \"WDL\": [\"1.0\", \"1.0\"],\n \"CWL\": [\"v1.0.2\"],\n \"NFL\"\ + : [\"DSL2\"]\n}\n" + title: Descriptor Type Version + id: + description: An identifier of the version of this tool for this particular + tool registry. + examples: + - v1 + title: Id + type: string + images: + anyOf: + - items: + $ref: '#/components/schemas/ImageData' + type: array + - type: 'null' + description: All known docker images (and versions/hashes) used by this + tool. If the tool has to evaluate any of the docker images strings at + runtime, those ones cannot be reported here. + title: Images + included_apps: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: An array of IDs for the applications that are stored inside + this tool. + examples: + - https://bio.tools/tool/mytum.de/SNAP2/1 + - https://bio.tools/bioexcel_seqqc + title: Included Apps + is_production: + anyOf: + - type: boolean + - type: 'null' + description: This version of a tool is guaranteed to not change over time + (for example, a tool built from a tag in git as opposed to a branch). + A production quality tool is required to have a checksum + title: Is Production + meta_version: + anyOf: + - type: string + - type: 'null' + description: The version of this tool version in the registry. Iterates + when fields like the description, author, etc. are updated. + title: Meta Version + name: + anyOf: + - type: string + - type: 'null' + description: The name of the version. + title: Name + signed: + anyOf: + - type: boolean + - type: 'null' + description: Reports whether this version of the tool has been signed. + title: Signed + url: + description: The URL for this tool version in this registry. + examples: + - http://agora.broadinstitute.org/tools/123456/versions/1 + title: Url + type: string + verified: + anyOf: + - type: boolean + - type: 'null' + description: Reports whether this tool has been verified by a specific organization + or individual. + title: Verified + verified_source: + anyOf: + - items: + type: string + type: array + - type: 'null' + description: Source of metadata that can support a verified tool, such as + an email or URL. + title: Verified Source + required: + - url + - id + title: ToolVersion + type: object + UiChangePasswordRequest: + properties: + current: + title: Current + type: string + password: + title: Password + type: string + required: + - current + - password + title: UiChangePasswordRequest + type: object + UiLoginRequest: + properties: + login: + title: Login + type: string + password: + title: Password + type: string + session_csrf_token: + title: Session Csrf Token + type: string + required: + - session_csrf_token + - login + - password + title: UiLoginRequest + type: object + UiLoginResponse: + properties: {} + title: UiLoginResponse + type: object + UiLogoutRequest: + properties: + logout_all: + default: false + title: Logout All + type: boolean + session_csrf_token: + title: Session Csrf Token + type: string + required: + - session_csrf_token + title: UiLogoutRequest + type: object + UiLogoutResponse: + properties: {} + title: UiLogoutResponse + type: object + UiRegisterRequest: + properties: + bear_field: + title: Bear Field + type: string + email: + title: Email + type: string + password: + title: Password + type: string + username: + title: Username + type: string + required: + - email + - username + - password + - bear_field + title: UiRegisterRequest + type: object + UiRegisterResponse: + properties: + activation_error: + default: false + title: Activation Error + type: boolean + activation_sent: + default: false + title: Activation Sent + type: boolean + contact_email: + anyOf: + - type: string + - type: 'null' + title: Contact Email + email: + title: Email + type: string + required: + - email + title: UiRegisterResponse + type: object + UserV2: + properties: + id: + title: Id + type: string + is_admin: + title: Is Admin + type: boolean + username: + title: Username + type: string + required: + - id + - username + - is_admin + title: UserV2 + type: object + ValidRepostiroyUpdateMessage: + properties: + message: + title: Message + type: string + required: + - message + title: ValidRepostiroyUpdateMessage + type: object + ValidTool: + properties: + add_to_tool_panel: + title: Add To Tool Panel + type: boolean + description: + title: Description + type: string + guid: + title: Guid + type: string + id: + title: Id + type: string + name: + title: Name + type: string + requirements: + items: {} + title: Requirements + type: array + tests: + items: {} + title: Tests + type: array + tool_config: + title: Tool Config + type: string + tool_type: + title: Tool Type + type: string + version: + title: Version + type: string + version_string_cmd: + anyOf: + - type: string + - type: 'null' + title: Version String Cmd + required: + - add_to_tool_panel + - description + - guid + - id + - name + - requirements + - tests + - tool_config + - tool_type + - version + title: ValidTool + type: object + ValidationError: + properties: + loc: + items: + anyOf: + - type: string + - type: integer + title: Location + type: array + msg: + title: Message + type: string + type: + title: Error Type + type: string + required: + - loc + - msg + - type + title: ValidationError + type: object + Version: + properties: + api_version: + default: v1 + title: Api Version + type: string + version: + title: Version + type: string + version_major: + title: Version Major + type: string + required: + - version_major + - version + title: Version + type: object + securitySchemes: + APIKeyCookie: + in: cookie + name: galaxycommunitysession + type: apiKey + APIKeyHeader: + in: header + name: x-api-key + type: apiKey + APIKeyQuery: + in: query + name: key + type: apiKey +info: + description: This API allows you to manage the Tool Shed repositories. + license: + name: MIT + url: https://github.com/galaxyproject/galaxy/blob/dev/LICENSE.txt + title: Galaxy Tool Shed API + version: 0.1.0 +openapi: 3.1.0 +paths: + /api/authenticate/baseauth: + get: + operationId: authenticate__baseauth + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/APIKeyResponse' + description: Successful Response + summary: Returns returns an API key for authenticated user based on BaseAuth + headers. + tags: + - authenticate + - authenticate + /api/categories: + get: + description: index category + operationId: categories__index + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/Category' + title: Response Categories Index + type: array + description: Successful Response + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Index + tags: + - categories + - categories + post: + description: create a category + operationId: categories__create + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/CreateCategoryRequest' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/Category' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Create + tags: + - categories + - categories + /api/categories/{encoded_category_id}: + get: + description: show category + operationId: categories__show + parameters: + - description: The encoded database identifier of the category. + in: path + name: encoded_category_id + required: true + schema: + description: The encoded database identifier of the category. + title: Category ID + type: string + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/Category' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + summary: Show + tags: + - categories + - categories + /api/categories/{encoded_category_id}/repositories: + get: + description: display repositories by category + operationId: categories__repositories + parameters: + - description: The encoded database identifier of the category. + in: path + name: encoded_category_id + required: true + schema: + description: The encoded database identifier of the category. + title: Category ID + type: string + - in: query + name: installable + required: false + schema: + default: false + title: Installable? + type: boolean + - in: query + name: sort_key + required: false + schema: + default: name + title: Sort Key + type: string + - in: query + name: sort_order + required: false + schema: + default: asc + title: Sort Order + type: string + - in: query + name: page + required: false + schema: + anyOf: + - type: integer + - type: 'null' + title: Page + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/RepositoriesByCategory' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Repositories + tags: + - categories + - categories + /api/ga4gh/trs/v2/service-info: + get: + operationId: tools_trs_service_info + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/Service' + description: Successful Response + summary: Service Info + tags: + - tools + - tools + /api/ga4gh/trs/v2/toolClasses: + get: + operationId: tools__trs_tool_classes + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/ToolClass' + title: Response Tools Trs Tool Classes + type: array + description: Successful Response + summary: Tool Classes + tags: + - tools + - tools + /api/ga4gh/trs/v2/tools: + get: + operationId: tools__trs_index + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + summary: Trs Index + tags: + - tools + - tools + /api/ga4gh/trs/v2/tools/{tool_id}: + get: + operationId: tools__trs_get + parameters: + - description: See also https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs-tool-and-trs-tool-version-ids + in: path + name: tool_id + required: true + schema: + description: See also https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs-tool-and-trs-tool-version-ids + title: GA4GH TRS Tool ID + type: string + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/Tool' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Trs Get + tags: + - tools + - tools + /api/ga4gh/trs/v2/tools/{tool_id}/versions: + get: + operationId: tools__trs_get_versions + parameters: + - description: See also https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs-tool-and-trs-tool-version-ids + in: path + name: tool_id + required: true + schema: + description: See also https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs-tool-and-trs-tool-version-ids + title: GA4GH TRS Tool ID + type: string + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/ToolVersion' + title: Response Tools Trs Get Versions + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Trs Get Versions + tags: + - tools + - tools + /api/repositories: + get: + description: Get a list of repositories or perform a search. + operationId: repositories__index + parameters: + - in: query + name: q + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Search Query + - in: query + name: page + required: false + schema: + anyOf: + - type: integer + - type: 'null' + default: 1 + title: Page + - in: query + name: page_size + required: false + schema: + anyOf: + - type: integer + - type: 'null' + default: 10 + title: Page Size + - in: query + name: deleted + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: false + title: Deleted? + - in: query + name: owner + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Owner + - in: query + name: name + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Name + responses: + '200': + content: + application/json: + schema: + anyOf: + - $ref: '#/components/schemas/RepositorySearchResults' + - items: + $ref: '#/components/schemas/Repository' + type: array + title: Response Repositories Index + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Index + tags: + - repositories + - repositories + post: + description: create a new repository + operationId: repositories__create + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/CreateRepositoryRequest' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/Repository' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Create + tags: + - repositories + - repositories + /api/repositories/get_ordered_installable_revisions: + get: + description: Get an ordered list of the repository changeset revisions that + are installable + operationId: repositories__get_ordered_installable_revisions + parameters: + - in: query + name: owner + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Owner + - in: query + name: name + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Name + - in: query + name: tsr_id + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: TSR ID + responses: + '200': + content: + application/json: + schema: + items: + type: string + title: Response Repositories Get Ordered Installable Revisions + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + summary: Get Ordered Installable Revisions + tags: + - repositories + - repositories + /api/repositories/get_repository_revision_install_info: + get: + description: Get information used by the install client to install this repository. + operationId: repositories__legacy_install_info + parameters: + - description: Name of the target repository. + in: query + name: name + required: true + schema: + description: Name of the target repository. + title: Name + type: string + - description: Owner of the target repository. + in: query + name: owner + required: true + schema: + description: Owner of the target repository. + title: owner + type: string + - description: Changeset of the target repository. + in: query + name: changeset_revision + required: true + schema: + description: Changeset of the target repository. + title: changeset + type: string + responses: + '200': + content: + application/json: + schema: + items: {} + title: Response Repositories Legacy Install Info + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Legacy Install Info + tags: + - repositories + - repositories + /api/repositories/install_info: + get: + description: Get information used by the install client to install this repository. + operationId: repositories__install_info + parameters: + - description: Name of the target repository. + in: query + name: name + required: true + schema: + description: Name of the target repository. + title: Name + type: string + - description: Owner of the target repository. + in: query + name: owner + required: true + schema: + description: Owner of the target repository. + title: owner + type: string + - description: Changeset of the target repository. + in: query + name: changeset_revision + required: true + schema: + description: Changeset of the target repository. + title: changeset + type: string + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/InstallInfo' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Install Info + tags: + - repositories + - repositories + /api/repositories/reset_metadata_on_repository: + post: + description: reset metadata on a repository + operationId: repositories__reset_legacy + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ResetMetadataOnRepositoryResponse' + description: Successful Response + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Reset Metadata On Repository Legacy + tags: + - repositories + - repositories + /api/repositories/updates: + get: + operationId: repositories__update + parameters: + - in: query + name: owner + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Owner + - in: query + name: name + required: false + schema: + anyOf: + - type: string + - type: 'null' + title: Name + - in: query + name: changeset_revision + required: true + schema: + title: Changeset Revision + type: string + - in: query + name: hexlify + required: false + schema: + anyOf: + - type: boolean + - type: 'null' + default: true + title: Hexlify response + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + summary: Updates + tags: + - repositories + - repositories + /api/repositories/{encoded_repository_id}: + get: + operationId: repositories__show + parameters: + - description: The encoded database identifier of the repository. + in: path + name: encoded_repository_id + required: true + schema: + description: The encoded database identifier of the repository. + title: Repository ID + type: string + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/DetailedRepository' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + summary: Show + tags: + - repositories + - repositories + /api/repositories/{encoded_repository_id}/allow_push: + get: + operationId: repositories__show_allow_push + parameters: + - description: The encoded database identifier of the repository. + in: path + name: encoded_repository_id + required: true + schema: + description: The encoded database identifier of the repository. + title: Repository ID + type: string + responses: + '200': + content: + application/json: + schema: + items: + type: string + title: Response Repositories Show Allow Push + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Show Allow Push + tags: + - repositories + - repositories + /api/repositories/{encoded_repository_id}/allow_push/{username}: + delete: + operationId: repositories__remove_allow_push + parameters: + - description: The encoded database identifier of the repository. + in: path + name: encoded_repository_id + required: true + schema: + description: The encoded database identifier of the repository. + title: Repository ID + type: string + - description: The target username. + in: path + name: username + required: true + schema: + description: The target username. + title: Username + type: string + responses: + '200': + content: + application/json: + schema: + items: + type: string + title: Response Repositories Remove Allow Push + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Remove Allow Push + tags: + - repositories + - repositories + post: + operationId: repositories__add_allow_push + parameters: + - description: The encoded database identifier of the repository. + in: path + name: encoded_repository_id + required: true + schema: + description: The encoded database identifier of the repository. + title: Repository ID + type: string + - description: The target username. + in: path + name: username + required: true + schema: + description: The target username. + title: Username + type: string + responses: + '200': + content: + application/json: + schema: + items: + type: string + title: Response Repositories Add Allow Push + type: array + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Add Allow Push + tags: + - repositories + - repositories + /api/repositories/{encoded_repository_id}/changeset_revision: + post: + description: upload new revision to the repository + operationId: repositories__create_revision + parameters: + - description: The encoded database identifier of the repository. + in: path + name: encoded_repository_id + required: true + schema: + description: The encoded database identifier of the repository. + title: Repository ID + type: string + - description: Set commit message as a query parameter. + in: query + name: commit_message + required: false + schema: + anyOf: + - type: string + - type: 'null' + description: Set commit message as a query parameter. + title: Commit Message + requestBody: + content: + multipart/form-data: + schema: + allOf: + - $ref: '#/components/schemas/Body_repositories__create_revision' + title: Body + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/RepositoryUpdate' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Create Changeset Revision + tags: + - repositories + - repositories + /api/repositories/{encoded_repository_id}/deprecated: + delete: + operationId: repositories__unset_deprecated + parameters: + - description: The encoded database identifier of the repository. + in: path + name: encoded_repository_id + required: true + schema: + description: The encoded database identifier of the repository. + title: Repository ID + type: string + responses: + '204': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Unset Deprecated + tags: + - repositories + - repositories + put: + operationId: repositories__set_deprecated + parameters: + - description: The encoded database identifier of the repository. + in: path + name: encoded_repository_id + required: true + schema: + description: The encoded database identifier of the repository. + title: Repository ID + type: string + responses: + '204': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Set Deprecated + tags: + - repositories + - repositories + /api/repositories/{encoded_repository_id}/metadata: + get: + description: Get information about repository metadata + operationId: repositories__metadata + parameters: + - description: The encoded database identifier of the repository. + in: path + name: encoded_repository_id + required: true + schema: + description: The encoded database identifier of the repository. + title: Repository ID + type: string + - description: Include only downloadable repositories. + in: query + name: downloadable_only + required: false + schema: + default: true + description: Include only downloadable repositories. + title: downloadable_only + type: boolean + responses: + '200': + content: + application/json: + schema: + title: Response Repositories Metadata + type: object + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + summary: Metadata + tags: + - repositories + - repositories + /api/repositories/{encoded_repository_id}/permissions: + get: + operationId: repositories__permissions + parameters: + - description: The encoded database identifier of the repository. + in: path + name: encoded_repository_id + required: true + schema: + description: The encoded database identifier of the repository. + title: Repository ID + type: string + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/RepositoryPermissions' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Permissions + tags: + - repositories + - repositories + /api/repositories/{encoded_repository_id}/reset_metadata: + post: + description: reset metadata on a repository + operationId: repositories__reset + parameters: + - description: The encoded database identifier of the repository. + in: path + name: encoded_repository_id + required: true + schema: + description: The encoded database identifier of the repository. + title: Repository ID + type: string + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/ResetMetadataOnRepositoryResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Reset Metadata On Repository + tags: + - repositories + - repositories + /api/repositories/{encoded_repository_id}/revisions/{changeset_revision}/malicious: + delete: + operationId: repositories__unset_malicious + parameters: + - description: The encoded database identifier of the repository. + in: path + name: encoded_repository_id + required: true + schema: + description: The encoded database identifier of the repository. + title: Repository ID + type: string + - description: The changeset revision corresponding to the target revision of + the target repository. + in: path + name: changeset_revision + required: true + schema: + description: The changeset revision corresponding to the target revision + of the target repository. + title: Change Revision + type: string + responses: + '204': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Unset Malicious + tags: + - repositories + - repositories + put: + operationId: repositories__set_malicious + parameters: + - description: The encoded database identifier of the repository. + in: path + name: encoded_repository_id + required: true + schema: + description: The encoded database identifier of the repository. + title: Repository ID + type: string + - description: The changeset revision corresponding to the target revision of + the target repository. + in: path + name: changeset_revision + required: true + schema: + description: The changeset revision corresponding to the target revision + of the target repository. + title: Change Revision + type: string + responses: + '204': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Set Malicious + tags: + - repositories + - repositories + /api/repositories/{encoded_repository_id}/revisions/{changeset_revision}/readmes: + get: + description: fetch readmes for repository revision + operationId: repositories__readmes + parameters: + - description: The encoded database identifier of the repository. + in: path + name: encoded_repository_id + required: true + schema: + description: The encoded database identifier of the repository. + title: Repository ID + type: string + - description: The changeset revision corresponding to the target revision of + the target repository. + in: path + name: changeset_revision + required: true + schema: + description: The changeset revision corresponding to the target revision + of the target repository. + title: Change Revision + type: string + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/RepositoryRevisionReadmes' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + summary: Get Readmes + tags: + - repositories + - repositories + /api/tools: + get: + operationId: tools__index + parameters: + - in: query + name: q + required: true + schema: + title: Search Query + type: string + - in: query + name: page + required: false + schema: + default: 1 + title: Page + type: integer + - in: query + name: page_size + required: false + schema: + default: 10 + title: Page Size + type: integer + responses: + '200': + content: + application/json: + schema: {} + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Index + tags: + - tools + - tools + /api/tools/build_search_index: + put: + description: 'Not part of the stable API, just something to simplify + + bootstrapping tool sheds, scripting, testing, etc...' + operationId: tools__build_search_index + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/BuildSearchIndexResponse' + description: Successful Response + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Build Search Index + tags: + - tools + - tools + /api/users: + get: + description: index users + operationId: users__index + responses: + '200': + content: + application/json: + schema: + items: + $ref: '#/components/schemas/UserV2' + title: Response Users Index + type: array + description: Successful Response + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Index + tags: + - users + - users + post: + description: create a user + operationId: users__create + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/CreateUserRequest' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/UserV2' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Create + tags: + - users + - users + /api/users/current: + get: + description: show current user + operationId: users__current + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/UserV2' + description: Successful Response + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Current + tags: + - users + - users + /api/users/{encoded_user_id}: + get: + description: show a user + operationId: users__show + parameters: + - description: The encoded database identifier of the user. + in: path + name: encoded_user_id + required: true + schema: + description: The encoded database identifier of the user. + title: User ID + type: string + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/UserV2' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Show + tags: + - users + - users + /api/users/{encoded_user_id}/api_key: + delete: + operationId: users__delete_api_key + parameters: + - description: The encoded database identifier of the user. + in: path + name: encoded_user_id + required: true + schema: + description: The encoded database identifier of the user. + title: User ID + type: string + responses: + '204': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Delete the current API key of the user + tags: + - users + - users + get: + operationId: users__get_or_create_api_key + parameters: + - description: The encoded database identifier of the user. + in: path + name: encoded_user_id + required: true + schema: + description: The encoded database identifier of the user. + title: User ID + type: string + responses: + '200': + content: + application/json: + schema: + title: Response Users Get Or Create Api Key + type: string + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Return the user's API key + tags: + - users + - users + post: + operationId: users__create_api_key + parameters: + - description: The encoded database identifier of the user. + in: path + name: encoded_user_id + required: true + schema: + description: The encoded database identifier of the user. + title: User ID + type: string + responses: + '200': + content: + application/json: + schema: + title: Response Users Create Api Key + type: string + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Creates a new API key for the user + tags: + - users + - users + /api/version: + get: + operationId: configuration__version + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/Version' + description: Successful Response + summary: Version + tags: + - configuration + - configuration + /api_internal/change_password: + put: + description: reset a user + operationId: users__internal_change_password + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/UiChangePasswordRequest' + required: true + responses: + '204': + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Change Password + tags: + - users + - users + /api_internal/login: + put: + description: login to web UI + operationId: users__internal_login + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/UiLoginRequest' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/UiLoginResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Internal Login + tags: + - users + - users + /api_internal/logout: + put: + description: logout of web UI + operationId: users__internal_logout + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/UiLogoutRequest' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/UiLogoutResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Internal Logout + tags: + - users + - users + /api_internal/register: + post: + description: register a user + operationId: users__internal_register + requestBody: + content: + application/json: + schema: + $ref: '#/components/schemas/UiRegisterRequest' + required: true + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/UiRegisterResponse' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + security: + - APIKeyCookie: [] + - APIKeyQuery: [] + - APIKeyHeader: [] + summary: Register + tags: + - users + - users + /api_internal/repositories/{encoded_repository_id}/metadata: + get: + description: Get information about repository metadata + operationId: repositories__internal_metadata + parameters: + - description: The encoded database identifier of the repository. + in: path + name: encoded_repository_id + required: true + schema: + description: The encoded database identifier of the repository. + title: Repository ID + type: string + - description: Include only downloadable repositories. + in: query + name: downloadable_only + required: false + schema: + default: true + description: Include only downloadable repositories. + title: downloadable_only + type: boolean + responses: + '200': + content: + application/json: + schema: + $ref: '#/components/schemas/RepositoryMetadata' + description: Successful Response + '422': + content: + application/json: + schema: + $ref: '#/components/schemas/HTTPValidationError' + description: Validation Error + summary: Metadata Internal + tags: + - repositories + - repositories From ad1cd342714bd628ddb52f5abb9d82cc8c4ed914 Mon Sep 17 00:00:00 2001 From: Mira Kuntz Date: Wed, 21 Feb 2024 10:01:51 +0100 Subject: [PATCH 5/8] fix wrong arg type --- _schema.yaml | 2 +- lib/galaxy/webapps/galaxy/api/configuration.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/_schema.yaml b/_schema.yaml index f3f8562ef745..694a6f286307 100644 --- a/_schema.yaml +++ b/_schema.yaml @@ -12937,7 +12937,7 @@ paths: schema: description: Decoded id to be encoded title: Decoded id - type: string + type: integer - description: The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. in: header diff --git a/lib/galaxy/webapps/galaxy/api/configuration.py b/lib/galaxy/webapps/galaxy/api/configuration.py index 47e6f43c1fdc..51c23813a007 100644 --- a/lib/galaxy/webapps/galaxy/api/configuration.py +++ b/lib/galaxy/webapps/galaxy/api/configuration.py @@ -115,7 +115,7 @@ def decode_id(self, encoded_id: str = EncodedIdPathParam) -> Dict[str, int]: summary="Encode a given id", response_description="Encoded id", ) - def encode_id(self, decoded_id: str = DecodedIdPathParam) -> Dict[str, str]: + def encode_id(self, decoded_id: int = DecodedIdPathParam) -> Dict[str, str]: """Decode a given id.""" return self.configuration_manager.encode_id(decoded_id) From 2179c317ed8f3ea13bec9c74fe0d7c89823d402d Mon Sep 17 00:00:00 2001 From: Mira <86979912+mira-miracoli@users.noreply.github.com> Date: Wed, 21 Feb 2024 10:19:25 +0100 Subject: [PATCH 6/8] Update lib/galaxy/managers/configuration.py Co-authored-by: Helena --- lib/galaxy/managers/configuration.py | 1 - 1 file changed, 1 deletion(-) diff --git a/lib/galaxy/managers/configuration.py b/lib/galaxy/managers/configuration.py index 513df907bcf0..88b37cf48851 100644 --- a/lib/galaxy/managers/configuration.py +++ b/lib/galaxy/managers/configuration.py @@ -61,7 +61,6 @@ def encode_id( self, decoded_id: int, ) -> Dict[str, str]: - # Handle the special case for library folders encoded_id = unicodify(self._app.security.encode_id(decoded_id)) return {"encoded_id": encoded_id} From 7f642d8496d4646609e3a4e30a59814195e91e89 Mon Sep 17 00:00:00 2001 From: Mira <86979912+mira-miracoli@users.noreply.github.com> Date: Wed, 21 Feb 2024 10:41:47 +0100 Subject: [PATCH 7/8] remove redundant unicodify MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: David López <46503462+davelopez@users.noreply.github.com> --- lib/galaxy/managers/configuration.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/managers/configuration.py b/lib/galaxy/managers/configuration.py index 88b37cf48851..d15eb0332b6a 100644 --- a/lib/galaxy/managers/configuration.py +++ b/lib/galaxy/managers/configuration.py @@ -61,7 +61,7 @@ def encode_id( self, decoded_id: int, ) -> Dict[str, str]: - encoded_id = unicodify(self._app.security.encode_id(decoded_id)) + encoded_id = self._app.security.encode_id(decoded_id) return {"encoded_id": encoded_id} def tool_lineages(self) -> List[Dict[str, Dict]]: From 8f788d94d690e5d263587b42bcbfa71c2649a658 Mon Sep 17 00:00:00 2001 From: Mira Kuntz Date: Wed, 21 Feb 2024 10:54:15 +0100 Subject: [PATCH 8/8] remove import unicodify --- _schema.yaml | 37009 ------------------------- _shed_schema.yaml | 3010 -- client/src/api/schema/schema.ts | 39 + lib/galaxy/managers/configuration.py | 1 - 4 files changed, 39 insertions(+), 40020 deletions(-) delete mode 100644 _schema.yaml delete mode 100644 _shed_schema.yaml diff --git a/_schema.yaml b/_schema.yaml deleted file mode 100644 index 694a6f286307..000000000000 --- a/_schema.yaml +++ /dev/null @@ -1,37009 +0,0 @@ -components: - schemas: - APIKeyModel: - properties: - create_time: - description: The time and date this API key was created. - format: date-time - title: Create Time - type: string - key: - description: API key to interact with the Galaxy API - title: Key - type: string - required: - - key - - create_time - title: APIKeyModel - type: object - APIKeyResponse: - properties: - api_key: - title: Api Key - type: string - required: - - api_key - title: APIKeyResponse - type: object - AccessMethod: - properties: - access_id: - anyOf: - - type: string - - type: 'null' - description: An arbitrary string to be passed to the `/access` method to - get an `AccessURL`. This string must be unique within the scope of a single - object. Note that at least one of `access_url` and `access_id` must be - provided. - title: Access Id - access_url: - anyOf: - - $ref: '#/components/schemas/AccessURL' - - type: 'null' - authorizations: - anyOf: - - $ref: '#/components/schemas/Authorizations' - - type: 'null' - region: - anyOf: - - type: string - - type: 'null' - description: Name of the region in the cloud service provider that the object - belongs to. - examples: - - us-east-1 - title: Region - type: - allOf: - - $ref: '#/components/schemas/AccessMethodType' - description: Type of the access method. - required: - - type - title: AccessMethod - type: object - AccessMethodType: - enum: - - s3 - - gs - - ftp - - gsiftp - - globus - - htsget - - https - - file - title: AccessMethodType - type: string - AccessURL: - properties: - headers: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: An optional list of headers to include in the HTTP request - to `url`. These headers can be used to provide auth tokens required to - fetch the object bytes. - examples: - - 'Authorization: Basic Z2E0Z2g6ZHJz' - title: Headers - url: - description: A fully resolvable URL that can be used to fetch the actual - object bytes. - title: Url - type: string - required: - - url - title: AccessURL - type: object - ActionLink: - description: An action link to be displayed in the notification as a button. - properties: - action_name: - description: The name of the action, will be the button title. - title: Action name - type: string - link: - description: The link to be opened when the button is clicked. - title: Link - type: string - required: - - action_name - - link - title: ActionLink - type: object - AnonUserModel: - properties: - nice_total_disk_usage: - description: Size of all non-purged, unique datasets of the user in a nice - format. - title: Nice total disc usage - type: string - quota_percent: - description: Percentage of the storage quota applicable to the user. - title: Quota percent - total_disk_usage: - description: Size of all non-purged, unique datasets of the user in bytes. - title: Total disk usage - type: number - required: - - total_disk_usage - - nice_total_disk_usage - title: AnonUserModel - type: object - ArchiveHistoryRequestPayload: - properties: - archive_export_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: The encoded ID of the export record to associate with this - history archival.This is used to be able to recover the history from the - export record. - title: Export Record ID - purge_history: - default: false - description: Whether to purge the history after archiving it. It requires - an `archive_export_id` to be set. - title: Purge History - type: boolean - title: ArchiveHistoryRequestPayload - type: object - ArchivedHistoryDetailed: - additionalProperties: true - properties: - annotation: - anyOf: - - type: string - - type: 'null' - description: An annotation to provide details or to help understand the - purpose and usage of this item. - title: Annotation - archived: - description: Whether this item has been archived and is no longer active. - title: Archived - type: boolean - contents_url: - description: The relative URL to access the contents of this History. - title: Contents URL - type: string - count: - description: The number of items in the history. - title: Count - type: integer - create_time: - description: The time and date this item was created. - format: date-time - title: Create Time - type: string - deleted: - description: Whether this item is marked as deleted. - title: Deleted - type: boolean - export_record_data: - anyOf: - - $ref: '#/components/schemas/ExportRecordData' - - type: 'null' - description: The export record data associated with this archived history. - Used to recover the history. - title: Export Record Data - genome_build: - anyOf: - - type: string - - type: 'null' - default: '?' - description: TODO - title: Genome Build - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: History ID - type: string - importable: - description: Whether this History can be imported by other users with a - shared link. - title: Importable - type: boolean - model_class: - const: History - description: The name of the database model class. - title: Model class - type: string - name: - description: The name of the history. - title: Name - type: string - preferred_object_store_id: - anyOf: - - type: string - - type: 'null' - description: The ID of the object store that should be used to store new - datasets in this history. - title: Preferred Object Store ID - published: - description: Whether this resource is currently publicly available to all - users. - title: Published - type: boolean - purged: - description: Whether this item has been permanently removed. - title: Purged - type: boolean - size: - description: The total size of the contents of this history in bytes. - title: Size - type: integer - slug: - anyOf: - - type: string - - type: 'null' - description: Part of the URL to uniquely identify this History by link in - a readable way. - title: Slug - state: - allOf: - - $ref: '#/components/schemas/DatasetState' - description: The current state of the History based on the states of the - datasets it contains. - title: State - state_details: - additionalProperties: - type: integer - description: A dictionary keyed to possible dataset states and valued with - the number of datasets in this history that have those states. - title: State Counts - type: object - state_ids: - additionalProperties: - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - type: array - description: A dictionary keyed to possible dataset states and valued with - lists containing the ids of each HDA in that state. - title: State IDs - type: object - tags: - $ref: '#/components/schemas/TagCollection' - update_time: - description: The last time and date this item was updated. - format: date-time - title: Update Time - type: string - url: - deprecated: true - description: The relative URL to access this item. - title: URL - type: string - user_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: The encoded ID of the user that owns this History. - title: User ID - username: - anyOf: - - type: string - - type: 'null' - description: Owner of the history - title: Username - username_and_slug: - anyOf: - - type: string - - type: 'null' - description: The relative URL in the form of /u/{username}/h/{slug} - title: Username and slug - required: - - model_class - - id - - name - - deleted - - purged - - archived - - url - - published - - count - - annotation - - tags - - update_time - - contents_url - - size - - create_time - - importable - - state - - state_ids - - state_details - title: ArchivedHistoryDetailed - type: object - ArchivedHistorySummary: - additionalProperties: true - properties: - annotation: - anyOf: - - type: string - - type: 'null' - description: An annotation to provide details or to help understand the - purpose and usage of this item. - title: Annotation - archived: - description: Whether this item has been archived and is no longer active. - title: Archived - type: boolean - count: - description: The number of items in the history. - title: Count - type: integer - deleted: - description: Whether this item is marked as deleted. - title: Deleted - type: boolean - export_record_data: - anyOf: - - $ref: '#/components/schemas/ExportRecordData' - - type: 'null' - description: The export record data associated with this archived history. - Used to recover the history. - title: Export Record Data - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: History ID - type: string - model_class: - const: History - description: The name of the database model class. - title: Model class - type: string - name: - description: The name of the history. - title: Name - type: string - preferred_object_store_id: - anyOf: - - type: string - - type: 'null' - description: The ID of the object store that should be used to store new - datasets in this history. - title: Preferred Object Store ID - published: - description: Whether this resource is currently publicly available to all - users. - title: Published - type: boolean - purged: - description: Whether this item has been permanently removed. - title: Purged - type: boolean - tags: - $ref: '#/components/schemas/TagCollection' - update_time: - description: The last time and date this item was updated. - format: date-time - title: Update Time - type: string - url: - deprecated: true - description: The relative URL to access this item. - title: URL - type: string - required: - - model_class - - id - - name - - deleted - - purged - - archived - - url - - published - - count - - annotation - - tags - - update_time - title: ArchivedHistorySummary - type: object - AsyncFile: - properties: - storage_request_id: - format: uuid - title: Storage Request Id - type: string - task: - $ref: '#/components/schemas/AsyncTaskResultSummary' - required: - - storage_request_id - - task - title: AsyncFile - type: object - AsyncTaskResultSummary: - properties: - id: - description: Celery AsyncResult ID for this task - title: ID - type: string - ignored: - description: Indicated whether the Celery AsyncResult will be available - for retrieval - title: Ignored - type: boolean - name: - anyOf: - - type: string - - type: 'null' - title: Name of task being done derived from Celery AsyncResult - queue: - anyOf: - - type: string - - type: 'null' - title: Queue of task being done derived from Celery AsyncResult - required: - - id - - ignored - title: AsyncTaskResultSummary - type: object - Authorizations: - properties: - bearer_auth_issuers: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: If authorizations contain `BearerAuth` this is an optional - list of issuers that may authorize access to this object. The caller must - provide a token from one of these issuers. If this is empty or missing - it assumed the caller knows which token to send via other means. It is - strongly recommended that the caller validate that it is appropriate to - send the requested token to the DRS server to mitigate attacks by malicious - DRS servers requesting credentials they should not have. - title: Bearer Auth Issuers - passport_auth_issuers: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: If authorizations contain `PassportAuth` this is a required - list of visa issuers (as found in a visa's `iss` claim) that may authorize - access to this object. The caller must only provide passports that contain - visas from this list. It is strongly recommended that the caller validate - that it is appropriate to send the requested passport/visa to the DRS - server to mitigate attacks by malicious DRS servers requesting credentials - they should not have. - title: Passport Auth Issuers - supported_types: - anyOf: - - items: - $ref: '#/components/schemas/SupportedType' - type: array - - type: 'null' - description: An Optional list of support authorization types. More than - one can be supported and tried in sequence. Defaults to `None` if empty - or missing. - title: Supported Types - title: Authorizations - type: object - BadgeDict: - properties: - message: - anyOf: - - type: string - - type: 'null' - title: Message - source: - enum: - - admin - - galaxy - title: Source - type: string - type: - anyOf: - - enum: - - faster - - slower - - short_term - - backed_up - - not_backed_up - - more_secure - - less_secure - - more_stable - - less_stable - type: string - - enum: - - cloud - - quota - - no_quota - - restricted - type: string - title: Type - required: - - type - - message - - source - title: BadgeDict - type: object - BasicRoleModel: - properties: - id: - description: Encoded ID of the role - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - name: - description: Name of the role - title: Name - type: string - type: - description: Type or category of the role - title: Type - type: string - required: - - id - - name - - type - title: BasicRoleModel - type: object - Body_create_api_histories_post: - properties: - all_datasets: - default: true - title: All Datasets - archive_file: - title: Archive File - archive_source: - title: Archive Source - archive_type: - default: url - title: Archive Type - history_id: - title: History Id - name: - title: Name - title: Body_create_api_histories_post - type: object - Body_fetch_form_api_tools_fetch_post: - properties: - files: - anyOf: - - items: - format: binary - type: string - type: array - - type: 'null' - title: Files - history_id: - title: History Id - targets: - title: Targets - required: - - history_id - - targets - title: Body_fetch_form_api_tools_fetch_post - type: object - BroadcastNotificationContent: - properties: - action_links: - anyOf: - - items: - $ref: '#/components/schemas/ActionLink' - type: array - - type: 'null' - description: The optional action links (buttons) to be displayed in the - notification. - title: Action links - category: - const: broadcast - default: broadcast - title: Category - message: - description: The message of the notification (supports Markdown). - title: Message - type: string - subject: - description: The subject of the notification. - title: Subject - type: string - required: - - subject - - message - title: BroadcastNotificationContent - type: object - BroadcastNotificationCreateRequest: - description: A notification create request specific for broadcasting. - properties: - category: - const: broadcast - default: broadcast - title: Category - content: - allOf: - - $ref: '#/components/schemas/BroadcastNotificationContent' - description: The content of the broadcast notification. Broadcast notifications - are displayed prominently to all users and can contain action links to - redirect the user to a specific page. - title: Content - expiration_time: - anyOf: - - format: date-time - type: string - - type: 'null' - description: The time when the notification should expire. By default it - will expire after 6 months. Expired notifications will be permanently - deleted. - title: Expiration time - publication_time: - anyOf: - - format: date-time - type: string - - type: 'null' - description: The time when the notification should be published. Notifications - can be created and then scheduled to be published at a later time. - title: Publication time - source: - description: The source of the notification. Represents the agent that created - the notification. E.g. 'galaxy' or 'admin'. - title: Source - type: string - variant: - allOf: - - $ref: '#/components/schemas/NotificationVariant' - description: The variant of the notification. Represents the intent or relevance - of the notification. E.g. 'info' or 'urgent'. - title: Variant - required: - - source - - variant - - content - title: BroadcastNotificationCreateRequest - type: object - BroadcastNotificationListResponse: - description: A list of broadcast notifications. - items: - $ref: '#/components/schemas/BroadcastNotificationResponse' - title: BroadcastNotificationListResponse - type: array - BroadcastNotificationResponse: - description: A notification response specific for broadcasting. - properties: - category: - const: broadcast - default: broadcast - title: Category - content: - $ref: '#/components/schemas/BroadcastNotificationContent' - create_time: - description: The time when the notification was created. - format: date-time - title: Create time - type: string - expiration_time: - anyOf: - - format: date-time - type: string - - type: 'null' - description: The time when the notification will expire. If not set, the - notification will never expire. Expired notifications will be permanently - deleted. - title: Expiration time - id: - description: The encoded ID of the notification. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - publication_time: - description: The time when the notification was published. Notifications - can be created and then published at a later time. - format: date-time - title: Publication time - type: string - source: - description: The source of the notification. Represents the agent that created - the notification. E.g. 'galaxy' or 'admin'. - title: Source - type: string - update_time: - description: The time when the notification was last updated. - format: date-time - title: Update time - type: string - variant: - allOf: - - $ref: '#/components/schemas/NotificationVariant' - description: The variant of the notification. Represents the intent or relevance - of the notification. E.g. 'info' or 'urgent'. - title: Variant - required: - - id - - source - - variant - - create_time - - update_time - - publication_time - - content - title: BroadcastNotificationResponse - type: object - BrowsableFilesSourcePlugin: - additionalProperties: true - properties: - browsable: - const: true - title: Browsable - doc: - description: Documentation or extended description for this plugin. - examples: - - Galaxy's library import directory - title: Documentation - type: string - id: - description: The `FilesSource` plugin identifier - examples: - - _import - title: ID - type: string - label: - description: The display label for this plugin. - examples: - - Library Import Directory - title: Label - type: string - requires_groups: - anyOf: - - type: string - - type: 'null' - description: Only users belonging to the groups specified here can access - this files source. - title: Requires groups - requires_roles: - anyOf: - - type: string - - type: 'null' - description: Only users with the roles specified here can access this files - source. - title: Requires roles - type: - description: The type of the plugin. - examples: - - gximport - title: Type - type: string - uri_root: - description: The URI root used by this type of plugin. - examples: - - gximport:// - title: URI root - type: string - writable: - description: Whether this files source plugin allows write access. - examples: - - false - title: Writeable - type: boolean - required: - - id - - type - - label - - doc - - browsable - - writable - - uri_root - title: BrowsableFilesSourcePlugin - type: object - BulkOperationItemError: - properties: - error: - title: Error - type: string - item: - $ref: '#/components/schemas/EncodedHistoryContentItem' - required: - - item - - error - title: BulkOperationItemError - type: object - ChangeDatatypeOperationParams: - properties: - datatype: - title: Datatype - type: string - type: - const: change_datatype - title: Type - required: - - type - - datatype - title: ChangeDatatypeOperationParams - type: object - ChangeDbkeyOperationParams: - properties: - dbkey: - title: Dbkey - type: string - type: - const: change_dbkey - title: Type - required: - - type - - dbkey - title: ChangeDbkeyOperationParams - type: object - CheckForUpdatesResponse: - properties: - message: - description: Unstructured description of tool shed updates discovered or - failure - title: Message - type: string - status: - description: '''ok'' or ''error''' - enum: - - ok - - error - title: Status - type: string - required: - - status - - message - title: CheckForUpdatesResponse - type: object - Checksum: - properties: - checksum: - description: The hex-string encoded checksum for the data - title: Checksum - type: string - type: - description: 'The digest method used to create the checksum. - - The value (e.g. `sha-256`) SHOULD be listed as `Hash Name String` in the - https://www.iana.org/assignments/named-information/named-information.xhtml#hash-alg[IANA - Named Information Hash Algorithm Registry]. Other values MAY be used, - as long as implementors are aware of the issues discussed in https://tools.ietf.org/html/rfc6920#section-9.4[RFC6920]. - - GA4GH may provide more explicit guidance for use of non-IANA-registered - algorithms in the future. Until then, if implementers do choose such an - algorithm (e.g. because it''s implemented by their storage provider), - they SHOULD use an existing standard `type` value such as `md5`, `etag`, - `crc32c`, `trunc512`, or `sha1`.' - examples: - - sha-256 - title: Type - type: string - required: - - checksum - - type - title: Checksum - type: object - CleanableItemsSummary: - properties: - total_items: - description: The total number of items that could be purged. - title: Total Items - type: integer - total_size: - description: The total size in bytes that can be recovered by purging all - the items. - title: Total Size - type: integer - required: - - total_size - - total_items - title: CleanableItemsSummary - type: object - CleanupStorageItemsRequest: - properties: - item_ids: - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - title: Item Ids - type: array - required: - - item_ids - title: CleanupStorageItemsRequest - type: object - CloudDatasets: - properties: - authz_id: - description: The ID of CloudAuthz to be used for authorizing access to the - resource provider. You may get a list of the defined authorizations via - `/api/cloud/authz`. Also, you can use `/api/cloud/authz/create` to define - a new authorization. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Authentication ID - type: string - bucket: - description: The name of a bucket to which data should be sent (e.g., a - bucket name on AWS S3). - title: Bucket - type: string - dataset_ids: - anyOf: - - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - type: array - - type: 'null' - description: A list of dataset IDs belonging to the specified history that - should be sent to the given bucket. If not provided, Galaxy sends all - the datasets belonging the specified history. - title: Objects - history_id: - description: The ID of history from which the object should be downloaded - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: History ID - type: string - overwrite_existing: - anyOf: - - type: boolean - - type: 'null' - default: false - description: A boolean value. If set to 'True', and an object with same - name of the dataset to be sent already exist in the bucket, Galaxy replaces - the existing object with the dataset to be sent. If set to 'False', Galaxy - appends datetime to the dataset name to prevent overwriting an existing - object. - title: Spaces to tabs - required: - - history_id - - bucket - - authz_id - title: CloudDatasets - type: object - CloudDatasetsResponse: - properties: - bucket_name: - description: The name of bucket to which the listed datasets are queued - to be sent - title: Bucket - type: string - failed_dataset_labels: - description: The datasets for which Galaxy failed to create (and queue) - send job - items: - type: string - title: Failed datasets - type: array - sent_dataset_labels: - description: The datasets for which Galaxy succeeded to create (and queue) - send job - items: - type: string - title: Send datasets - type: array - required: - - sent_dataset_labels - - failed_dataset_labels - - bucket_name - title: CloudDatasetsResponse - type: object - CloudObjects: - properties: - authz_id: - description: The ID of CloudAuthz to be used for authorizing access to the - resource provider. You may get a list of the defined authorizations via - `/api/cloud/authz`. Also, you can use `/api/cloud/authz/create` to define - a new authorization. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Authentication ID - type: string - bucket: - description: The name of a bucket from which data should be fetched from - (e.g., a bucket name on AWS S3). - title: Bucket - type: string - history_id: - description: The ID of history to which the object should be received to. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: History ID - type: string - input_args: - anyOf: - - $ref: '#/components/schemas/InputArguments' - - type: 'null' - description: A summary of the input arguments, which is optional and will - default to {}. - title: Input arguments - objects: - description: A list of the names of objects to be fetched. - items: - type: string - title: Objects - type: array - required: - - history_id - - bucket - - objects - - authz_id - title: CloudObjects - type: object - CollectionElementIdentifier: - properties: - collection_type: - anyOf: - - type: string - - type: 'null' - description: The type of the collection, can be `list`, `paired`, or define - subcollections using `:` as separator like `list:paired` or `list:list`. - title: Collection Type - element_identifiers: - anyOf: - - items: - $ref: '#/components/schemas/CollectionElementIdentifier' - type: array - - type: 'null' - description: List of elements that should be in the new sub-collection. - title: Element Identifiers - id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: The encoded ID of the element. - title: ID - name: - anyOf: - - type: string - - type: 'null' - description: The name of the element. - title: Name - src: - allOf: - - $ref: '#/components/schemas/ColletionSourceType' - description: The source of the element. - title: Source - tags: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: The list of tags associated with the element. - title: Tags - required: - - src - title: CollectionElementIdentifier - type: object - ColletionSourceType: - enum: - - hda - - ldda - - hdca - - new_collection - title: ColletionSourceType - type: string - CompositeDataElement: - additionalProperties: false - properties: - MD5: - anyOf: - - type: string - - type: 'null' - title: Md5 - auto_decompress: - default: false - description: Decompress compressed data before sniffing? - title: Auto Decompress - type: boolean - collection_type: - anyOf: - - type: string - - type: 'null' - title: Collection Type - composite: - $ref: '#/components/schemas/CompositeItems' - created_from_basename: - anyOf: - - type: string - - type: 'null' - title: Created From Basename - dbkey: - default: '?' - title: Dbkey - type: string - deferred: - default: false - title: Deferred - type: boolean - description: - anyOf: - - type: string - - type: 'null' - title: Description - elements_from: - anyOf: - - $ref: '#/components/schemas/ElementsFromType' - - type: 'null' - ext: - default: auto - title: Ext - type: string - extra_files: - anyOf: - - $ref: '#/components/schemas/ExtraFiles' - - type: 'null' - info: - anyOf: - - type: string - - type: 'null' - title: Info - name: - anyOf: - - type: string - - type: integer - - type: number - - type: boolean - - type: 'null' - title: Name - space_to_tab: - default: false - title: Space To Tab - type: boolean - src: - const: composite - title: Src - tags: - anyOf: - - items: - type: string - type: array - - type: 'null' - title: Tags - to_posix_lines: - default: false - title: To Posix Lines - type: boolean - required: - - src - - composite - title: CompositeDataElement - type: object - CompositeFileInfo: - properties: - description: - anyOf: - - type: string - - type: 'null' - description: Summary description of the purpouse of this file - title: Description - is_binary: - description: Whether this file is a binary file - title: Is binary - type: boolean - mimetype: - anyOf: - - type: string - - type: 'null' - description: The MIME type of this file - title: MIME type - name: - description: The name of this composite file - title: Name - type: string - optional: - description: '' - title: Optional - type: boolean - space_to_tab: - description: '' - title: Spaces to tabulation - type: boolean - substitute_name_with_metadata: - anyOf: - - type: string - - type: 'null' - description: '' - title: Substitute name with metadata - to_posix_lines: - description: '' - title: To posix lines - type: boolean - required: - - name - - optional - - mimetype - - description - - substitute_name_with_metadata - - is_binary - - to_posix_lines - - space_to_tab - title: CompositeFileInfo - type: object - CompositeItems: - properties: - elements: - items: - anyOf: - - $ref: '#/components/schemas/FileDataElement' - - $ref: '#/components/schemas/PastedDataElement' - - $ref: '#/components/schemas/UrlDataElement' - - $ref: '#/components/schemas/PathDataElement' - - $ref: '#/components/schemas/ServerDirElement' - - $ref: '#/components/schemas/FtpImportElement' - title: Elements - type: array - required: - - elements - title: CompositeItems - type: object - ComputeDatasetHashPayload: - properties: - extra_files_path: - anyOf: - - type: string - - type: 'null' - description: If set, extra files path to compute a hash for. - title: Extra Files Path - hash_function: - anyOf: - - $ref: '#/components/schemas/HashFunctionNameEnum' - - type: 'null' - default: MD5 - description: Hash function name to use to compute dataset hashes. - title: ComputeDatasetHashPayload - type: object - ConcreteObjectStoreModel: - properties: - badges: - items: - $ref: '#/components/schemas/BadgeDict' - title: Badges - type: array - description: - anyOf: - - type: string - - type: 'null' - title: Description - device: - anyOf: - - type: string - - type: 'null' - title: Device - name: - anyOf: - - type: string - - type: 'null' - title: Name - object_store_id: - anyOf: - - type: string - - type: 'null' - title: Object Store Id - private: - title: Private - type: boolean - quota: - $ref: '#/components/schemas/QuotaModel' - required: - - private - - quota - - badges - title: ConcreteObjectStoreModel - type: object - ConcreteObjectStoreQuotaSourceDetails: - properties: - enabled: - description: Whether the object store tracks quota on the data (independent - of Galaxy's configuration) - title: Enabled - type: boolean - source: - anyOf: - - type: string - - type: 'null' - description: The quota source label corresponding to the object store the - dataset is stored in (or would be stored in) - title: Source - required: - - source - - enabled - title: ConcreteObjectStoreQuotaSourceDetails - type: object - ContentsObject: - properties: - contents: - anyOf: - - items: - $ref: '#/components/schemas/ContentsObject' - type: array - - type: 'null' - description: If this ContentsObject describes a nested bundle and the caller - specified "?expand=true" on the request, then this contents array must - be present and describe the objects within the nested bundle. - title: Contents - drs_uri: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: A list of full DRS identifier URI paths that may be used to - obtain the object. These URIs may be external to this DRS instance. - examples: - - drs://drs.example.org/314159 - title: Drs Uri - id: - anyOf: - - type: string - - type: 'null' - description: A DRS identifier of a `DrsObject` (either a single blob or - a nested bundle). If this ContentsObject is an object within a nested - bundle, then the id is optional. Otherwise, the id is required. - title: Id - name: - description: A name declared by the bundle author that must be used when - materialising this object, overriding any name directly associated with - the object itself. The name must be unique within the containing bundle. - This string is made up of uppercase and lowercase letters, decimal digits, - hyphen, period, and underscore [A-Za-z0-9.-_]. See http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap03.html#tag_03_282[portable - filenames]. - title: Name - type: string - required: - - name - title: ContentsObject - type: object - ConvertedDatasetsMap: - additionalProperties: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - description: Map of `file extension` -> `converted dataset encoded id` - example: - csv: dataset_id - title: ConvertedDatasetsMap - type: object - CreateEntryPayload: - properties: - name: - description: The name of the entry to create. - examples: - - my_new_entry - title: Name - type: string - target: - description: The target file source to create the entry in. - title: Target - type: string - required: - - target - - name - title: CreateEntryPayload - type: object - CreateHistoryContentFromStore: - properties: - model_store_format: - anyOf: - - $ref: '#/components/schemas/ModelStoreFormat' - - type: 'null' - store_content_uri: - anyOf: - - type: string - - type: 'null' - title: Store Content Uri - store_dict: - anyOf: - - type: object - - type: 'null' - title: Store Dict - title: CreateHistoryContentFromStore - type: object - CreateHistoryContentPayload: - additionalProperties: true - properties: - collection_type: - anyOf: - - type: string - - type: 'null' - description: The type of the collection, can be `list`, `paired`, or define - subcollections using `:` as separator like `list:paired` or `list:list`. - title: Collection Type - content: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: 'Depending on the `source` it can be: - - - The encoded id from the library dataset - - - The encoded id from the library folder - - - The encoded id from the HDA - - - The encoded id from the HDCA - - ' - title: Content - copy_elements: - anyOf: - - type: boolean - - type: 'null' - default: true - description: If the source is a collection, whether to copy child HDAs into - the target history as well. Prior to the galaxy release 23.1 this defaulted - to false. - title: Copy Elements - dbkey: - anyOf: - - type: string - - type: 'null' - description: TODO - title: DBKey - element_identifiers: - anyOf: - - items: - $ref: '#/components/schemas/CollectionElementIdentifier' - type: array - - type: 'null' - description: List of elements that should be in the new collection. - title: Element Identifiers - folder_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: The ID of the library folder that will contain the collection. - Required if `instance_type=library`. - title: Folder Id - hide_source_items: - anyOf: - - type: boolean - - type: 'null' - default: false - description: Whether to mark the original HDAs as hidden. - title: Hide Source Items - history_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: The ID of the history that will contain the collection. Required - if `instance_type=history`. - title: History Id - instance_type: - anyOf: - - enum: - - history - - library - type: string - - type: 'null' - default: history - description: The type of the instance, either `history` (default) or `library`. - title: Instance Type - name: - anyOf: - - type: string - - type: 'null' - description: The name of the new collection. - title: Name - source: - anyOf: - - $ref: '#/components/schemas/HistoryContentSource' - - type: 'null' - description: The source of the content. Can be other history element to - be copied or library elements. - title: Source - type: - anyOf: - - $ref: '#/components/schemas/HistoryContentType' - - type: 'null' - default: dataset - description: The type of content to be created in the history. - title: Type - title: CreateHistoryContentPayload - type: object - CreateHistoryFromStore: - properties: - model_store_format: - anyOf: - - $ref: '#/components/schemas/ModelStoreFormat' - - type: 'null' - store_content_uri: - anyOf: - - type: string - - type: 'null' - title: Store Content Uri - store_dict: - anyOf: - - type: object - - type: 'null' - title: Store Dict - title: CreateHistoryFromStore - type: object - CreateInvocationsFromStorePayload: - properties: - history_id: - description: The ID of the history associated with the invocations. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: History ID - type: string - legacy_job_state: - default: false - deprecated: true - description: "Populate the invocation step state with the job state instead\ - \ of the invocation step state.\n This will also produce one step\ - \ per job in mapping jobs to mimic the older behavior with respect to\ - \ collections.\n Partially scheduled steps may provide incomplete\ - \ information and the listed steps outputs\n are not the mapped\ - \ over step outputs but the individual job outputs." - title: Legacy Job State - type: boolean - model_store_format: - anyOf: - - $ref: '#/components/schemas/ModelStoreFormat' - - type: 'null' - step_details: - default: false - description: Include details for individual invocation steps and populate - a steps attribute in the resulting dictionary - title: Include step details - type: boolean - store_content_uri: - anyOf: - - type: string - - type: 'null' - title: Store Content Uri - store_dict: - anyOf: - - type: object - - type: 'null' - title: Store Dict - view: - anyOf: - - $ref: '#/components/schemas/InvocationSerializationView' - - type: 'null' - description: The name of the view used to serialize this item. This will - return a predefined set of attributes of the item. - examples: - - element - title: View - required: - - history_id - title: CreateInvocationsFromStorePayload - type: object - CreateLibrariesFromStore: - properties: - model_store_format: - anyOf: - - $ref: '#/components/schemas/ModelStoreFormat' - - type: 'null' - store_content_uri: - anyOf: - - type: string - - type: 'null' - title: Store Content Uri - store_dict: - anyOf: - - type: object - - type: 'null' - title: Store Dict - title: CreateLibrariesFromStore - type: object - CreateLibraryFilePayload: - properties: - from_hda_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: The ID of an accessible HDA to copy into the library. - title: From HDA ID - from_hdca_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: The ID of an accessible HDCA to copy into the library. Nested - collections are not allowed, you must flatten the collection first. - title: From HDCA ID - ldda_message: - anyOf: - - type: string - - type: 'null' - default: '' - description: The new message attribute of the LDDA created. - title: LDDA Message - title: CreateLibraryFilePayload - type: object - CreateLibraryFolderPayload: - properties: - description: - anyOf: - - type: string - - type: 'null' - default: '' - description: A detailed description of the library folder. - title: Description - name: - description: The name of the library folder. - title: Name - type: string - required: - - name - title: CreateLibraryFolderPayload - type: object - CreateLibraryPayload: - properties: - description: - anyOf: - - type: string - - type: 'null' - default: '' - description: A detailed description of the Library. - title: Description - name: - description: The name of the Library. - title: Name - type: string - synopsis: - anyOf: - - type: string - - type: 'null' - default: '' - description: A short text describing the contents of the Library. - title: Synopsis - required: - - name - title: CreateLibraryPayload - type: object - CreateMetricsPayload: - properties: - metrics: - default: [] - examples: - - args: '{"test":"value"}' - level: 0 - namespace: test-source - time: '2021-01-23T18:25:43.511Z' - items: - $ref: '#/components/schemas/Metric' - title: List of metrics to be recorded. - type: array - title: CreateMetricsPayload - type: object - CreateNewCollectionPayload: - properties: - collection_type: - anyOf: - - type: string - - type: 'null' - description: The type of the collection, can be `list`, `paired`, or define - subcollections using `:` as separator like `list:paired` or `list:list`. - title: Collection Type - copy_elements: - anyOf: - - type: boolean - - type: 'null' - default: true - description: Whether to create a copy of the source HDAs for the new collection. - title: Copy Elements - element_identifiers: - anyOf: - - items: - $ref: '#/components/schemas/CollectionElementIdentifier' - type: array - - type: 'null' - description: List of elements that should be in the new collection. - title: Element Identifiers - folder_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: The ID of the library folder that will contain the collection. - Required if `instance_type=library`. - title: Folder Id - hide_source_items: - anyOf: - - type: boolean - - type: 'null' - default: false - description: Whether to mark the original HDAs as hidden. - title: Hide Source Items - history_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: The ID of the history that will contain the collection. Required - if `instance_type=history`. - title: History Id - instance_type: - anyOf: - - enum: - - history - - library - type: string - - type: 'null' - default: history - description: The type of the instance, either `history` (default) or `library`. - title: Instance Type - name: - anyOf: - - type: string - - type: 'null' - description: The name of the new collection. - title: Name - title: CreateNewCollectionPayload - type: object - CreatePagePayload: - additionalProperties: true - properties: - annotation: - anyOf: - - type: string - - type: 'null' - description: Annotation that will be attached to the page. - title: Annotation - content: - anyOf: - - type: string - - type: 'null' - default: '' - description: Raw text contents of the last page revision (type dependent - on content_format). - title: Content - content_format: - allOf: - - $ref: '#/components/schemas/PageContentFormat' - default: html - description: Either `markdown` or `html`. - title: Content format - invocation_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: Encoded ID used by workflow generated reports. - title: Workflow invocation ID - slug: - description: The title slug for the page URL, must be unique. - pattern: ^[a-z0-9\-]+$ - title: Identifier - type: string - title: - description: The name of the page. - title: Title - type: string - required: - - title - - slug - title: CreatePagePayload - type: object - CreateQuotaParams: - properties: - amount: - description: Quota size (E.g. ``10000MB``, ``99 gb``, ``0.2T``, ``unlimited``) - title: Amount - type: string - default: - allOf: - - $ref: '#/components/schemas/DefaultQuotaValues' - default: 'no' - description: Whether or not this is a default quota. Valid values are ``no``, - ``unregistered``, ``registered``. None is equivalent to ``no``. - title: Default - description: - description: Detailed text description for this Quota. - title: Description - type: string - in_groups: - anyOf: - - items: - type: string - type: array - - type: 'null' - default: [] - description: A list of group IDs or names to associate with this quota. - title: Groups - in_users: - anyOf: - - items: - type: string - type: array - - type: 'null' - default: [] - description: A list of user IDs or user emails to associate with this quota. - title: Users - name: - description: The name of the quota. This must be unique within a Galaxy - instance. - title: Name - type: string - operation: - allOf: - - $ref: '#/components/schemas/QuotaOperation' - default: '=' - description: 'Quotas can have one of three `operations`:- `=` : The quota - is exactly the amount specified- `+` : The amount specified will be added - to the amounts of the user''s other associated quota definitions- `-` - : The amount specified will be subtracted from the amounts of the user''s - other associated quota definitions' - title: Operation - quota_source_label: - anyOf: - - type: string - - type: 'null' - description: If set, quota source label to apply this quota operation to. - Otherwise, the default quota is used. - title: Quota Source Label - required: - - name - - description - - amount - title: CreateQuotaParams - type: object - CreateQuotaResult: - properties: - id: - description: The `encoded identifier` of the quota. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - message: - description: Text message describing the result of the operation. - title: Message - type: string - model_class: - const: Quota - description: The name of the database model class. - title: Model class - type: string - name: - description: The name of the quota. This must be unique within a Galaxy - instance. - title: Name - type: string - quota_source_label: - anyOf: - - type: string - - type: 'null' - description: Quota source label - title: Quota Source Label - url: - deprecated: true - description: The relative URL to get this particular Quota details from - the rest API. - title: URL - type: string - required: - - model_class - - id - - name - - url - - message - title: CreateQuotaResult - type: object - CreatedEntryResponse: - properties: - external_link: - anyOf: - - type: string - - type: 'null' - description: An optional external link to the created entry if available. - title: External link - name: - description: The name of the created entry. - examples: - - my_new_entry - title: Name - type: string - uri: - description: The URI of the created entry. - examples: - - gxfiles://my_new_entry - title: URI - type: string - required: - - name - - uri - title: CreatedEntryResponse - type: object - CreatedUserModel: - properties: - active: - description: User is active - title: Active - type: boolean - deleted: - description: ' User is deleted' - title: Deleted - type: boolean - email: - description: Email of the user - title: Email - type: string - id: - description: Encoded ID of the user - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - last_password_change: - anyOf: - - format: date-time - type: string - - type: 'null' - description: '' - title: Last password change - model_class: - const: User - description: The name of the database model class. - title: Model class - type: string - nice_total_disk_usage: - description: Size of all non-purged, unique datasets of the user in a nice - format. - title: Nice total disc usage - type: string - preferred_object_store_id: - anyOf: - - type: string - - type: 'null' - description: The ID of the object store that should be used to store new - datasets in this history. - title: Preferred Object Store ID - total_disk_usage: - description: Size of all non-purged, unique datasets of the user in bytes. - title: Total disk usage - type: number - username: - description: The name of the user. - title: user_name - type: string - required: - - model_class - - total_disk_usage - - nice_total_disk_usage - - id - - username - - email - - deleted - - active - - last_password_change - title: CreatedUserModel - type: object - CustomBuildCreationPayload: - properties: - len|type: - allOf: - - $ref: '#/components/schemas/CustomBuildLenType' - description: The type of the len file. - title: Length type - len|value: - description: The content of the length file. - title: Length value - type: string - name: - description: The name of the custom build. - title: Name - type: string - required: - - name - - len|type - - len|value - title: CustomBuildCreationPayload - type: object - CustomBuildLenType: - enum: - - file - - fasta - - text - title: CustomBuildLenType - type: string - CustomBuildModel: - properties: - count: - anyOf: - - type: string - - type: 'null' - description: The number of chromosomes/contigs. - title: Count - fasta: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: The primary id of the fasta file from a history. - title: Fasta - id: - description: The ID of the custom build. - title: ID - type: string - len: - description: The primary id of the len file. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Length - type: string - linecount: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: The primary id of a linecount dataset. - title: Line count - name: - description: The name of the custom build. - title: Name - type: string - required: - - name - - len - - id - title: CustomBuildModel - type: object - CustomBuildsCollection: - items: - $ref: '#/components/schemas/CustomBuildModel' - title: CustomBuildsCollection - type: array - CustomBuildsMetadataResponse: - properties: - fasta_hdas: - description: "A list of label/value pairs with all the datasets of type\ - \ `FASTA` contained in the History.\n - `label` is item position followed\ - \ by the name of the dataset.\n - `value` is the encoded database ID of\ - \ the dataset.\n" - items: - $ref: '#/components/schemas/LabelValuePair' - title: Fasta HDAs - type: array - installed_builds: - description: TODO - items: - $ref: '#/components/schemas/LabelValuePair' - title: Installed Builds - type: array - required: - - installed_builds - - fasta_hdas - title: CustomBuildsMetadataResponse - type: object - CustomHistoryItem: - additionalProperties: true - description: 'Can contain any serializable property of the item. - - - Allows arbitrary custom keys to be specified in the serialization - - parameters without a particular view (predefined set of keys).' - properties: {} - title: CustomHistoryItem - type: object - DCESummary: - description: Dataset Collection Element summary information. - properties: - element_identifier: - description: The actual name of this element. - title: Element Identifier - type: string - element_index: - description: The position index of this element inside the collection. - title: Element Index - type: integer - element_type: - allOf: - - $ref: '#/components/schemas/DCEType' - description: The type of the element. Used to interpret the `object` field. - title: Element Type - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Dataset Collection Element ID - type: string - model_class: - const: DatasetCollectionElement - description: The name of the database model class. - title: Model class - type: string - object: - anyOf: - - $ref: '#/components/schemas/HDAObject' - - $ref: '#/components/schemas/HDADetailed' - - $ref: '#/components/schemas/DCObject' - description: The element's specific data depending on the value of `element_type`. - title: Object - required: - - model_class - - id - - element_index - - element_identifier - - element_type - - object - title: DCESummary - type: object - DCEType: - description: Available types of dataset collection elements. - enum: - - hda - - dataset_collection - title: DCEType - type: string - DCObject: - description: Dataset Collection Object - properties: - collection_type: - description: The type of the collection, can be `list`, `paired`, or define - subcollections using `:` as separator like `list:paired` or `list:list`. - title: Collection Type - type: string - contents_url: - anyOf: - - description: The relative URL to access the contents of this History. - title: Contents URL - type: string - - type: 'null' - title: Contents Url - element_count: - anyOf: - - type: integer - - type: 'null' - description: The number of elements contained in the dataset collection. - It may be None or undefined if the collection could not be populated. - title: Element Count - elements: - default: [] - description: The summary information of each of the elements inside the - dataset collection. - items: - $ref: '#/components/schemas/DCESummary' - title: Elements - type: array - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Dataset Collection ID - type: string - model_class: - const: DatasetCollection - description: The name of the database model class. - title: Model class - type: string - populated: - description: Whether the dataset collection elements (and any subcollections - elements) were successfully populated. - title: Populated - type: boolean - required: - - model_class - - id - - collection_type - title: DCObject - type: object - DataElementsFromTarget: - properties: - auto_decompress: - default: false - description: Decompress compressed data before sniffing? - title: Auto Decompress - type: boolean - destination: - discriminator: - mapping: - hdas: '#/components/schemas/HdaDestination' - library: '#/components/schemas/LibraryDestination' - library_folder: '#/components/schemas/LibraryFolderDestination' - propertyName: type - oneOf: - - $ref: '#/components/schemas/HdaDestination' - - $ref: '#/components/schemas/LibraryFolderDestination' - - $ref: '#/components/schemas/LibraryDestination' - title: Destination - elements_from: - $ref: '#/components/schemas/ElementsFromType' - ftp_path: - anyOf: - - type: string - - type: 'null' - title: Ftp Path - path: - anyOf: - - type: string - - type: 'null' - title: Path - server_dir: - anyOf: - - type: string - - type: 'null' - title: Server Dir - src: - $ref: '#/components/schemas/ItemsFromSrc' - url: - anyOf: - - type: string - - type: 'null' - title: Url - required: - - src - - destination - - elements_from - title: DataElementsFromTarget - type: object - DataElementsTarget: - properties: - auto_decompress: - default: false - description: Decompress compressed data before sniffing? - title: Auto Decompress - type: boolean - destination: - discriminator: - mapping: - hdas: '#/components/schemas/HdaDestination' - library: '#/components/schemas/LibraryDestination' - library_folder: '#/components/schemas/LibraryFolderDestination' - propertyName: type - oneOf: - - $ref: '#/components/schemas/HdaDestination' - - $ref: '#/components/schemas/LibraryFolderDestination' - - $ref: '#/components/schemas/LibraryDestination' - title: Destination - elements: - items: - anyOf: - - discriminator: - mapping: - composite: '#/components/schemas/CompositeDataElement' - files: '#/components/schemas/FileDataElement' - ftp_import: '#/components/schemas/FtpImportElement' - pasted: '#/components/schemas/PastedDataElement' - path: '#/components/schemas/PathDataElement' - server_dir: '#/components/schemas/ServerDirElement' - url: '#/components/schemas/UrlDataElement' - propertyName: src - oneOf: - - $ref: '#/components/schemas/FileDataElement' - - $ref: '#/components/schemas/PastedDataElement' - - $ref: '#/components/schemas/UrlDataElement' - - $ref: '#/components/schemas/PathDataElement' - - $ref: '#/components/schemas/ServerDirElement' - - $ref: '#/components/schemas/FtpImportElement' - - $ref: '#/components/schemas/CompositeDataElement' - - $ref: '#/components/schemas/NestedElement' - title: Elements - type: array - required: - - destination - - elements - title: DataElementsTarget - type: object - DataItemSourceType: - enum: - - hda - - ldda - - hdca - - dce - - dc - title: DataItemSourceType - type: string - DatasetAssociationRoles: - properties: - access_dataset_roles: - default: [] - description: A list of roles that can access the dataset. The user has to - **have all these roles** in order to access this dataset. Users without - access permission **cannot** have other permissions on this dataset. If - there are no access roles set on the dataset it is considered **unrestricted**. - items: - items: - type: string - type: array - title: Access Roles - type: array - manage_dataset_roles: - default: [] - description: A list of roles that can manage permissions on the dataset. - Users with **any** of these roles can manage permissions of this dataset. - If you remove yourself you will lose the ability to manage this dataset - unless you are an admin. - items: - items: - type: string - type: array - title: Manage Roles - type: array - modify_item_roles: - default: [] - description: A list of roles that can modify the library item. This is a - library related permission. User with **any** of these roles can modify - name, metadata, and other information about this library item. - items: - items: - type: string - type: array - title: Modify Roles - type: array - title: DatasetAssociationRoles - type: object - DatasetCollectionAttributesResult: - properties: - dbkey: - description: TODO - title: Dbkey - type: string - dbkeys: - anyOf: - - items: - type: string - type: array - uniqueItems: true - - type: 'null' - title: Dbkeys - extension: - description: The dataset file extension. - examples: - - txt - title: Extension - type: string - extensions: - anyOf: - - items: - type: string - type: array - uniqueItems: true - - type: 'null' - title: Extensions - model_class: - const: HistoryDatasetCollectionAssociation - description: The name of the database model class. - title: Model class - type: string - tags: - $ref: '#/components/schemas/TagCollection' - required: - - dbkey - - extension - - model_class - - dbkeys - - extensions - - tags - title: DatasetCollectionAttributesResult - type: object - DatasetCollectionContentElements: - description: Represents a collection of elements contained in the dataset collection. - items: - $ref: '#/components/schemas/DCESummary' - title: DatasetCollectionContentElements - type: array - DatasetCollectionPopulatedState: - enum: - - new - - ok - - failed - title: DatasetCollectionPopulatedState - type: string - DatasetContentType: - description: For retrieving content from a structured dataset (e.g. HDF5) - enum: - - meta - - attr - - stats - - data - title: DatasetContentType - type: string - DatasetErrorMessage: - properties: - dataset: - allOf: - - $ref: '#/components/schemas/EncodedDatasetSourceId' - description: The encoded ID of the dataset and its source. - error_message: - description: The error message returned while processing this dataset. - title: Error Message - type: string - required: - - dataset - - error_message - title: DatasetErrorMessage - type: object - DatasetExtraFiles: - description: A list of extra files associated with a dataset. - items: - $ref: '#/components/schemas/ExtraFileEntry' - title: DatasetExtraFiles - type: array - DatasetInheritanceChain: - default: [] - items: - $ref: '#/components/schemas/DatasetInheritanceChainEntry' - title: DatasetInheritanceChain - type: array - DatasetInheritanceChainEntry: - properties: - dep: - description: Name of the source of the referenced dataset at this point - of the inheritance chain. - title: Dep - type: string - name: - description: Name of the referenced dataset - title: Name - type: string - required: - - name - - dep - title: DatasetInheritanceChainEntry - type: object - DatasetPermissions: - description: Role-based permissions for accessing and managing a dataset. - properties: - access: - default: [] - description: The set of roles (encoded IDs) that can access this dataset. - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - title: Access - type: array - manage: - default: [] - description: The set of roles (encoded IDs) that can manage this dataset. - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - title: Management - type: array - title: DatasetPermissions - type: object - DatasetSourceId: - properties: - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Id - type: string - src: - allOf: - - $ref: '#/components/schemas/DatasetSourceType' - description: The source of this dataset, either `hda` or `ldda` depending - of its origin. - title: Source - required: - - src - - id - title: DatasetSourceId - type: object - DatasetSourceType: - enum: - - hda - - ldda - title: DatasetSourceType - type: string - DatasetState: - enum: - - new - - upload - - queued - - running - - ok - - empty - - error - - paused - - setting_metadata - - failed_metadata - - deferred - - discarded - title: DatasetState - type: string - DatasetStorageDetails: - properties: - badges: - description: A list of badges describing object store properties for concrete - object store dataset is stored in. - items: - $ref: '#/components/schemas/BadgeDict' - title: Badges - type: array - dataset_state: - description: The model state of the supplied dataset instance. - title: Dataset State - type: string - description: - anyOf: - - type: string - - type: 'null' - description: A description of how this dataset is stored. - title: Description - hashes: - description: The file contents hashes associated with the supplied dataset - instance. - items: - type: object - title: Hashes - type: array - name: - anyOf: - - type: string - - type: 'null' - description: The display name of the destination ObjectStore for this dataset. - title: Name - object_store_id: - anyOf: - - type: string - - type: 'null' - description: The identifier of the destination ObjectStore for this dataset. - title: Object Store Id - percent_used: - anyOf: - - type: number - - type: 'null' - description: The percentage indicating how full the store is. - title: Percent Used - quota: - allOf: - - $ref: '#/components/schemas/ConcreteObjectStoreQuotaSourceDetails' - description: Information about quota sources around dataset storage. - relocatable: - description: Indicator of whether the objectstore for this dataset can be - switched by this user. - title: Relocatable - type: boolean - shareable: - description: Is this dataset shareable. - title: Shareable - type: boolean - sources: - description: The file sources associated with the supplied dataset instance. - items: - type: object - title: Sources - type: array - required: - - object_store_id - - name - - description - - percent_used - - dataset_state - - hashes - - sources - - shareable - - quota - - badges - - relocatable - title: DatasetStorageDetails - type: object - DatasetSummary: - properties: - create_time: - anyOf: - - format: date-time - type: string - - type: 'null' - description: The time and date this item was created. - title: Create Time - deleted: - title: Deleted - type: boolean - file_size: - title: File Size - type: integer - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Id - type: string - purgable: - title: Purgable - type: boolean - purged: - title: Purged - type: boolean - state: - allOf: - - $ref: '#/components/schemas/DatasetState' - description: The current state of this dataset. - title: State - total_size: - title: Total Size - type: integer - update_time: - anyOf: - - format: date-time - type: string - - type: 'null' - description: The last time and date this item was updated. - title: Update Time - uuid: - description: Universal unique identifier for this dataset. - format: uuid4 - title: UUID - type: string - required: - - id - - create_time - - update_time - - state - - deleted - - purged - - purgable - - file_size - - total_size - - uuid - title: DatasetSummary - type: object - DatasetSummaryList: - items: - $ref: '#/components/schemas/DatasetSummary' - title: DatasetSummaryList - type: array - DatasetTextContentDetails: - properties: - item_data: - anyOf: - - type: string - - type: 'null' - description: First chunk of text content (maximum 1MB) of the dataset. - title: Item Data - item_url: - description: URL to access this dataset. - title: Item Url - type: string - truncated: - description: Whether the text in `item_data` has been truncated or contains - the whole contents. - title: Truncated - type: boolean - required: - - item_data - - truncated - - item_url - title: DatasetTextContentDetails - type: object - DatasetValidatedState: - enum: - - unknown - - invalid - - ok - title: DatasetValidatedState - type: string - DatatypeConverter: - properties: - source: - description: Source type for conversion - examples: - - bam - title: Source - type: string - target: - description: Target type for conversion - examples: - - bai - title: Target - type: string - tool_id: - description: The converter tool identifier - examples: - - CONVERTER_Bam_Bai_0 - title: Tool identifier - type: string - required: - - source - - target - - tool_id - title: DatatypeConverter - type: object - DatatypeConverterList: - default: [] - items: - $ref: '#/components/schemas/DatatypeConverter' - title: DatatypeConverterList - type: array - DatatypeDetails: - properties: - composite_files: - anyOf: - - items: - $ref: '#/components/schemas/CompositeFileInfo' - type: array - - type: 'null' - description: A collection of files composing this data type - title: Composite files - description: - anyOf: - - type: string - - type: 'null' - description: A summary description for this data type - title: Description - description_url: - anyOf: - - format: uri - maxLength: 2083 - minLength: 1 - type: string - - type: 'null' - description: The URL to a detailed description for this datatype - examples: - - https://wiki.galaxyproject.org/Learn/Datatypes#Bed - title: Description URL - display_in_upload: - default: false - description: If True, the associated file extension will be displayed in - the `File Format` select list in the `Upload File from your computer` - tool in the `Get Data` tool section of the tool panel - title: Display in upload - type: boolean - extension: - description: "The data type\u2019s Dataset file extension" - examples: - - bed - title: Extension - type: string - upload_warning: - anyOf: - - type: string - - type: 'null' - description: End-user information regarding potential pitfalls with this - upload type. - title: Upload warning - required: - - extension - - description - - description_url - title: DatatypeDetails - type: object - DatatypeEDAMDetails: - properties: - definition: - anyOf: - - type: string - - type: 'null' - description: The EDAM definition - examples: - - Entry (gene) format of the NCBI database. - title: Definition - label: - anyOf: - - type: string - - type: 'null' - description: The EDAM label - examples: - - NCBI gene report format - title: Label - prefix_IRI: - description: The EDAM prefixed Resource Identifier - examples: - - format_1782 - title: Prefix IRI - type: string - required: - - prefix_IRI - - label - - definition - title: DatatypeEDAMDetails - type: object - DatatypesCombinedMap: - properties: - datatypes: - description: List of datatypes extensions - items: - type: string - title: Datatypes - type: array - datatypes_mapping: - allOf: - - $ref: '#/components/schemas/DatatypesMap' - description: Dictionaries for mapping datatype's extensions/classes with - their implementation classes - title: Datatypes Mapping - required: - - datatypes - - datatypes_mapping - title: DatatypesCombinedMap - type: object - DatatypesEDAMDetailsDict: - additionalProperties: - $ref: '#/components/schemas/DatatypeEDAMDetails' - default: {} - title: DatatypesEDAMDetailsDict - type: object - DatatypesMap: - properties: - class_to_classes: - additionalProperties: - additionalProperties: - type: boolean - type: object - description: Dictionary mapping datatype's classes with their base classes - title: Classes Map - type: object - ext_to_class_name: - additionalProperties: - type: string - description: Dictionary mapping datatype's extensions with implementation - classes - title: Extension Map - type: object - required: - - ext_to_class_name - - class_to_classes - title: DatatypesMap - type: object - DefaultQuota: - properties: - model_class: - const: DefaultQuotaAssociation - description: The name of the database model class. - title: Model class - type: string - type: - allOf: - - $ref: '#/components/schemas/DefaultQuotaTypes' - description: "The type of the default quota. Either one of:\n - `registered`:\ - \ the associated quota will affect registered users.\n - `unregistered`:\ - \ the associated quota will affect unregistered users.\n" - title: Type - required: - - model_class - - type - title: DefaultQuota - type: object - DefaultQuotaTypes: - enum: - - unregistered - - registered - title: DefaultQuotaTypes - type: string - DefaultQuotaValues: - enum: - - unregistered - - registered - - 'no' - title: DefaultQuotaValues - type: string - DeleteDatasetBatchPayload: - properties: - datasets: - description: The list of datasets IDs with their sources to be deleted/purged. - items: - $ref: '#/components/schemas/DatasetSourceId' - title: Datasets - type: array - purge: - anyOf: - - type: boolean - - type: 'null' - default: false - description: 'Whether to permanently delete from disk the specified datasets. - *Warning*: this is a destructive operation.' - title: Purge - required: - - datasets - title: DeleteDatasetBatchPayload - type: object - DeleteDatasetBatchResult: - properties: - errors: - anyOf: - - items: - $ref: '#/components/schemas/DatasetErrorMessage' - type: array - - type: 'null' - description: A list of dataset IDs and the corresponding error message if - something went wrong while processing the dataset. - title: Errors - success_count: - description: The number of datasets successfully processed. - title: Success Count - type: integer - required: - - success_count - title: DeleteDatasetBatchResult - type: object - DeleteHistoriesPayload: - properties: - ids: - description: List of history IDs to be deleted. - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - title: IDs - type: array - purge: - default: false - description: Whether to definitely remove this history from disk. - title: Purge - type: boolean - required: - - ids - title: DeleteHistoriesPayload - type: object - DeleteHistoryContentPayload: - properties: - purge: - default: false - description: Whether to remove the dataset from storage. Datasets will only - be removed from storage once all HDAs or LDDAs that refer to this datasets - are deleted. - title: Purge - type: boolean - recursive: - default: false - description: When deleting a dataset collection, whether to also delete - containing datasets. - title: Recursive - type: boolean - stop_job: - default: false - description: Whether to stop the creating job if all the job's outputs are - deleted. - title: Stop Job - type: boolean - title: DeleteHistoryContentPayload - type: object - DeleteHistoryContentResult: - additionalProperties: true - description: 'Contains minimum information about the deletion state of a history - item. - - - Can also contain any other properties of the item.' - properties: - deleted: - description: True if the item was successfully deleted. - title: Deleted - type: boolean - id: - description: The encoded ID of the history item. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - purged: - anyOf: - - type: boolean - - type: 'null' - description: True if the item was successfully removed from disk. - title: Purged - required: - - id - - deleted - title: DeleteHistoryContentResult - type: object - DeleteHistoryPayload: - properties: - purge: - default: false - description: Whether to definitely remove this history from disk. - title: Purge - type: boolean - title: DeleteHistoryPayload - type: object - DeleteJobPayload: - properties: - message: - anyOf: - - type: string - - type: 'null' - description: Stop message - title: Job message - title: DeleteJobPayload - type: object - DeleteLibraryPayload: - properties: - undelete: - description: Whether to restore this previously deleted library. - title: Undelete - type: boolean - required: - - undelete - title: DeleteLibraryPayload - type: object - DeleteQuotaPayload: - properties: - purge: - default: false - description: Whether to also purge the Quota after deleting it. - title: Purge - type: boolean - title: DeleteQuotaPayload - type: object - DeletedCustomBuild: - properties: - message: - description: Confirmation of the custom build deletion. - title: Deletion message - type: string - required: - - message - title: DeletedCustomBuild - type: object - DetailedUserModel: - properties: - deleted: - description: ' User is deleted' - title: Deleted - type: boolean - email: - description: Email of the user - title: Email - type: string - id: - description: Encoded ID of the user - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - is_admin: - description: User is admin - title: Is admin - type: boolean - nice_total_disk_usage: - description: Size of all non-purged, unique datasets of the user in a nice - format. - title: Nice total disc usage - type: string - preferences: - description: Preferences of the user - title: Preferences - type: object - preferred_object_store_id: - anyOf: - - type: string - - type: 'null' - description: The ID of the object store that should be used to store new - datasets in this history. - title: Preferred Object Store ID - purged: - description: User is purged - title: Purged - type: boolean - quota: - description: Quota applicable to the user - title: Quota - type: string - quota_bytes: - description: Quota applicable to the user in bytes. - title: Quota in bytes - quota_percent: - description: Percentage of the storage quota applicable to the user. - title: Quota percent - tags_used: - description: Tags used by the user - items: - type: string - title: Tags used - type: array - total_disk_usage: - description: Size of all non-purged, unique datasets of the user in bytes. - title: Total disk usage - type: number - username: - description: The name of the user. - title: user_name - type: string - required: - - total_disk_usage - - nice_total_disk_usage - - id - - username - - email - - deleted - - is_admin - - purged - - preferences - - quota - - quota_bytes - - tags_used - title: DetailedUserModel - type: object - DisplayApp: - description: Basic linked information about an application that can display - certain datatypes. - properties: - label: - description: The label or title of the Display Application. - title: Label - type: string - links: - description: The collection of link details for this Display Application. - items: - $ref: '#/components/schemas/Hyperlink' - title: Links - type: array - required: - - label - - links - title: DisplayApp - type: object - DisplayApplication: - properties: - filename_: - title: 'Filename ' - type: string - id: - title: Id - type: string - links: - items: - $ref: '#/components/schemas/Link' - title: Links - type: array - name: - title: Name - type: string - version: - title: Version - type: string - required: - - id - - name - - version - - filename_ - - links - title: DisplayApplication - type: object - DrsObject: - properties: - access_methods: - anyOf: - - items: - $ref: '#/components/schemas/AccessMethod' - minItems: 1 - type: array - - type: 'null' - description: 'The list of access methods that can be used to fetch the `DrsObject`. - - Required for single blobs; optional for bundles.' - title: Access Methods - aliases: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: A list of strings that can be used to find other metadata about - this `DrsObject` from external metadata sources. These aliases can be - used to represent secondary accession numbers or external GUIDs. - title: Aliases - checksums: - description: 'The checksum of the `DrsObject`. At least one checksum must - be provided. - - For blobs, the checksum is computed over the bytes in the blob. - - For bundles, the checksum is computed over a sorted concatenation of the - checksums of its top-level contained objects (not recursive, names not - included). The list of checksums is sorted alphabetically (hex-code) before - concatenation and a further checksum is performed on the concatenated - checksum value. - - For example, if a bundle contains blobs with the following checksums: - - md5(blob1) = 72794b6d - - md5(blob2) = 5e089d29 - - Then the checksum of the bundle is: - - md5( concat( sort( md5(blob1), md5(blob2) ) ) ) - - = md5( concat( sort( 72794b6d, 5e089d29 ) ) ) - - = md5( concat( 5e089d29, 72794b6d ) ) - - = md5( 5e089d2972794b6d ) - - = f7a29a04' - items: - $ref: '#/components/schemas/Checksum' - minItems: 1 - title: Checksums - type: array - contents: - anyOf: - - items: - $ref: '#/components/schemas/ContentsObject' - type: array - - type: 'null' - description: 'If not set, this `DrsObject` is a single blob. - - If set, this `DrsObject` is a bundle containing the listed `ContentsObject` - s (some of which may be further nested).' - title: Contents - created_time: - description: 'Timestamp of content creation in RFC3339. - - (This is the creation time of the underlying content, not of the JSON - object.)' - format: date-time - title: Created Time - type: string - description: - anyOf: - - type: string - - type: 'null' - description: A human readable description of the `DrsObject`. - title: Description - id: - description: An identifier unique to this `DrsObject` - title: Id - type: string - mime_type: - anyOf: - - type: string - - type: 'null' - description: A string providing the mime-type of the `DrsObject`. - examples: - - application/json - title: Mime Type - name: - anyOf: - - type: string - - type: 'null' - description: 'A string that can be used to name a `DrsObject`. - - This string is made up of uppercase and lowercase letters, decimal digits, - hyphen, period, and underscore [A-Za-z0-9.-_]. See http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap03.html#tag_03_282[portable - filenames].' - title: Name - self_uri: - description: 'A drs:// hostname-based URI, as defined in the DRS documentation, - that tells clients how to access this object. - - The intent of this field is to make DRS objects self-contained, and therefore - easier for clients to store and pass around. For example, if you arrive - at this DRS JSON by resolving a compact identifier-based DRS URI, the - `self_uri` presents you with a hostname and properly encoded DRS ID for - use in subsequent `access` endpoint calls.' - examples: - - drs://drs.example.org/314159 - title: Self Uri - type: string - size: - description: 'For blobs, the blob size in bytes. - - For bundles, the cumulative size, in bytes, of items in the `contents` - field.' - title: Size - type: integer - updated_time: - anyOf: - - format: date-time - type: string - - type: 'null' - description: Timestamp of content update in RFC3339, identical to `created_time` - in systems that do not support updates. (This is the update time of the - underlying content, not of the JSON object.) - title: Updated Time - version: - anyOf: - - type: string - - type: 'null' - description: 'A string representing a version. - - (Some systems may use checksum, a RFC3339 timestamp, or an incrementing - version number.)' - title: Version - required: - - id - - self_uri - - size - - created_time - - checksums - title: DrsObject - type: object - ElementsFromType: - enum: - - archive - - bagit - - bagit_archive - - directory - title: ElementsFromType - type: string - EncodedDataItemSourceId: - properties: - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Id - type: string - src: - allOf: - - $ref: '#/components/schemas/DataItemSourceType' - description: The source of this dataset, either `hda`, `ldda`, `hdca`, `dce` - or `dc` depending of its origin. - title: Source - required: - - id - - src - title: EncodedDataItemSourceId - type: object - EncodedDatasetJobInfo: - properties: - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Id - type: string - src: - allOf: - - $ref: '#/components/schemas/DataItemSourceType' - description: The source of this dataset, either `hda`, `ldda`, `hdca`, `dce` - or `dc` depending of its origin. - title: Source - uuid: - anyOf: - - format: uuid4 - type: string - - type: 'null' - deprecated: true - description: Universal unique identifier for this dataset. - title: UUID - required: - - id - - src - title: EncodedDatasetJobInfo - type: object - EncodedDatasetSourceId: - properties: - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Id - type: string - src: - allOf: - - $ref: '#/components/schemas/DatasetSourceType' - description: The source of this dataset, either `hda` or `ldda` depending - of its origin. - title: Source - required: - - src - - id - title: EncodedDatasetSourceId - type: object - EncodedHdcaSourceId: - properties: - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Id - type: string - src: - const: hdca - description: The source of this dataset, which in the case of the model - can only be `hdca`. - title: Source - required: - - src - - id - title: EncodedHdcaSourceId - type: object - EncodedHistoryContentItem: - properties: - history_content_type: - allOf: - - $ref: '#/components/schemas/HistoryContentType' - description: The type of this item. - title: Content Type - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Id - type: string - required: - - history_content_type - - id - title: EncodedHistoryContentItem - type: object - EncodedJobDetails: - properties: - command_line: - anyOf: - - type: string - - type: 'null' - description: The command line produced by the job. Users can see this value - if allowed in the configuration, administrator can always see this value. - title: Command Line - command_version: - anyOf: - - type: string - - type: 'null' - description: Tool version indicated during job execution. - title: Command Version - copied_from_job_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: Reference to cached job if job execution was cached. - title: Copied from Job-ID - create_time: - description: The time and date this item was created. - format: date-time - title: Create Time - type: string - exit_code: - anyOf: - - type: integer - - type: 'null' - description: The exit code returned by the tool. Can be unset if the job - is not completed yet. - title: Exit Code - external_id: - anyOf: - - type: string - - type: 'null' - description: The job id used by the external job runner (Condor, Pulsar, - etc.). Only administrator can see this value. - title: External ID - galaxy_version: - anyOf: - - type: string - - type: 'null' - description: The (major) version of Galaxy used to create this job. - examples: - - '21.05' - title: Galaxy Version - handler: - anyOf: - - type: string - - type: 'null' - description: The job handler process assigned to handle this job. Only administrator - can see this value. - title: Job Handler - history_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: The encoded ID of the history associated with this item. - title: History ID - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Job ID - type: string - inputs: - additionalProperties: - $ref: '#/components/schemas/EncodedDatasetJobInfo' - default: {} - description: Dictionary mapping all the tool inputs (by name) to the corresponding - data references. - title: Inputs - type: object - job_runner_name: - anyOf: - - type: string - - type: 'null' - description: Name of the job runner plugin that handles this job. Only administrator - can see this value. - title: Job Runner Name - model_class: - const: Job - description: The name of the database model class. - title: Model class - type: string - output_collections: - additionalProperties: - $ref: '#/components/schemas/EncodedHdcaSourceId' - default: {} - description: '' - title: Output collections - type: object - outputs: - additionalProperties: - $ref: '#/components/schemas/EncodedDatasetJobInfo' - default: {} - description: Dictionary mapping all the tool outputs (by name) to the corresponding - data references. - title: Outputs - type: object - params: - description: Object containing all the parameters of the tool associated - with this job. The specific parameters depend on the tool itself. - title: Parameters - state: - allOf: - - $ref: '#/components/schemas/JobState' - description: Current state of the job. - title: State - tool_id: - description: Identifier of the tool that generated this job. - title: Tool ID - type: string - update_time: - description: The last time and date this item was updated. - format: date-time - title: Update Time - type: string - user_email: - anyOf: - - type: string - - type: 'null' - description: The email of the user that owns this job. Only the owner of - the job and administrators can see this value. - title: User Email - required: - - model_class - - id - - tool_id - - state - - create_time - - update_time - - params - title: EncodedJobDetails - type: object - EncodedJobParameterHistoryItem: - properties: - hid: - anyOf: - - type: integer - - type: 'null' - title: Hid - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Id - type: string - name: - title: Name - type: string - src: - allOf: - - $ref: '#/components/schemas/DataItemSourceType' - description: The source of this dataset, either `hda`, `ldda`, `hdca`, `dce` - or `dc` depending of its origin. - title: Source - required: - - id - - src - - name - title: EncodedJobParameterHistoryItem - type: object - ExportHistoryArchivePayload: - properties: - directory_uri: - anyOf: - - type: string - - type: 'null' - description: A writable directory destination where the history will be - exported using the `galaxy.files` URI infrastructure. - title: Directory URI - file_name: - anyOf: - - type: string - - type: 'null' - description: The name of the file containing the exported history. - title: File Name - force: - anyOf: - - type: boolean - - type: 'null' - description: Whether to force a rebuild of the history archive. - title: Force Rebuild - gzip: - anyOf: - - type: boolean - - type: 'null' - default: true - description: Whether to export as gzip archive. - title: GZip - include_deleted: - anyOf: - - type: boolean - - type: 'null' - default: false - description: Whether to include deleted datasets in the exported archive. - title: Include Deleted - include_hidden: - anyOf: - - type: boolean - - type: 'null' - default: false - description: Whether to include hidden datasets in the exported archive. - title: Include Hidden - title: ExportHistoryArchivePayload - type: object - ExportObjectMetadata: - properties: - request_data: - $ref: '#/components/schemas/ExportObjectRequestMetadata' - result_data: - anyOf: - - $ref: '#/components/schemas/ExportObjectResultMetadata' - - type: 'null' - required: - - request_data - title: ExportObjectMetadata - type: object - ExportObjectRequestMetadata: - properties: - object_id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Object Id - type: string - object_type: - $ref: '#/components/schemas/ExportObjectType' - payload: - anyOf: - - $ref: '#/components/schemas/WriteStoreToPayload' - - $ref: '#/components/schemas/ShortTermStoreExportPayload' - title: Payload - user_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - title: User Id - required: - - object_id - - object_type - - payload - title: ExportObjectRequestMetadata - type: object - ExportObjectResultMetadata: - properties: - error: - anyOf: - - type: string - - type: 'null' - title: Error - success: - title: Success - type: boolean - required: - - success - title: ExportObjectResultMetadata - type: object - ExportObjectType: - description: Types of objects that can be exported. - enum: - - history - - invocation - title: ExportObjectType - type: string - ExportRecordData: - description: Data of an export record associated with a history that was archived. - properties: - include_deleted: - default: false - description: Include file contents for deleted datasets (if include_files - is True). - title: Include deleted - type: boolean - include_files: - default: true - description: include materialized files in export when available - title: Include Files - type: boolean - include_hidden: - default: false - description: Include file contents for hidden datasets (if include_files - is True). - title: Include hidden - type: boolean - model_store_format: - allOf: - - $ref: '#/components/schemas/ModelStoreFormat' - default: tar.gz - description: format of model store to export - target_uri: - description: Galaxy Files URI to write mode store content to. - title: Target URI - type: string - required: - - target_uri - title: ExportRecordData - type: object - ExportTaskListResponse: - items: - $ref: '#/components/schemas/ObjectExportTaskResponse' - title: ExportTaskListResponse - type: array - ExtraFileEntry: - properties: - class: - allOf: - - $ref: '#/components/schemas/ExtraFilesEntryClass' - description: The class of this entry, either File or Directory. - path: - description: Relative path to the file or directory. - title: Path - type: string - required: - - class - - path - title: ExtraFileEntry - type: object - ExtraFiles: - properties: - fuzzy_root: - anyOf: - - type: boolean - - type: 'null' - default: true - description: Prevent Galaxy from checking for a single file in a directory - and re-interpreting the archive - title: Fuzzy Root - items_from: - anyOf: - - type: string - - type: 'null' - title: Items From - src: - $ref: '#/components/schemas/Src' - required: - - src - title: ExtraFiles - type: object - ExtraFilesEntryClass: - enum: - - Directory - - File - title: ExtraFilesEntryClass - type: string - FavoriteObject: - properties: - object_id: - description: The id of an object the user wants to favorite. - title: Object ID - type: string - required: - - object_id - title: FavoriteObject - type: object - FavoriteObjectType: - const: tools - title: FavoriteObjectType - type: string - FavoriteObjectsSummary: - properties: - tools: - description: The name of the tools the user favored. - items: - type: string - title: Favorite tools - type: array - required: - - tools - title: FavoriteObjectsSummary - type: object - FetchDataPayload: - additionalProperties: true - properties: - history_id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: History Id - type: string - targets: - items: - anyOf: - - $ref: '#/components/schemas/DataElementsTarget' - - $ref: '#/components/schemas/HdcaDataItemsTarget' - - $ref: '#/components/schemas/DataElementsFromTarget' - - $ref: '#/components/schemas/HdcaDataItemsFromTarget' - - $ref: '#/components/schemas/FtpImportTarget' - title: Targets - type: array - required: - - history_id - - targets - title: FetchDataPayload - type: object - FileDataElement: - additionalProperties: false - properties: - MD5: - anyOf: - - type: string - - type: 'null' - title: Md5 - auto_decompress: - default: false - description: Decompress compressed data before sniffing? - title: Auto Decompress - type: boolean - collection_type: - anyOf: - - type: string - - type: 'null' - title: Collection Type - created_from_basename: - anyOf: - - type: string - - type: 'null' - title: Created From Basename - dbkey: - default: '?' - title: Dbkey - type: string - deferred: - default: false - title: Deferred - type: boolean - description: - anyOf: - - type: string - - type: 'null' - title: Description - elements_from: - anyOf: - - $ref: '#/components/schemas/ElementsFromType' - - type: 'null' - ext: - default: auto - title: Ext - type: string - extra_files: - anyOf: - - $ref: '#/components/schemas/ExtraFiles' - - type: 'null' - info: - anyOf: - - type: string - - type: 'null' - title: Info - name: - anyOf: - - type: string - - type: integer - - type: number - - type: boolean - - type: 'null' - title: Name - space_to_tab: - default: false - title: Space To Tab - type: boolean - src: - const: files - title: Src - tags: - anyOf: - - items: - type: string - type: array - - type: 'null' - title: Tags - to_posix_lines: - default: false - title: To Posix Lines - type: boolean - required: - - src - title: FileDataElement - type: object - FileLibraryFolderItem: - properties: - can_manage: - title: Can Manage - type: boolean - create_time: - description: The time and date this item was created. - format: date-time - title: Create Time - type: string - date_uploaded: - format: date-time - title: Date Uploaded - type: string - deleted: - title: Deleted - type: boolean - file_ext: - title: File Ext - type: string - file_size: - title: File Size - type: string - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Id - type: string - is_private: - title: Is Private - type: boolean - is_unrestricted: - title: Is Unrestricted - type: boolean - ldda_id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Ldda Id - type: string - message: - anyOf: - - type: string - - type: 'null' - title: Message - name: - title: Name - type: string - raw_size: - title: Raw Size - type: integer - state: - allOf: - - $ref: '#/components/schemas/DatasetState' - description: The current state of this dataset. - title: State - tags: - $ref: '#/components/schemas/TagCollection' - type: - const: file - title: Type - update_time: - description: The last time and date this item was updated. - format: date-time - title: Update Time - type: string - required: - - name - - type - - create_time - - update_time - - can_manage - - deleted - - id - - file_ext - - date_uploaded - - is_unrestricted - - is_private - - state - - file_size - - raw_size - - ldda_id - - tags - title: FileLibraryFolderItem - type: object - FilesSourcePlugin: - properties: - browsable: - description: Whether this file source plugin can list items. - title: Browsable - type: boolean - doc: - description: Documentation or extended description for this plugin. - examples: - - Galaxy's library import directory - title: Documentation - type: string - id: - description: The `FilesSource` plugin identifier - examples: - - _import - title: ID - type: string - label: - description: The display label for this plugin. - examples: - - Library Import Directory - title: Label - type: string - requires_groups: - anyOf: - - type: string - - type: 'null' - description: Only users belonging to the groups specified here can access - this files source. - title: Requires groups - requires_roles: - anyOf: - - type: string - - type: 'null' - description: Only users with the roles specified here can access this files - source. - title: Requires roles - type: - description: The type of the plugin. - examples: - - gximport - title: Type - type: string - writable: - description: Whether this files source plugin allows write access. - examples: - - false - title: Writeable - type: boolean - required: - - id - - type - - label - - doc - - browsable - - writable - title: FilesSourcePlugin - type: object - FilesSourcePluginList: - default: [] - items: - anyOf: - - $ref: '#/components/schemas/BrowsableFilesSourcePlugin' - - $ref: '#/components/schemas/FilesSourcePlugin' - title: FilesSourcePluginList - type: array - FolderLibraryFolderItem: - properties: - can_manage: - title: Can Manage - type: boolean - can_modify: - title: Can Modify - type: boolean - create_time: - description: The time and date this item was created. - format: date-time - title: Create Time - type: string - deleted: - title: Deleted - type: boolean - description: - anyOf: - - type: string - - type: 'null' - default: '' - description: A detailed description of the library folder. - title: Description - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Id - type: string - name: - title: Name - type: string - type: - const: folder - title: Type - update_time: - description: The last time and date this item was updated. - format: date-time - title: Update Time - type: string - required: - - name - - type - - create_time - - update_time - - can_manage - - deleted - - id - - can_modify - title: FolderLibraryFolderItem - type: object - FtpImportElement: - additionalProperties: false - properties: - MD5: - anyOf: - - type: string - - type: 'null' - title: Md5 - auto_decompress: - default: false - description: Decompress compressed data before sniffing? - title: Auto Decompress - type: boolean - collection_type: - anyOf: - - type: string - - type: 'null' - title: Collection Type - created_from_basename: - anyOf: - - type: string - - type: 'null' - title: Created From Basename - dbkey: - default: '?' - title: Dbkey - type: string - deferred: - default: false - title: Deferred - type: boolean - description: - anyOf: - - type: string - - type: 'null' - title: Description - elements_from: - anyOf: - - $ref: '#/components/schemas/ElementsFromType' - - type: 'null' - ext: - default: auto - title: Ext - type: string - extra_files: - anyOf: - - $ref: '#/components/schemas/ExtraFiles' - - type: 'null' - ftp_path: - title: Ftp Path - type: string - info: - anyOf: - - type: string - - type: 'null' - title: Info - name: - anyOf: - - type: string - - type: integer - - type: number - - type: boolean - - type: 'null' - title: Name - space_to_tab: - default: false - title: Space To Tab - type: boolean - src: - const: ftp_import - title: Src - tags: - anyOf: - - items: - type: string - type: array - - type: 'null' - title: Tags - to_posix_lines: - default: false - title: To Posix Lines - type: boolean - required: - - src - - ftp_path - title: FtpImportElement - type: object - FtpImportTarget: - properties: - auto_decompress: - default: false - description: Decompress compressed data before sniffing? - title: Auto Decompress - type: boolean - collection_type: - anyOf: - - type: string - - type: 'null' - title: Collection Type - destination: - $ref: '#/components/schemas/HdcaDestination' - elements_from: - anyOf: - - $ref: '#/components/schemas/ElementsFromType' - - type: 'null' - ftp_path: - title: Ftp Path - type: string - name: - anyOf: - - type: string - - type: 'null' - title: Name - src: - const: ftp_import - title: Src - tags: - anyOf: - - items: - type: string - type: array - - type: 'null' - title: Tags - required: - - destination - - src - - ftp_path - title: FtpImportTarget - type: object - GroupCreatePayload: - description: Payload schema for creating a group. - properties: - name: - title: name of the group - type: string - role_ids: - default: [] - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - title: role IDs - type: array - user_ids: - default: [] - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - title: user IDs - type: array - required: - - name - title: GroupCreatePayload - type: object - GroupListResponse: - description: Response schema for listing groups. - items: - $ref: '#/components/schemas/GroupResponse' - title: GroupListResponse - type: array - GroupModel: - description: User group model - properties: - id: - description: Encoded group ID - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - model_class: - const: Group - description: The name of the database model class. - title: Model class - type: string - name: - description: The name of the group. - title: Name - type: string - required: - - model_class - - id - - name - title: GroupModel - type: object - GroupQuota: - properties: - group: - allOf: - - $ref: '#/components/schemas/GroupModel' - description: Information about a user group associated with a quota. - title: Group - model_class: - const: GroupQuotaAssociation - description: The name of the database model class. - title: Model class - type: string - required: - - model_class - - group - title: GroupQuota - type: object - GroupResponse: - description: Response schema for a group. - properties: - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: group ID - type: string - model_class: - const: Group - description: The name of the database model class. - title: Model class - type: string - name: - title: name of the group - type: string - roles_url: - anyOf: - - type: string - - type: 'null' - title: URL for the roles of the group - url: - title: URL for the group - type: string - users_url: - anyOf: - - type: string - - type: 'null' - title: URL for the users of the group - required: - - model_class - - id - - name - - url - title: GroupResponse - type: object - GroupRoleListResponse: - items: - $ref: '#/components/schemas/GroupRoleResponse' - title: GroupRoleListResponse - type: array - GroupRoleResponse: - properties: - id: - description: Encoded ID of the role - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - name: - description: Name of the role - title: Name - type: string - url: - deprecated: true - description: The relative URL to access this item. - title: URL - type: string - required: - - id - - name - - url - title: GroupRoleResponse - type: object - GroupUserListResponse: - items: - $ref: '#/components/schemas/GroupUserResponse' - title: GroupUserListResponse - type: array - GroupUserResponse: - properties: - email: - description: Email of the user - title: Email - type: string - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Id - type: string - url: - deprecated: true - description: The relative URL to access this item. - title: URL - type: string - required: - - id - - email - - url - title: GroupUserResponse - type: object - HDABasicInfo: - properties: - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Id - type: string - name: - title: Name - type: string - required: - - id - - name - title: HDABasicInfo - type: object - HDADetailed: - additionalProperties: true - description: History Dataset Association detailed information. - properties: - accessible: - description: Whether this item is accessible to the current user due to - permissions. - title: Accessible - type: boolean - annotation: - anyOf: - - type: string - - type: 'null' - description: An annotation to provide details or to help understand the - purpose and usage of this item. - title: Annotation - api_type: - const: file - default: file - deprecated: true - description: TODO - title: API Type - copied_from_ldda_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - title: Copied From Ldda Id - create_time: - anyOf: - - format: date-time - type: string - - type: 'null' - description: The time and date this item was created. - title: Create Time - created_from_basename: - anyOf: - - type: string - - type: 'null' - description: The basename of the output that produced this dataset. - title: Created from basename - creating_job: - description: The encoded ID of the job that created this dataset. - title: Creating Job ID - type: string - data_type: - description: The fully qualified name of the class implementing the data - type of this dataset. - examples: - - galaxy.datatypes.data.Text - title: Data Type - type: string - dataset_id: - description: The encoded ID of the dataset associated with this item. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Dataset ID - type: string - deleted: - description: Whether this item is marked as deleted. - title: Deleted - type: boolean - display_apps: - description: Contains new-style display app urls. - items: - $ref: '#/components/schemas/DisplayApp' - title: Display Applications - type: array - display_types: - description: Contains old-style display app urls. - items: - $ref: '#/components/schemas/DisplayApp' - title: Legacy Display Applications - type: array - download_url: - description: The URL to download this item from the server. - title: Download URL - type: string - extension: - anyOf: - - type: string - - type: 'null' - description: The extension of the dataset. - examples: - - txt - title: Extension - file_ext: - description: The extension of the file. - title: File extension - type: string - file_name: - anyOf: - - type: string - - type: 'null' - description: The full path to the dataset file. - title: File Name - file_size: - description: The file size in bytes. - title: File Size - type: integer - genome_build: - anyOf: - - type: string - - type: 'null' - default: '?' - description: TODO - title: Genome Build - hda_ldda: - allOf: - - $ref: '#/components/schemas/DatasetSourceType' - default: hda - description: Whether this dataset belongs to a history (HDA) or a library - (LDDA). - title: HDA or LDDA - hid: - description: The index position of this item in the History. - title: HID - type: integer - history_content_type: - const: dataset - description: This is always `dataset` for datasets. - title: History Content Type - history_id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: History ID - type: string - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Id - type: string - meta_files: - description: Collection of metadata files associated with this dataset. - items: - $ref: '#/components/schemas/MetadataFile' - title: Metadata Files - type: array - metadata: - anyOf: - - {} - - type: 'null' - description: The metadata associated with this dataset. - title: Metadata - metadata_data_lines: - default: 0 - description: TODO - title: Metadata Data Lines - type: integer - metadata_dbkey: - anyOf: - - type: string - - type: 'null' - default: '?' - description: TODO - title: Metadata DBKey - misc_blurb: - anyOf: - - type: string - - type: 'null' - description: TODO - title: Miscellaneous Blurb - misc_info: - anyOf: - - type: string - - type: 'null' - description: TODO - title: Miscellaneous Information - model_class: - const: HistoryDatasetAssociation - description: The name of the database model class. - title: Model class - type: string - name: - anyOf: - - type: string - - type: 'null' - description: The name of the item. - title: Name - peek: - anyOf: - - type: string - - type: 'null' - description: A few lines of contents from the start of the file. - title: Peek - permissions: - allOf: - - $ref: '#/components/schemas/DatasetPermissions' - description: Role-based access and manage control permissions for the dataset. - title: Permissions - purged: - description: Whether this dataset has been removed from disk. - title: Purged - type: boolean - rerunnable: - description: Whether the job creating this dataset can be run again. - title: Rerunnable - type: boolean - resubmitted: - description: Whether the job creating this dataset has been resubmitted. - title: Resubmitted - type: boolean - state: - allOf: - - $ref: '#/components/schemas/DatasetState' - description: The current state of this dataset. - title: State - tags: - $ref: '#/components/schemas/TagCollection' - type: - const: file - default: file - description: This is always `file` for datasets. - title: Type - type_id: - anyOf: - - type: string - - type: 'null' - description: The type and the encoded ID of this item. Used for caching. - examples: - - dataset-616e371b2cc6c62e - title: Type - ID - update_time: - anyOf: - - format: date-time - type: string - - type: 'null' - description: The last time and date this item was updated. - title: Update Time - url: - deprecated: true - description: The relative URL to access this item. - title: URL - type: string - uuid: - description: Universal unique identifier for this dataset. - format: uuid4 - title: UUID - type: string - validated_state: - allOf: - - $ref: '#/components/schemas/DatasetValidatedState' - description: The state of the datatype validation for this dataset. - title: Validated State - validated_state_message: - anyOf: - - type: string - - type: 'null' - description: The message with details about the datatype validation result - for this dataset. - title: Validated State Message - visible: - description: Whether this item is visible or hidden to the user by default. - title: Visible - type: boolean - visualizations: - description: The collection of visualizations that can be applied to this - dataset. - items: - $ref: '#/components/schemas/Visualization' - title: Visualizations - type: array - required: - - model_class - - id - - name - - history_id - - hid - - deleted - - visible - - create_time - - update_time - - url - - tags - - history_content_type - - dataset_id - - state - - extension - - purged - - accessible - - file_ext - - file_size - - resubmitted - - meta_files - - data_type - - creating_job - - rerunnable - - uuid - - permissions - - display_apps - - display_types - - visualizations - - validated_state - - annotation - - download_url - title: HDADetailed - type: object - HDAObject: - additionalProperties: true - description: History Dataset Association Object - properties: - copied_from_ldda_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - title: Copied From Ldda Id - hda_ldda: - allOf: - - $ref: '#/components/schemas/DatasetSourceType' - default: hda - description: Whether this dataset belongs to a history (HDA) or a library - (LDDA). - title: HDA or LDDA - history_id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: History ID - type: string - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: History Dataset Association ID - type: string - model_class: - const: HistoryDatasetAssociation - description: The name of the database model class. - title: Model class - type: string - state: - allOf: - - $ref: '#/components/schemas/DatasetState' - description: The current state of this dataset. - title: State - tags: - items: - type: string - title: Tags - type: array - required: - - model_class - - id - - state - - history_id - - tags - title: HDAObject - type: object - HDASummary: - additionalProperties: true - description: History Dataset Association summary information. - properties: - copied_from_ldda_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - title: Copied From Ldda Id - create_time: - anyOf: - - format: date-time - type: string - - type: 'null' - description: The time and date this item was created. - title: Create Time - dataset_id: - description: The encoded ID of the dataset associated with this item. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Dataset ID - type: string - deleted: - description: Whether this item is marked as deleted. - title: Deleted - type: boolean - extension: - anyOf: - - type: string - - type: 'null' - description: The extension of the dataset. - examples: - - txt - title: Extension - hid: - description: The index position of this item in the History. - title: HID - type: integer - history_content_type: - const: dataset - description: This is always `dataset` for datasets. - title: History Content Type - history_id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: History ID - type: string - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Id - type: string - name: - anyOf: - - type: string - - type: 'null' - description: The name of the item. - title: Name - purged: - description: Whether this dataset has been removed from disk. - title: Purged - type: boolean - state: - allOf: - - $ref: '#/components/schemas/DatasetState' - description: The current state of this dataset. - title: State - tags: - $ref: '#/components/schemas/TagCollection' - type: - description: The type of this item. - title: Type - type: string - type_id: - anyOf: - - type: string - - type: 'null' - description: The type and the encoded ID of this item. Used for caching. - examples: - - dataset-616e371b2cc6c62e - title: Type - ID - update_time: - anyOf: - - format: date-time - type: string - - type: 'null' - description: The last time and date this item was updated. - title: Update Time - url: - deprecated: true - description: The relative URL to access this item. - title: URL - type: string - visible: - description: Whether this item is visible or hidden to the user by default. - title: Visible - type: boolean - required: - - id - - name - - history_id - - hid - - deleted - - visible - - type - - create_time - - update_time - - url - - tags - - history_content_type - - dataset_id - - state - - extension - - purged - title: HDASummary - type: object - HDCADetailed: - additionalProperties: true - description: History Dataset Collection Association detailed information. - properties: - collection_id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Dataset Collection ID - type: string - collection_type: - description: The type of the collection, can be `list`, `paired`, or define - subcollections using `:` as separator like `list:paired` or `list:list`. - title: Collection Type - type: string - contents_url: - description: The relative URL to access the contents of this History. - title: Contents URL - type: string - create_time: - anyOf: - - format: date-time - type: string - - type: 'null' - description: The time and date this item was created. - title: Create Time - deleted: - description: Whether this item is marked as deleted. - title: Deleted - type: boolean - element_count: - anyOf: - - type: integer - - type: 'null' - description: The number of elements contained in the dataset collection. - It may be None or undefined if the collection could not be populated. - title: Element Count - elements: - default: [] - description: The summary information of each of the elements inside the - dataset collection. - items: - $ref: '#/components/schemas/DCESummary' - title: Elements - type: array - elements_datatypes: - description: A set containing all the different element datatypes in the - collection. - items: - type: string - title: Elements Datatypes - type: array - uniqueItems: true - hid: - description: The index position of this item in the History. - title: HID - type: integer - history_content_type: - const: dataset_collection - description: This is always `dataset_collection` for dataset collections. - title: History Content Type - history_id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: History ID - type: string - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Id - type: string - implicit_collection_jobs_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: Encoded ID for the ICJ object describing the collection of - jobs corresponding to this collection - title: Implicit Collection Jobs Id - job_source_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: The encoded ID of the Job that produced this dataset collection. - Used to track the state of the job. - title: Job Source ID - job_source_type: - anyOf: - - $ref: '#/components/schemas/JobSourceType' - - type: 'null' - description: The type of job (model class) that produced this dataset collection. - Used to track the state of the job. - title: Job Source Type - job_state_summary: - anyOf: - - $ref: '#/components/schemas/HDCJobStateSummary' - - type: 'null' - description: Overview of the job states working inside the dataset collection. - title: Job State Summary - model_class: - const: HistoryDatasetCollectionAssociation - description: The name of the database model class. - title: Model class - type: string - name: - anyOf: - - type: string - - type: 'null' - description: The name of the item. - title: Name - populated: - description: Whether the dataset collection elements (and any subcollections - elements) were successfully populated. - title: Populated - type: boolean - populated_state: - allOf: - - $ref: '#/components/schemas/DatasetCollectionPopulatedState' - description: 'Indicates the general state of the elements in the dataset - collection:- ''new'': new dataset collection, unpopulated elements.- ''ok'': - collection elements populated (HDAs may or may not have errors).- ''failed'': - some problem populating, won''t be populated.' - title: Populated State - populated_state_message: - anyOf: - - type: string - - type: 'null' - description: Optional message with further information in case the population - of the dataset collection failed. - title: Populated State Message - tags: - $ref: '#/components/schemas/TagCollection' - type: - const: collection - default: collection - description: This is always `collection` for dataset collections. - title: Type - type_id: - anyOf: - - type: string - - type: 'null' - description: The type and the encoded ID of this item. Used for caching. - examples: - - dataset-616e371b2cc6c62e - title: Type - ID - update_time: - anyOf: - - format: date-time - type: string - - type: 'null' - description: The last time and date this item was updated. - title: Update Time - url: - deprecated: true - description: The relative URL to access this item. - title: URL - type: string - visible: - description: Whether this item is visible or hidden to the user by default. - title: Visible - type: boolean - required: - - model_class - - id - - name - - history_id - - hid - - deleted - - visible - - create_time - - update_time - - url - - tags - - history_content_type - - collection_type - - populated_state - - contents_url - - collection_id - - elements_datatypes - title: HDCADetailed - type: object - HDCASummary: - additionalProperties: true - description: History Dataset Collection Association summary information. - properties: - collection_id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Dataset Collection ID - type: string - collection_type: - description: The type of the collection, can be `list`, `paired`, or define - subcollections using `:` as separator like `list:paired` or `list:list`. - title: Collection Type - type: string - contents_url: - description: The relative URL to access the contents of this History. - title: Contents URL - type: string - create_time: - anyOf: - - format: date-time - type: string - - type: 'null' - description: The time and date this item was created. - title: Create Time - deleted: - description: Whether this item is marked as deleted. - title: Deleted - type: boolean - element_count: - anyOf: - - type: integer - - type: 'null' - description: The number of elements contained in the dataset collection. - It may be None or undefined if the collection could not be populated. - title: Element Count - hid: - description: The index position of this item in the History. - title: HID - type: integer - history_content_type: - const: dataset_collection - description: This is always `dataset_collection` for dataset collections. - title: History Content Type - history_id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: History ID - type: string - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Id - type: string - job_source_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: The encoded ID of the Job that produced this dataset collection. - Used to track the state of the job. - title: Job Source ID - job_source_type: - anyOf: - - $ref: '#/components/schemas/JobSourceType' - - type: 'null' - description: The type of job (model class) that produced this dataset collection. - Used to track the state of the job. - title: Job Source Type - job_state_summary: - anyOf: - - $ref: '#/components/schemas/HDCJobStateSummary' - - type: 'null' - description: Overview of the job states working inside the dataset collection. - title: Job State Summary - model_class: - const: HistoryDatasetCollectionAssociation - description: The name of the database model class. - title: Model class - type: string - name: - anyOf: - - type: string - - type: 'null' - description: The name of the item. - title: Name - populated_state: - allOf: - - $ref: '#/components/schemas/DatasetCollectionPopulatedState' - description: 'Indicates the general state of the elements in the dataset - collection:- ''new'': new dataset collection, unpopulated elements.- ''ok'': - collection elements populated (HDAs may or may not have errors).- ''failed'': - some problem populating, won''t be populated.' - title: Populated State - populated_state_message: - anyOf: - - type: string - - type: 'null' - description: Optional message with further information in case the population - of the dataset collection failed. - title: Populated State Message - tags: - $ref: '#/components/schemas/TagCollection' - type: - const: collection - default: collection - description: This is always `collection` for dataset collections. - title: Type - type_id: - anyOf: - - type: string - - type: 'null' - description: The type and the encoded ID of this item. Used for caching. - examples: - - dataset-616e371b2cc6c62e - title: Type - ID - update_time: - anyOf: - - format: date-time - type: string - - type: 'null' - description: The last time and date this item was updated. - title: Update Time - url: - deprecated: true - description: The relative URL to access this item. - title: URL - type: string - visible: - description: Whether this item is visible or hidden to the user by default. - title: Visible - type: boolean - required: - - model_class - - id - - name - - history_id - - hid - - deleted - - visible - - create_time - - update_time - - url - - tags - - history_content_type - - collection_type - - populated_state - - contents_url - - collection_id - title: HDCASummary - type: object - HDCJobStateSummary: - description: Overview of the job states working inside a dataset collection. - properties: - all_jobs: - default: 0 - description: Total number of jobs associated with a dataset collection. - title: All jobs - type: integer - deleted: - default: 0 - description: Number of jobs in the `deleted` state. - title: Deleted jobs - type: integer - deleted_new: - default: 0 - description: Number of jobs in the `deleted_new` state. - title: Deleted new jobs - type: integer - error: - default: 0 - description: Number of jobs in the `error` state. - title: Jobs with errors - type: integer - failed: - default: 0 - description: Number of jobs in the `failed` state. - title: Failed jobs - type: integer - new: - default: 0 - description: Number of jobs in the `new` state. - title: New jobs - type: integer - ok: - default: 0 - description: Number of jobs in the `ok` state. - title: OK jobs - type: integer - paused: - default: 0 - description: Number of jobs in the `paused` state. - title: Paused jobs - type: integer - queued: - default: 0 - description: Number of jobs in the `queued` state. - title: Queued jobs - type: integer - resubmitted: - default: 0 - description: Number of jobs in the `resubmitted` state. - title: Resubmitted jobs - type: integer - running: - default: 0 - description: Number of jobs in the `running` state. - title: Running jobs - type: integer - skipped: - default: 0 - description: Number of jobs that were skipped due to conditional workflow - step execution. - title: Skipped jobs - type: integer - upload: - default: 0 - description: Number of jobs in the `upload` state. - title: Upload jobs - type: integer - waiting: - default: 0 - description: Number of jobs in the `waiting` state. - title: Waiting jobs - type: integer - title: HDCJobStateSummary - type: object - HTTPValidationError: - properties: - detail: - items: - $ref: '#/components/schemas/ValidationError' - title: Detail - type: array - title: HTTPValidationError - type: object - HashFunctionNameEnum: - description: Particular pieces of information that can be requested for a dataset. - enum: - - MD5 - - SHA-1 - - SHA-256 - - SHA-512 - title: HashFunctionNameEnum - type: string - HdaDestination: - properties: - type: - const: hdas - title: Type - required: - - type - title: HdaDestination - type: object - HdcaDataItemsFromTarget: - properties: - auto_decompress: - default: false - description: Decompress compressed data before sniffing? - title: Auto Decompress - type: boolean - collection_type: - anyOf: - - type: string - - type: 'null' - title: Collection Type - destination: - $ref: '#/components/schemas/HdcaDestination' - elements_from: - $ref: '#/components/schemas/ElementsFromType' - ftp_path: - anyOf: - - type: string - - type: 'null' - title: Ftp Path - name: - anyOf: - - type: string - - type: 'null' - title: Name - path: - anyOf: - - type: string - - type: 'null' - title: Path - server_dir: - anyOf: - - type: string - - type: 'null' - title: Server Dir - src: - $ref: '#/components/schemas/ItemsFromSrc' - tags: - anyOf: - - items: - type: string - type: array - - type: 'null' - title: Tags - url: - anyOf: - - type: string - - type: 'null' - title: Url - required: - - src - - destination - - elements_from - title: HdcaDataItemsFromTarget - type: object - HdcaDataItemsTarget: - properties: - auto_decompress: - default: false - description: Decompress compressed data before sniffing? - title: Auto Decompress - type: boolean - collection_type: - anyOf: - - type: string - - type: 'null' - title: Collection Type - destination: - $ref: '#/components/schemas/HdcaDestination' - elements: - items: - anyOf: - - discriminator: - mapping: - composite: '#/components/schemas/CompositeDataElement' - files: '#/components/schemas/FileDataElement' - ftp_import: '#/components/schemas/FtpImportElement' - pasted: '#/components/schemas/PastedDataElement' - path: '#/components/schemas/PathDataElement' - server_dir: '#/components/schemas/ServerDirElement' - url: '#/components/schemas/UrlDataElement' - propertyName: src - oneOf: - - $ref: '#/components/schemas/FileDataElement' - - $ref: '#/components/schemas/PastedDataElement' - - $ref: '#/components/schemas/UrlDataElement' - - $ref: '#/components/schemas/PathDataElement' - - $ref: '#/components/schemas/ServerDirElement' - - $ref: '#/components/schemas/FtpImportElement' - - $ref: '#/components/schemas/CompositeDataElement' - - $ref: '#/components/schemas/NestedElement' - title: Elements - type: array - name: - anyOf: - - type: string - - type: 'null' - title: Name - tags: - anyOf: - - items: - type: string - type: array - - type: 'null' - title: Tags - required: - - destination - - elements - title: HdcaDataItemsTarget - type: object - HdcaDestination: - properties: - type: - const: hdca - title: Type - required: - - type - title: HdcaDestination - type: object - HelpForumCategory: - additionalProperties: true - description: Model for a category in the help forum. - properties: {} - title: HelpForumCategory - type: object - HelpForumGroup: - additionalProperties: true - description: Model for a group in the help forum. - properties: {} - title: HelpForumGroup - type: object - HelpForumGroupedSearchResult: - additionalProperties: true - description: Model for a grouped search result. - properties: {} - title: HelpForumGroupedSearchResult - type: object - HelpForumPost: - additionalProperties: true - description: Model for a post in the help forum. - properties: - avatar_template: - description: The avatar template of the user. - title: Avatar Template - type: string - blurb: - description: The blurb of the post. - title: Blurb - type: string - created_at: - description: The creation date of the post. - title: Created At - type: string - id: - description: The ID of the post. - title: Id - type: integer - like_count: - description: The number of likes of the post. - title: Like Count - type: integer - name: - description: The name of the post. - title: Name - type: string - post_number: - description: The post number of the post. - title: Post Number - type: integer - topic_id: - description: The ID of the topic of the post. - title: Topic Id - type: integer - username: - description: The username of the post author. - title: Username - type: string - required: - - id - - name - - username - - avatar_template - - created_at - - like_count - - blurb - - post_number - - topic_id - title: HelpForumPost - type: object - HelpForumSearchResponse: - description: 'Response model for the help search API endpoint. - - - This model is based on the Discourse API response for the search endpoint.' - properties: - categories: - anyOf: - - items: - $ref: '#/components/schemas/HelpForumCategory' - type: array - - type: 'null' - title: Categories - grouped_search_result: - anyOf: - - $ref: '#/components/schemas/HelpForumGroupedSearchResult' - - type: 'null' - groups: - anyOf: - - items: - $ref: '#/components/schemas/HelpForumGroup' - type: array - - type: 'null' - title: Groups - posts: - anyOf: - - items: - $ref: '#/components/schemas/HelpForumPost' - type: array - - type: 'null' - title: Posts - tags: - anyOf: - - items: - $ref: '#/components/schemas/HelpForumTag' - type: array - - type: 'null' - title: Tags - topics: - anyOf: - - items: - $ref: '#/components/schemas/HelpForumTopic' - type: array - - type: 'null' - title: Topics - users: - anyOf: - - items: - $ref: '#/components/schemas/HelpForumUser' - type: array - - type: 'null' - title: Users - required: - - posts - - topics - - users - - categories - - tags - - groups - - grouped_search_result - title: HelpForumSearchResponse - type: object - HelpForumTag: - additionalProperties: true - description: Model for a tag in the help forum. - properties: {} - title: HelpForumTag - type: object - HelpForumTopic: - description: Model for a topic in the help forum compatible with Discourse API. - properties: - archetype: - description: The archetype of the topic. - title: Archetype - archived: - description: Whether the topic is archived. - title: Archived - type: boolean - bookmarked: - anyOf: - - type: boolean - - type: 'null' - description: Whether the topic is bookmarked. - title: Bookmarked - bumped: - description: Whether the topic was bumped. - title: Bumped - type: boolean - bumped_at: - description: The date of the last bump of the topic. - title: Bumped At - type: string - category_id: - description: The ID of the category of the topic. - title: Category Id - type: integer - closed: - description: Whether the topic is closed. - title: Closed - type: boolean - created_at: - description: The creation date of the topic. - title: Created At - type: string - fancy_title: - description: The fancy title of the topic. - title: Fancy Title - type: string - has_accepted_answer: - description: Whether the topic has an accepted answer. - title: Has Accepted Answer - type: boolean - highest_post_number: - description: The highest post number in the topic. - title: Highest Post Number - type: integer - id: - description: The ID of the topic. - title: Id - type: integer - last_posted_at: - description: The date of the last post in the topic. - title: Last Posted At - type: string - liked: - anyOf: - - type: boolean - - type: 'null' - description: Whether the topic is liked. - title: Liked - pinned: - description: Whether the topic is pinned. - title: Pinned - type: boolean - posts_count: - description: The number of posts in the topic. - title: Posts Count - type: integer - reply_count: - description: The number of replies in the topic. - title: Reply Count - type: integer - slug: - description: The slug of the topic. - title: Slug - type: string - tags: - description: The tags of the topic. - items: - type: string - title: Tags - type: array - tags_descriptions: - anyOf: - - {} - - type: 'null' - description: The descriptions of the tags of the topic. - title: Tags Descriptions - title: - description: The title of the topic. - title: Title - type: string - unpinned: - anyOf: - - type: boolean - - type: 'null' - description: Whether the topic is unpinned. - title: Unpinned - unseen: - description: Whether the topic is unseen. - title: Unseen - type: boolean - visible: - description: Whether the topic is visible. - title: Visible - type: boolean - required: - - id - - title - - fancy_title - - slug - - posts_count - - reply_count - - highest_post_number - - created_at - - last_posted_at - - bumped - - bumped_at - - archetype - - unseen - - pinned - - unpinned - - visible - - closed - - archived - - bookmarked - - liked - - tags - - tags_descriptions - - category_id - - has_accepted_answer - title: HelpForumTopic - type: object - HelpForumUser: - additionalProperties: true - description: Model for a user in the help forum. - properties: {} - title: HelpForumUser - type: object - HistoryContentBulkOperationPayload: - properties: - items: - anyOf: - - items: - $ref: '#/components/schemas/HistoryContentItem' - type: array - - type: 'null' - title: Items - operation: - $ref: '#/components/schemas/HistoryContentItemOperation' - params: - anyOf: - - $ref: '#/components/schemas/ChangeDatatypeOperationParams' - - $ref: '#/components/schemas/ChangeDbkeyOperationParams' - - $ref: '#/components/schemas/TagOperationParams' - - type: 'null' - title: Params - required: - - operation - title: HistoryContentBulkOperationPayload - type: object - HistoryContentBulkOperationResult: - properties: - errors: - items: - $ref: '#/components/schemas/BulkOperationItemError' - title: Errors - type: array - success_count: - title: Success Count - type: integer - required: - - success_count - - errors - title: HistoryContentBulkOperationResult - type: object - HistoryContentItem: - properties: - history_content_type: - allOf: - - $ref: '#/components/schemas/HistoryContentType' - description: The type of this item. - title: Content Type - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Id - type: string - required: - - history_content_type - - id - title: HistoryContentItem - type: object - HistoryContentItemOperation: - enum: - - hide - - unhide - - delete - - undelete - - purge - - change_datatype - - change_dbkey - - add_tags - - remove_tags - title: HistoryContentItemOperation - type: string - HistoryContentSource: - enum: - - hda - - hdca - - library - - library_folder - - new_collection - title: HistoryContentSource - type: string - HistoryContentStats: - properties: - total_matches: - description: The total number of items that match the search query without - any pagination - title: Total Matches - type: integer - required: - - total_matches - title: HistoryContentStats - type: object - HistoryContentType: - description: Available types of History contents. - enum: - - dataset - - dataset_collection - title: HistoryContentType - type: string - HistoryContentsResult: - description: 'List of history content items. - - Can contain different views and kinds of items.' - items: - anyOf: - - $ref: '#/components/schemas/HDADetailed' - - $ref: '#/components/schemas/HDASummary' - - $ref: '#/components/schemas/HDCADetailed' - - $ref: '#/components/schemas/HDCASummary' - - $ref: '#/components/schemas/CustomHistoryItem' - title: HistoryContentsResult - type: array - HistoryContentsWithStatsResult: - description: Includes stats with items counting - properties: - contents: - description: The items matching the search query. Only the items fitting - in the current page limit will be returned. - items: - anyOf: - - $ref: '#/components/schemas/HDADetailed' - - $ref: '#/components/schemas/HDASummary' - - $ref: '#/components/schemas/HDCADetailed' - - $ref: '#/components/schemas/HDCASummary' - - $ref: '#/components/schemas/CustomHistoryItem' - title: Contents - type: array - stats: - allOf: - - $ref: '#/components/schemas/HistoryContentStats' - description: Contains counting stats for the query. - title: Stats - required: - - stats - - contents - title: HistoryContentsWithStatsResult - type: object - HistoryDetailed: - additionalProperties: true - description: History detailed information. - properties: - annotation: - anyOf: - - type: string - - type: 'null' - description: An annotation to provide details or to help understand the - purpose and usage of this item. - title: Annotation - archived: - description: Whether this item has been archived and is no longer active. - title: Archived - type: boolean - contents_url: - description: The relative URL to access the contents of this History. - title: Contents URL - type: string - count: - description: The number of items in the history. - title: Count - type: integer - create_time: - description: The time and date this item was created. - format: date-time - title: Create Time - type: string - deleted: - description: Whether this item is marked as deleted. - title: Deleted - type: boolean - genome_build: - anyOf: - - type: string - - type: 'null' - default: '?' - description: TODO - title: Genome Build - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: History ID - type: string - importable: - description: Whether this History can be imported by other users with a - shared link. - title: Importable - type: boolean - model_class: - const: History - description: The name of the database model class. - title: Model class - type: string - name: - description: The name of the history. - title: Name - type: string - preferred_object_store_id: - anyOf: - - type: string - - type: 'null' - description: The ID of the object store that should be used to store new - datasets in this history. - title: Preferred Object Store ID - published: - description: Whether this resource is currently publicly available to all - users. - title: Published - type: boolean - purged: - description: Whether this item has been permanently removed. - title: Purged - type: boolean - size: - description: The total size of the contents of this history in bytes. - title: Size - type: integer - slug: - anyOf: - - type: string - - type: 'null' - description: Part of the URL to uniquely identify this History by link in - a readable way. - title: Slug - state: - allOf: - - $ref: '#/components/schemas/DatasetState' - description: The current state of the History based on the states of the - datasets it contains. - title: State - state_details: - additionalProperties: - type: integer - description: A dictionary keyed to possible dataset states and valued with - the number of datasets in this history that have those states. - title: State Counts - type: object - state_ids: - additionalProperties: - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - type: array - description: A dictionary keyed to possible dataset states and valued with - lists containing the ids of each HDA in that state. - title: State IDs - type: object - tags: - $ref: '#/components/schemas/TagCollection' - update_time: - description: The last time and date this item was updated. - format: date-time - title: Update Time - type: string - url: - deprecated: true - description: The relative URL to access this item. - title: URL - type: string - user_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: The encoded ID of the user that owns this History. - title: User ID - username: - anyOf: - - type: string - - type: 'null' - description: Owner of the history - title: Username - username_and_slug: - anyOf: - - type: string - - type: 'null' - description: The relative URL in the form of /u/{username}/h/{slug} - title: Username and slug - required: - - model_class - - id - - name - - deleted - - purged - - archived - - url - - published - - count - - annotation - - tags - - update_time - - contents_url - - size - - create_time - - importable - - state - - state_ids - - state_details - title: HistoryDetailed - type: object - HistoryMinimal: - additionalProperties: true - description: Minimal History Response with optional fields - properties: - id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - title: Id - model_class: - const: History - description: The name of the database model class. - title: Model class - type: string - user_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: The encoded ID of the user that owns this History. - title: User ID - required: - - model_class - title: HistoryMinimal - type: object - HistorySummary: - additionalProperties: true - description: History summary information. - properties: - annotation: - anyOf: - - type: string - - type: 'null' - description: An annotation to provide details or to help understand the - purpose and usage of this item. - title: Annotation - archived: - description: Whether this item has been archived and is no longer active. - title: Archived - type: boolean - count: - description: The number of items in the history. - title: Count - type: integer - deleted: - description: Whether this item is marked as deleted. - title: Deleted - type: boolean - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: History ID - type: string - model_class: - const: History - description: The name of the database model class. - title: Model class - type: string - name: - description: The name of the history. - title: Name - type: string - preferred_object_store_id: - anyOf: - - type: string - - type: 'null' - description: The ID of the object store that should be used to store new - datasets in this history. - title: Preferred Object Store ID - published: - description: Whether this resource is currently publicly available to all - users. - title: Published - type: boolean - purged: - description: Whether this item has been permanently removed. - title: Purged - type: boolean - tags: - $ref: '#/components/schemas/TagCollection' - update_time: - description: The last time and date this item was updated. - format: date-time - title: Update Time - type: string - url: - deprecated: true - description: The relative URL to access this item. - title: URL - type: string - required: - - model_class - - id - - name - - deleted - - purged - - archived - - url - - published - - count - - annotation - - tags - - update_time - title: HistorySummary - type: object - Hyperlink: - description: Represents some text with an Hyperlink. - properties: - href: - description: Specifies the linked document, resource, or location. - format: uri - minLength: 1 - title: HRef - type: string - target: - description: Specifies where to open the linked document. - examples: - - _blank - title: Target - type: string - text: - description: The text placeholder for the link. - title: Text - type: string - required: - - target - - href - - text - title: Hyperlink - type: object - ImplicitCollectionJobsStateSummary: - properties: - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Id - type: string - model: - const: ImplicitCollectionJobs - description: The name of the database model class. - title: Model class - type: string - populated_state: - allOf: - - $ref: '#/components/schemas/DatasetCollectionPopulatedState' - description: 'Indicates the general state of the elements in the dataset - collection:- ''new'': new dataset collection, unpopulated elements.- ''ok'': - collection elements populated (HDAs may or may not have errors).- ''failed'': - some problem populating, won''t be populated.' - title: Populated State - states: - additionalProperties: - type: integer - default: {} - description: A dictionary of job states and the number of jobs in that state. - title: States - type: object - required: - - id - - populated_state - - model - title: ImplicitCollectionJobsStateSummary - type: object - ImportToolDataBundle: - properties: - source: - discriminator: - mapping: - hda: '#/components/schemas/ImportToolDataBundleDatasetSource' - ldda: '#/components/schemas/ImportToolDataBundleDatasetSource' - uri: '#/components/schemas/ImportToolDataBundleUriSource' - propertyName: src - oneOf: - - $ref: '#/components/schemas/ImportToolDataBundleDatasetSource' - - $ref: '#/components/schemas/ImportToolDataBundleUriSource' - title: Source - required: - - source - title: ImportToolDataBundle - type: object - ImportToolDataBundleDatasetSource: - properties: - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Id - type: string - src: - description: Indicates that the tool data should be resolved from a dataset. - enum: - - hda - - ldda - title: src - type: string - required: - - src - - id - title: ImportToolDataBundleDatasetSource - type: object - ImportToolDataBundleUriSource: - properties: - src: - const: uri - description: Indicates that the tool data should be resolved by a URI. - title: src - uri: - description: URI to fetch tool data bundle from (file:// URIs are fine because - this is an admin-only operation) - title: uri - type: string - required: - - src - - uri - title: ImportToolDataBundleUriSource - type: object - InputArguments: - properties: - dbkey: - anyOf: - - type: string - - type: 'null' - default: '?' - description: Sets the database key of the objects being fetched to Galaxy. - title: Database Key - file_type: - anyOf: - - type: string - - type: 'null' - default: auto - description: 'Sets the Galaxy datatype (e.g., `bam`) for the objects being - fetched to Galaxy. See the following link for a complete list of Galaxy - data types: https://galaxyproject.org/learn/datatypes/.' - title: File Type - space_to_tab: - anyOf: - - type: boolean - - type: 'null' - default: false - description: A boolean value ('true' or 'false') that sets if spaces should - be converted to tab in the objects being fetched to Galaxy. Applicable - only if `to_posix_lines` is True - title: Spaces to tabs - to_posix_lines: - anyOf: - - const: 'Yes' - - type: boolean - - type: 'null' - default: 'Yes' - description: A boolean value ('true' or 'false'); if 'Yes', converts universal - line endings to POSIX line endings. Set to 'False' if you upload a gzip, - bz2 or zip archive containing a binary file. - title: POSIX line endings - title: InputArguments - type: object - InstalledRepositoryToolShedStatus: - properties: - latest_installable_revision: - anyOf: - - type: string - - type: 'null' - description: Most recent version available on the tool shed - title: Latest installed revision - repository_deprecated: - anyOf: - - type: string - - type: 'null' - description: Repository has been depreciated on the tool shed - title: Repository deprecated - revision_update: - title: Revision Update - type: string - revision_upgrade: - anyOf: - - type: string - - type: 'null' - title: Revision Upgrade - required: - - latest_installable_revision - - revision_update - - repository_deprecated - title: InstalledRepositoryToolShedStatus - type: object - InstalledToolShedRepository: - properties: - changeset_revision: - description: Changeset revision of the repository - a mercurial commit hash - title: Changeset revision - type: string - ctx_rev: - anyOf: - - type: string - - type: 'null' - description: The linearized 0-based index of the changeset on the tool shed - (0, 1, 2,...) - title: Changeset revision number - deleted: - title: Deleted - type: boolean - dist_to_shed: - title: Dist To Shed - type: boolean - error_message: - default: Installation error message, the empty string means no error was - recorded - title: Error Message - type: string - id: - description: Encoded ID of the install tool shed repository. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - installed_changeset_revision: - description: Initially installed changeset revision. Used to construct path - to repository within Galaxies filesystem. Does not change if a repository - is updated. - title: Installed changeset revision - type: string - model_class: - const: ToolShedRepository - description: The name of the database model class. - title: Model class - type: string - name: - description: Name of repository - title: Name - type: string - owner: - description: Owner of repository - title: Owner - type: string - status: - title: Status - type: string - tool_shed: - description: Hostname of the tool shed this was installed from - title: Tool shed - type: string - tool_shed_status: - anyOf: - - $ref: '#/components/schemas/InstalledRepositoryToolShedStatus' - - type: 'null' - title: Latest updated status from the tool shed - uninstalled: - title: Uninstalled - type: boolean - required: - - model_class - - id - - status - - name - - owner - - deleted - - ctx_rev - - installed_changeset_revision - - tool_shed - - dist_to_shed - - uninstalled - - changeset_revision - - tool_shed_status - title: InstalledToolShedRepository - type: object - InvocationCancellationHistoryDeletedResponse: - properties: - history_id: - description: History ID of history that was deleted. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: History ID - type: string - reason: - const: history_deleted - title: Reason - required: - - reason - - history_id - title: InvocationCancellationHistoryDeletedResponse - type: object - InvocationCancellationReviewFailedResponse: - properties: - reason: - const: cancelled_on_review - title: Reason - workflow_step_id: - description: Workflow step id of paused step that did not pass review. - title: Workflow Step Id - type: integer - required: - - reason - - workflow_step_id - title: InvocationCancellationReviewFailedResponse - type: object - InvocationCancellationUserRequestResponse: - properties: - reason: - const: user_request - title: Reason - required: - - reason - title: InvocationCancellationUserRequestResponse - type: object - InvocationEvaluationWarningWorkflowOutputNotFoundResponse: - properties: - output_name: - description: Output that was designated as workflow output but that has - not been found - title: Output Name - type: string - reason: - const: workflow_output_not_found - title: Reason - workflow_step_id: - title: Workflow step id of step that caused a warning. - type: integer - required: - - reason - - workflow_step_id - - output_name - title: InvocationEvaluationWarningWorkflowOutputNotFoundResponse - type: object - InvocationFailureCollectionFailedResponse: - properties: - dependent_workflow_step_id: - description: Workflow step id of step that caused failure. - title: Dependent Workflow Step Id - type: integer - hdca_id: - description: HistoryDatasetCollectionAssociation ID that relates to failure. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: HistoryDatasetCollectionAssociation ID - type: string - reason: - const: collection_failed - title: Reason - workflow_step_id: - description: Workflow step id of step that failed. - title: Workflow Step Id - type: integer - required: - - reason - - workflow_step_id - - hdca_id - - dependent_workflow_step_id - title: InvocationFailureCollectionFailedResponse - type: object - InvocationFailureDatasetFailedResponse: - properties: - dependent_workflow_step_id: - anyOf: - - type: integer - - type: 'null' - description: Workflow step id of step that caused failure. - title: Dependent Workflow Step Id - hda_id: - description: HistoryDatasetAssociation ID that relates to failure. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: HistoryDatasetAssociation ID - type: string - reason: - const: dataset_failed - title: Reason - workflow_step_id: - description: Workflow step id of step that failed. - title: Workflow Step Id - type: integer - required: - - reason - - workflow_step_id - - hda_id - title: InvocationFailureDatasetFailedResponse - type: object - InvocationFailureExpressionEvaluationFailedResponse: - properties: - details: - anyOf: - - type: string - - type: 'null' - description: May contain details to help troubleshoot this problem. - title: Details - reason: - const: expression_evaluation_failed - title: Reason - workflow_step_id: - description: Workflow step id of step that failed. - title: Workflow Step Id - type: integer - required: - - reason - - workflow_step_id - title: InvocationFailureExpressionEvaluationFailedResponse - type: object - InvocationFailureJobFailedResponse: - properties: - dependent_workflow_step_id: - description: Workflow step id of step that caused failure. - title: Dependent Workflow Step Id - type: integer - job_id: - description: Job ID that relates to failure. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Job ID - type: string - reason: - const: job_failed - title: Reason - workflow_step_id: - description: Workflow step id of step that failed. - title: Workflow Step Id - type: integer - required: - - reason - - workflow_step_id - - job_id - - dependent_workflow_step_id - title: InvocationFailureJobFailedResponse - type: object - InvocationFailureOutputNotFoundResponse: - properties: - dependent_workflow_step_id: - description: Workflow step id of step that caused failure. - title: Dependent Workflow Step Id - type: integer - output_name: - title: Tool or module output name that was referenced but not produced - type: string - reason: - const: output_not_found - title: Reason - workflow_step_id: - description: Workflow step id of step that failed. - title: Workflow Step Id - type: integer - required: - - reason - - workflow_step_id - - output_name - - dependent_workflow_step_id - title: InvocationFailureOutputNotFoundResponse - type: object - InvocationFailureWhenNotBooleanResponse: - properties: - details: - description: Contains details to help troubleshoot this problem. - title: Details - type: string - reason: - const: when_not_boolean - title: Reason - workflow_step_id: - description: Workflow step id of step that failed. - title: Workflow Step Id - type: integer - required: - - reason - - workflow_step_id - - details - title: InvocationFailureWhenNotBooleanResponse - type: object - InvocationInput: - properties: - id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: The encoded ID of the dataset/dataset collection. - title: ID - label: - anyOf: - - type: string - - type: 'null' - description: Label of the workflow step associated with the input dataset/dataset - collection. - title: Label - src: - anyOf: - - const: hda - - const: hdca - description: Source type of the input dataset/dataset collection. - title: Source - workflow_step_id: - description: The encoded ID of the workflow step associated with the dataset/dataset - collection. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Workflow step ID - type: string - required: - - workflow_step_id - - src - title: InvocationInput - type: object - InvocationInputParameter: - properties: - label: - description: Label of the workflow step associated with the input parameter. - title: Label - type: string - parameter_value: - description: Value of the input parameter. - title: Parameter value - workflow_step_id: - description: The encoded ID of the workflow step associated with the input - parameter. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Workflow step ID - type: string - required: - - parameter_value - - label - - workflow_step_id - title: InvocationInputParameter - type: object - InvocationJobsResponse: - properties: - id: - description: The encoded ID of the workflow invocation. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - model: - const: WorkflowInvocation - title: Model - populated_state: - allOf: - - $ref: '#/components/schemas/JobState' - description: The absolute state of all the jobs related to the Invocation. - title: Populated state - states: - additionalProperties: - type: integer - description: The states of all the jobs related to the Invocation. - title: States - type: object - required: - - id - - states - - populated_state - - model - title: InvocationJobsResponse - type: object - InvocationOutput: - properties: - id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: The encoded ID of the dataset/dataset collection. - title: ID - src: - const: hda - description: Source model of the output dataset. - title: Source - workflow_step_id: - description: The encoded ID of the workflow step associated with the dataset/dataset - collection. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Workflow step ID - type: string - required: - - workflow_step_id - - src - title: InvocationOutput - type: object - InvocationOutputCollection: - properties: - id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: The encoded ID of the dataset/dataset collection. - title: ID - src: - const: hdca - description: Source model of the output dataset collection. - title: Source - workflow_step_id: - description: The encoded ID of the workflow step associated with the dataset/dataset - collection. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Workflow step ID - type: string - required: - - workflow_step_id - - src - title: InvocationOutputCollection - type: object - InvocationReport: - description: Report describing workflow invocation - properties: - errors: - anyOf: - - type: object - - type: 'null' - description: Errors associated with the invocation. - title: Errors - generate_time: - anyOf: - - type: string - - type: 'null' - description: The version of Galaxy this object was generated with. - title: Galaxy Version - generate_version: - anyOf: - - type: string - - type: 'null' - description: The version of Galaxy this object was generated with. - title: Galaxy Version - histories: - anyOf: - - type: object - - type: 'null' - description: Histories associated with the invocation. - title: Histories - history_dataset_collections: - anyOf: - - type: object - - type: 'null' - description: History dataset collections associated with the invocation. - title: History dataset collections - history_datasets: - anyOf: - - type: object - - type: 'null' - description: History datasets associated with the invocation. - title: History datasets - id: - description: The workflow this invocation has been triggered for. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Workflow ID - type: string - invocation_markdown: - anyOf: - - type: string - - type: 'null' - description: Raw galaxy-flavored markdown contents of the report. - title: Markdown - invocations: - anyOf: - - type: object - - type: 'null' - description: Other invocations associated with the invocation. - title: Invocations - jobs: - anyOf: - - type: object - - type: 'null' - description: Jobs associated with the invocation. - title: Jobs - markdown: - anyOf: - - type: string - - type: 'null' - description: Raw galaxy-flavored markdown contents of the report. - title: Markdown - model_class: - const: Report - description: The name of the database model class. - title: Model class - type: string - render_format: - const: markdown - default: markdown - description: Format of the invocation report. - title: Render format - title: - description: The name of the report. - title: Title - type: string - username: - description: The name of the user who owns this report. - title: Username - type: string - workflows: - anyOf: - - type: object - - type: 'null' - description: Workflows associated with the invocation. - title: Workflows - required: - - model_class - - id - - username - - title - title: InvocationReport - type: object - InvocationSerializationView: - enum: - - element - - collection - title: InvocationSerializationView - type: string - InvocationSortByEnum: - enum: - - create_time - - update_time - - None - title: InvocationSortByEnum - type: string - InvocationState: - enum: - - new - - ready - - scheduled - - cancelled - - cancelling - - failed - title: InvocationState - type: string - InvocationStep: - description: Information about workflow invocation step - properties: - action: - anyOf: - - type: boolean - - type: 'null' - description: Whether to take action on the invocation step. - title: Action - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation Step ID - type: string - job_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - title: Job Id - jobs: - default: [] - description: Jobs associated with the workflow invocation step. - items: - $ref: '#/components/schemas/JobBaseModel' - title: Jobs - type: array - model_class: - const: WorkflowInvocationStep - description: The name of the database model class. - title: Model class - type: string - order_index: - description: The index of the workflow step in the workflow. - title: Order index - type: integer - output_collections: - additionalProperties: - $ref: '#/components/schemas/InvocationStepCollectionOutput' - default: {} - description: The dataset collection outputs of the workflow invocation step. - title: Output collections - type: object - outputs: - additionalProperties: - $ref: '#/components/schemas/InvocationStepOutput' - default: {} - description: The outputs of the workflow invocation step. - title: Outputs - type: object - state: - anyOf: - - $ref: '#/components/schemas/InvocationStepState' - - $ref: '#/components/schemas/JobState' - - type: 'null' - description: Describes where in the scheduling process the workflow invocation - step is. - title: State of the invocation step - subworkflow_invocation_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - title: Subworkflow Invocation Id - update_time: - anyOf: - - format: date-time - type: string - - type: 'null' - description: The last time and date this item was updated. - title: Update Time - workflow_step_id: - description: The encoded ID of the workflow step associated with this workflow - invocation step. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Workflow step ID - type: string - workflow_step_label: - anyOf: - - type: string - - type: 'null' - description: The label of the workflow step - title: Step label - workflow_step_uuid: - anyOf: - - format: uuid4 - type: string - - type: 'null' - description: Universal unique identifier of the workflow step. - title: UUID - required: - - model_class - - id - - update_time - - job_id - - workflow_step_id - - subworkflow_invocation_id - - action - - order_index - title: InvocationStep - type: object - InvocationStepCollectionOutput: - properties: - id: - description: Dataset Collection ID of the workflow step output. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Dataset Collection ID - type: string - src: - const: hdca - default: hdca - description: The source model of the output. - title: src - required: - - id - title: InvocationStepCollectionOutput - type: object - InvocationStepJobsResponseCollectionJobsModel: - properties: - id: - description: The encoded ID of the workflow invocation. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - model: - const: ImplicitCollectionJobs - title: Model - populated_state: - allOf: - - $ref: '#/components/schemas/JobState' - description: The absolute state of all the jobs related to the Invocation. - title: Populated state - states: - additionalProperties: - type: integer - description: The states of all the jobs related to the Invocation. - title: States - type: object - required: - - id - - states - - populated_state - - model - title: InvocationStepJobsResponseCollectionJobsModel - type: object - InvocationStepJobsResponseJobModel: - properties: - id: - description: The encoded ID of the workflow invocation. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - model: - const: Job - title: Model - populated_state: - allOf: - - $ref: '#/components/schemas/JobState' - description: The absolute state of all the jobs related to the Invocation. - title: Populated state - states: - additionalProperties: - type: integer - description: The states of all the jobs related to the Invocation. - title: States - type: object - required: - - id - - states - - populated_state - - model - title: InvocationStepJobsResponseJobModel - type: object - InvocationStepJobsResponseStepModel: - properties: - id: - description: The encoded ID of the workflow invocation. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - model: - const: WorkflowInvocationStep - title: Model - populated_state: - allOf: - - $ref: '#/components/schemas/JobState' - description: The absolute state of all the jobs related to the Invocation. - title: Populated state - states: - additionalProperties: - type: integer - description: The states of all the jobs related to the Invocation. - title: States - type: object - required: - - id - - states - - populated_state - - model - title: InvocationStepJobsResponseStepModel - type: object - InvocationStepOutput: - properties: - id: - description: Dataset ID of the workflow step output. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Dataset ID - type: string - src: - const: hda - default: hda - description: The source model of the output. - title: src - uuid: - anyOf: - - format: uuid4 - type: string - - type: 'null' - description: Universal unique identifier of the workflow step output dataset. - title: UUID - required: - - id - title: InvocationStepOutput - type: object - InvocationStepState: - enum: - - new - - ready - - scheduled - title: InvocationStepState - type: string - InvocationUnexpectedFailureResponse: - properties: - details: - anyOf: - - type: string - - type: 'null' - description: May contains details to help troubleshoot this problem. - title: Details - reason: - const: unexpected_failure - title: Reason - workflow_step_id: - anyOf: - - type: integer - - type: 'null' - description: Workflow step id of step that failed. - title: Workflow Step Id - required: - - reason - title: InvocationUnexpectedFailureResponse - type: object - InvocationUpdatePayload: - properties: - action: - description: Whether to take action on the invocation step. - title: Action - type: boolean - required: - - action - title: InvocationUpdatePayload - type: object - ItemTagsCreatePayload: - description: Payload schema for creating an item tag. - properties: - value: - anyOf: - - type: string - - type: 'null' - title: value of the item tag - title: ItemTagsCreatePayload - type: object - ItemTagsListResponse: - description: Response schema for listing item tags. - items: - $ref: '#/components/schemas/ItemTagsResponse' - title: ItemTagsListResponse - type: array - ItemTagsPayload: - properties: - item_class: - allOf: - - $ref: '#/components/schemas/TaggableItemClass' - description: The name of the class of the item that will be tagged. - title: Item class - item_id: - description: The `encoded identifier` of the item whose tags will be updated. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Item ID - type: string - item_tags: - anyOf: - - $ref: '#/components/schemas/TagCollection' - - type: 'null' - description: The list of tags that will replace the current tags associated - with the item. - title: Item tags - required: - - item_id - - item_class - title: ItemTagsPayload - type: object - ItemTagsResponse: - description: Response schema for showing an item tag. - properties: - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: item tag ID - type: string - model_class: - title: model class - type: string - user_tname: - title: name of the item tag - type: string - user_value: - anyOf: - - type: string - - type: 'null' - title: value of the item tag - required: - - model_class - - id - - user_tname - title: ItemTagsResponse - type: object - ItemsFromSrc: - enum: - - url - - files - - path - - ftp_import - - server_dir - title: ItemsFromSrc - type: string - JobBaseModel: - properties: - create_time: - description: The time and date this item was created. - format: date-time - title: Create Time - type: string - exit_code: - anyOf: - - type: integer - - type: 'null' - description: The exit code returned by the tool. Can be unset if the job - is not completed yet. - title: Exit Code - galaxy_version: - anyOf: - - type: string - - type: 'null' - description: The (major) version of Galaxy used to create this job. - examples: - - '21.05' - title: Galaxy Version - history_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: The encoded ID of the history associated with this item. - title: History ID - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Job ID - type: string - model_class: - const: Job - description: The name of the database model class. - title: Model class - type: string - state: - allOf: - - $ref: '#/components/schemas/JobState' - description: Current state of the job. - title: State - tool_id: - description: Identifier of the tool that generated this job. - title: Tool ID - type: string - update_time: - description: The last time and date this item was updated. - format: date-time - title: Update Time - type: string - required: - - model_class - - id - - tool_id - - state - - create_time - - update_time - title: JobBaseModel - type: object - JobDestinationParams: - additionalProperties: true - properties: - Handler: - anyOf: - - type: string - - type: 'null' - description: Name of the process that handled the job. - title: Handler - Runner: - anyOf: - - type: string - - type: 'null' - description: Job runner class - title: Runner - Runner Job ID: - anyOf: - - type: string - - type: 'null' - description: ID assigned to submitted job by external job running system - title: Runner Job ID - title: JobDestinationParams - type: object - JobDisplayParametersSummary: - properties: - has_parameter_errors: - description: The job has parameter errors - title: Has parameter errors - type: boolean - outputs: - additionalProperties: - items: - $ref: '#/components/schemas/JobOutput' - type: array - description: Dictionary mapping all the tool outputs (by name) with the - corresponding dataset information in a nested format. - title: Outputs - type: object - parameters: - description: The parameters of the job in a nested format. - items: - $ref: '#/components/schemas/JobParameter' - title: Parameters - type: array - required: - - parameters - - has_parameter_errors - - outputs - title: JobDisplayParametersSummary - type: object - JobErrorSummary: - properties: - messages: - description: The error messages for the specified job. - items: - items: - type: string - type: array - title: Error messages - type: array - required: - - messages - title: JobErrorSummary - type: object - JobExportHistoryArchiveListResponse: - items: - $ref: '#/components/schemas/JobExportHistoryArchiveModel' - title: JobExportHistoryArchiveListResponse - type: array - JobExportHistoryArchiveModel: - properties: - download_url: - description: Relative API URL to download the exported history archive. - title: Download URL - type: string - external_download_latest_url: - description: Fully qualified URL to download the latests version of the - exported history archive. - format: uri - minLength: 1 - title: External Download Latest URL - type: string - external_download_permanent_url: - description: Fully qualified URL to download this particular version of - the exported history archive. - format: uri - minLength: 1 - title: External Download Permanent URL - type: string - id: - description: The encoded database ID of the export request. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - job_id: - description: The encoded database ID of the job that generated this history - export archive. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Job ID - type: string - preparing: - description: Whether the archive is currently being built or in preparation. - title: Preparing - type: boolean - ready: - description: Whether the export has completed successfully and the archive - is ready - title: Ready - type: boolean - up_to_date: - description: False, if a new export archive should be generated. - title: Up to Date - type: boolean - required: - - id - - ready - - preparing - - up_to_date - - job_id - - download_url - - external_download_latest_url - - external_download_permanent_url - title: JobExportHistoryArchiveModel - type: object - JobIdResponse: - description: Contains the ID of the job associated with a particular request. - properties: - job_id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Job ID - type: string - required: - - job_id - title: JobIdResponse - type: object - JobImportHistoryResponse: - properties: - create_time: - description: The time and date this item was created. - format: date-time - title: Create Time - type: string - exit_code: - anyOf: - - type: integer - - type: 'null' - description: The exit code returned by the tool. Can be unset if the job - is not completed yet. - title: Exit Code - galaxy_version: - anyOf: - - type: string - - type: 'null' - description: The (major) version of Galaxy used to create this job. - examples: - - '21.05' - title: Galaxy Version - history_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: The encoded ID of the history associated with this item. - title: History ID - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Job ID - type: string - message: - description: Text message containing information about the history import. - title: Message - type: string - model_class: - const: Job - description: The name of the database model class. - title: Model class - type: string - state: - allOf: - - $ref: '#/components/schemas/JobState' - description: Current state of the job. - title: State - tool_id: - description: Identifier of the tool that generated this job. - title: Tool ID - type: string - update_time: - description: The last time and date this item was updated. - format: date-time - title: Update Time - type: string - required: - - model_class - - id - - tool_id - - state - - create_time - - update_time - - message - title: JobImportHistoryResponse - type: object - JobIndexSortByEnum: - enum: - - create_time - - update_time - title: JobIndexSortByEnum - type: string - JobIndexViewEnum: - enum: - - collection - - admin_job_list - title: JobIndexViewEnum - type: string - JobInputAssociation: - properties: - dataset: - allOf: - - $ref: '#/components/schemas/EncodedDataItemSourceId' - description: Reference to the associated item. - title: dataset - name: - description: Name of the job input parameter. - title: name - type: string - required: - - name - - dataset - title: JobInputAssociation - type: object - JobInputSummary: - properties: - has_duplicate_inputs: - description: Job has duplicate inputs. - title: Duplicate inputs - type: boolean - has_empty_inputs: - description: Job has empty inputs. - title: Empty inputs - type: boolean - required: - - has_empty_inputs - - has_duplicate_inputs - title: JobInputSummary - type: object - JobLock: - properties: - active: - description: If active, jobs will not dispatch - title: Job lock status - type: boolean - required: - - active - title: JobLock - type: object - JobMetric: - example: - name: start_epoch - plugin: core - raw_value: '1614261340.0000000' - title: Job Start Time - value: '2021-02-25 14:55:40' - properties: - name: - description: The name of the metric variable. - title: Name - type: string - plugin: - description: The instrumenter plugin that generated this metric. - title: Plugin - type: string - raw_value: - description: The raw value of the metric as a string. - title: Raw Value - type: string - title: - description: A descriptive title for this metric. - title: Title - type: string - value: - description: The textual representation of the metric value. - title: Value - type: string - required: - - title - - value - - plugin - - name - - raw_value - title: JobMetric - type: object - JobMetricCollection: - default: [] - description: Represents a collection of metrics associated with a Job. - items: - $ref: '#/components/schemas/JobMetric' - title: JobMetricCollection - type: array - JobOutput: - properties: - label: - description: The output label - title: Output label - value: - allOf: - - $ref: '#/components/schemas/EncodedDataItemSourceId' - description: The associated dataset. - title: Dataset - required: - - label - - value - title: JobOutput - type: object - JobOutputAssociation: - properties: - dataset: - allOf: - - $ref: '#/components/schemas/EncodedDataItemSourceId' - description: Reference to the associated item. - title: dataset - name: - description: Name of the job output parameter. - title: name - type: string - required: - - name - - dataset - title: JobOutputAssociation - type: object - JobParameter: - properties: - depth: - description: The depth of the job parameter. - title: Depth - type: integer - notes: - anyOf: - - type: string - - type: 'null' - description: Notes associated with the job parameter. - title: Notes - text: - description: Text associated with the job parameter. - title: Text - type: string - value: - anyOf: - - items: - $ref: '#/components/schemas/EncodedJobParameterHistoryItem' - type: array - - type: number - - type: integer - - type: boolean - - type: string - - type: 'null' - description: The values of the job parameter - title: Value - required: - - text - - depth - title: JobParameter - type: object - JobSourceType: - description: Available types of job sources (model classes) that produce dataset - collections. - enum: - - Job - - ImplicitCollectionJobs - - WorkflowInvocation - title: JobSourceType - type: string - JobState: - enum: - - new - - resubmitted - - upload - - waiting - - queued - - running - - ok - - error - - failed - - paused - - deleting - - deleted - - stop - - stopped - - skipped - title: JobState - type: string - JobStateSummary: - properties: - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Id - type: string - model: - const: Job - description: The name of the database model class. - title: Model class - type: string - populated_state: - allOf: - - $ref: '#/components/schemas/DatasetCollectionPopulatedState' - description: 'Indicates the general state of the elements in the dataset - collection:- ''new'': new dataset collection, unpopulated elements.- ''ok'': - collection elements populated (HDAs may or may not have errors).- ''failed'': - some problem populating, won''t be populated.' - title: Populated State - states: - additionalProperties: - type: integer - default: {} - description: A dictionary of job states and the number of jobs in that state. - title: States - type: object - required: - - id - - populated_state - - model - title: JobStateSummary - type: object - JobSummary: - description: Basic information about a job. - properties: - command_line: - anyOf: - - type: string - - type: 'null' - description: The command line produced by the job. Users can see this value - if allowed in the configuration, administrator can always see this value. - title: Command Line - create_time: - description: The time and date this item was created. - format: date-time - title: Create Time - type: string - exit_code: - anyOf: - - type: integer - - type: 'null' - description: The exit code returned by the tool. Can be unset if the job - is not completed yet. - title: Exit Code - external_id: - anyOf: - - type: string - - type: 'null' - description: The job id used by the external job runner (Condor, Pulsar, - etc.). Only administrator can see this value. - title: External ID - galaxy_version: - anyOf: - - type: string - - type: 'null' - description: The (major) version of Galaxy used to create this job. - examples: - - '21.05' - title: Galaxy Version - handler: - anyOf: - - type: string - - type: 'null' - description: The job handler process assigned to handle this job. Only administrator - can see this value. - title: Job Handler - history_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: The encoded ID of the history associated with this item. - title: History ID - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Job ID - type: string - job_runner_name: - anyOf: - - type: string - - type: 'null' - description: Name of the job runner plugin that handles this job. Only administrator - can see this value. - title: Job Runner Name - model_class: - const: Job - description: The name of the database model class. - title: Model class - type: string - state: - allOf: - - $ref: '#/components/schemas/JobState' - description: Current state of the job. - title: State - tool_id: - description: Identifier of the tool that generated this job. - title: Tool ID - type: string - update_time: - description: The last time and date this item was updated. - format: date-time - title: Update Time - type: string - user_email: - anyOf: - - type: string - - type: 'null' - description: The email of the user that owns this job. Only the owner of - the job and administrators can see this value. - title: User Email - required: - - model_class - - id - - tool_id - - state - - create_time - - update_time - title: JobSummary - type: object - LabelValuePair: - description: Generic Label/Value pair model. - properties: - label: - description: The label of the item. - title: Label - type: string - value: - description: The value of the item. - title: Value - type: string - required: - - label - - value - title: LabelValuePair - type: object - LegacyLibraryPermissionsPayload: - properties: - LIBRARY_ACCESS_in: - anyOf: - - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - type: array - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - default: [] - description: A list of role encoded IDs defining roles that should have - access permission on the library. - title: Access IDs - LIBRARY_ADD_in: - anyOf: - - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - type: array - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - default: [] - description: A list of role encoded IDs defining roles that should have - manage permission on the library. - title: Manage IDs - LIBRARY_MANAGE_in: - anyOf: - - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - type: array - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - default: [] - description: A list of role encoded IDs defining roles that should have - modify permission on the library. - title: Modify IDs - LIBRARY_MODIFY_in: - anyOf: - - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - type: array - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - default: [] - description: A list of role encoded IDs defining roles that should be able - to add items to the library. - title: Add IDs - title: LegacyLibraryPermissionsPayload - type: object - LibraryAvailablePermissions: - properties: - page: - description: Current page. - title: Page - type: integer - page_limit: - description: Maximum number of items per page. - title: Page Limit - type: integer - roles: - description: A list available roles that can be assigned to a particular - permission. - items: - $ref: '#/components/schemas/BasicRoleModel' - title: Roles - type: array - total: - description: Total number of items - title: Total - type: integer - required: - - roles - - page - - page_limit - - total - title: LibraryAvailablePermissions - type: object - LibraryCurrentPermissions: - properties: - access_library_role_list: - description: A list containing pairs of role names and corresponding encoded - IDs which have access to the Library. - items: - items: - type: string - type: array - title: Access Role List - type: array - add_library_item_role_list: - description: A list containing pairs of role names and corresponding encoded - IDs which can add items to the Library. - items: - items: - type: string - type: array - title: Add Role List - type: array - manage_library_role_list: - description: A list containing pairs of role names and corresponding encoded - IDs which can manage the Library. - items: - items: - type: string - type: array - title: Manage Role List - type: array - modify_library_role_list: - description: A list containing pairs of role names and corresponding encoded - IDs which can modify the Library. - items: - items: - type: string - type: array - title: Modify Role List - type: array - required: - - access_library_role_list - - modify_library_role_list - - manage_library_role_list - - add_library_item_role_list - title: LibraryCurrentPermissions - type: object - LibraryDestination: - properties: - description: - anyOf: - - type: string - - type: 'null' - description: Description for library to create - title: Description - name: - description: Must specify a library name - title: Name - type: string - synopsis: - anyOf: - - type: string - - type: 'null' - description: Description for library to create - title: Synopsis - type: - const: library - title: Type - required: - - type - - name - title: LibraryDestination - type: object - LibraryFolderContentsIndexResult: - properties: - folder_contents: - items: - discriminator: - mapping: - file: '#/components/schemas/FileLibraryFolderItem' - folder: '#/components/schemas/FolderLibraryFolderItem' - propertyName: type - oneOf: - - $ref: '#/components/schemas/FileLibraryFolderItem' - - $ref: '#/components/schemas/FolderLibraryFolderItem' - title: Folder Contents - type: array - metadata: - $ref: '#/components/schemas/LibraryFolderMetadata' - required: - - metadata - - folder_contents - title: LibraryFolderContentsIndexResult - type: object - LibraryFolderCurrentPermissions: - properties: - add_library_item_role_list: - description: A list containing pairs of role names and corresponding encoded - IDs which can add items to the Library folder. - items: - items: - type: string - type: array - title: Add Role List - type: array - manage_folder_role_list: - description: A list containing pairs of role names and corresponding encoded - IDs which can manage the Library folder. - items: - items: - type: string - type: array - title: Manage Role List - type: array - modify_folder_role_list: - description: A list containing pairs of role names and corresponding encoded - IDs which can modify the Library folder. - items: - items: - type: string - type: array - title: Modify Role List - type: array - required: - - modify_folder_role_list - - manage_folder_role_list - - add_library_item_role_list - title: LibraryFolderCurrentPermissions - type: object - LibraryFolderDestination: - properties: - library_folder_id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Library Folder Id - type: string - type: - const: library_folder - title: Type - required: - - type - - library_folder_id - title: LibraryFolderDestination - type: object - LibraryFolderDetails: - properties: - deleted: - description: Whether this folder is marked as deleted. - title: Deleted - type: boolean - description: - anyOf: - - type: string - - type: 'null' - default: '' - description: A detailed description of the library folder. - title: Description - genome_build: - anyOf: - - type: string - - type: 'null' - default: '?' - description: TODO - title: Genome Build - id: - description: Encoded ID of the library folder. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - item_count: - description: A detailed description of the library folder. - title: Item Count - type: integer - library_path: - default: [] - description: The list of folder names composing the path to this folder. - items: - type: string - title: Path - type: array - model_class: - const: LibraryFolder - description: The name of the database model class. - title: Model class - type: string - name: - description: The name of the library folder. - title: Name - type: string - parent_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: Encoded ID of the parent folder. Empty if it's the root folder. - title: Parent Folder ID - parent_library_id: - description: Encoded ID of the Library this folder belongs to. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Parent Library ID - type: string - update_time: - description: The last time and date this item was updated. - format: date-time - title: Update Time - type: string - required: - - model_class - - id - - name - - item_count - - parent_library_id - - update_time - - deleted - title: LibraryFolderDetails - type: object - LibraryFolderMetadata: - properties: - can_add_library_item: - title: Can Add Library Item - type: boolean - can_modify_folder: - title: Can Modify Folder - type: boolean - folder_description: - title: Folder Description - type: string - folder_name: - title: Folder Name - type: string - full_path: - items: - maxItems: 2 - minItems: 2 - prefixItems: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: string - type: array - title: Full Path - type: array - parent_library_id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Parent Library Id - type: string - total_rows: - title: Total Rows - type: integer - required: - - parent_library_id - - folder_name - - folder_description - - total_rows - - can_modify_folder - - can_add_library_item - - full_path - title: LibraryFolderMetadata - type: object - LibraryFolderPermissionAction: - const: set_permissions - title: LibraryFolderPermissionAction - type: string - LibraryFolderPermissionsPayload: - properties: - action: - anyOf: - - $ref: '#/components/schemas/LibraryFolderPermissionAction' - - type: 'null' - description: Indicates what action should be performed on the library folder. - title: Action - add_ids[]: - anyOf: - - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - type: array - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - default: [] - description: A list of role encoded IDs defining roles that should be able - to add items to the library. - title: Add IDs - manage_ids[]: - anyOf: - - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - type: array - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - default: [] - description: A list of role encoded IDs defining roles that should have - manage permission on the library. - title: Manage IDs - modify_ids[]: - anyOf: - - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - type: array - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - default: [] - description: A list of role encoded IDs defining roles that should have - modify permission on the library. - title: Modify IDs - title: LibraryFolderPermissionsPayload - type: object - LibraryLegacySummary: - properties: - create_time: - description: The time and date this item was created. - format: date-time - title: Create Time - type: string - deleted: - description: Whether this Library has been deleted. - title: Deleted - type: boolean - description: - anyOf: - - type: string - - type: 'null' - default: '' - description: A detailed description of the Library. - title: Description - id: - description: Encoded ID of the Library. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - model_class: - const: Library - description: The name of the database model class. - title: Model class - type: string - name: - description: The name of the Library. - title: Name - type: string - root_folder_id: - description: Encoded ID of the Library's base folder. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Root Folder ID - type: string - synopsis: - anyOf: - - type: string - - type: 'null' - description: A short text describing the contents of the Library. - title: Description - required: - - model_class - - id - - name - - root_folder_id - - create_time - - deleted - title: LibraryLegacySummary - type: object - LibraryPermissionAction: - enum: - - set_permissions - - remove_restrictions - title: LibraryPermissionAction - type: string - LibraryPermissionScope: - enum: - - current - - available - title: LibraryPermissionScope - type: string - LibraryPermissionsPayload: - properties: - access_ids[]: - anyOf: - - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - type: array - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - default: [] - description: A list of role encoded IDs defining roles that should have - access permission on the library. - title: Access IDs - action: - anyOf: - - $ref: '#/components/schemas/LibraryPermissionAction' - - type: 'null' - description: Indicates what action should be performed on the Library. - title: Action - add_ids[]: - anyOf: - - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - type: array - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - default: [] - description: A list of role encoded IDs defining roles that should be able - to add items to the library. - title: Add IDs - manage_ids[]: - anyOf: - - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - type: array - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - default: [] - description: A list of role encoded IDs defining roles that should have - manage permission on the library. - title: Manage IDs - modify_ids[]: - anyOf: - - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - type: array - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - default: [] - description: A list of role encoded IDs defining roles that should have - modify permission on the library. - title: Modify IDs - title: LibraryPermissionsPayload - type: object - LibrarySummary: - properties: - can_user_add: - description: Whether the current user can add contents to this Library. - title: Can User Add - type: boolean - can_user_manage: - description: Whether the current user can manage the Library and its contents. - title: Can User Manage - type: boolean - can_user_modify: - description: Whether the current user can modify this Library. - title: Can User Modify - type: boolean - create_time: - description: The time and date this item was created. - format: date-time - title: Create Time - type: string - create_time_pretty: - description: Nice time representation of the creation date. - examples: - - 2 months ago - title: Create Time Pretty - type: string - deleted: - description: Whether this Library has been deleted. - title: Deleted - type: boolean - description: - anyOf: - - type: string - - type: 'null' - default: '' - description: A detailed description of the Library. - title: Description - id: - description: Encoded ID of the Library. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - model_class: - const: Library - description: The name of the database model class. - title: Model class - type: string - name: - description: The name of the Library. - title: Name - type: string - public: - description: Whether this Library has been deleted. - title: Public - type: boolean - root_folder_id: - description: Encoded ID of the Library's base folder. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Root Folder ID - type: string - synopsis: - anyOf: - - type: string - - type: 'null' - description: A short text describing the contents of the Library. - title: Description - required: - - model_class - - id - - name - - root_folder_id - - create_time - - deleted - - create_time_pretty - - public - - can_user_add - - can_user_modify - - can_user_manage - title: LibrarySummary - type: object - LibrarySummaryList: - default: [] - items: - $ref: '#/components/schemas/LibrarySummary' - title: LibrarySummaryList - type: array - LicenseMetadataModel: - properties: - detailsUrl: - description: URL to the SPDX json details for this license - examples: - - http://spdx.org/licenses/Apache-2.0.json - format: uri - maxLength: 2083 - minLength: 1 - title: Details URL - type: string - isDeprecatedLicenseId: - description: True if the entire license is deprecated - examples: - - false - title: Deprecated License - type: boolean - isOsiApproved: - description: Indicates if the [OSI](https://opensource.org/) has approved - the license - examples: - - true - title: OSI approved - type: boolean - licenseId: - description: SPDX Identifier - examples: - - Apache-2.0 - title: Identifier - type: string - name: - description: Full name of the license - examples: - - Apache License 2.0 - title: Name - type: string - recommended: - description: True if this license is recommended to be used - title: Recommended - type: boolean - reference: - description: Reference to the HTML format for the license file - examples: - - ./Apache-2.0.html - title: Reference - type: string - referenceNumber: - description: '*Deprecated* - this field is generated and is no longer in - use' - title: Reference number - type: integer - seeAlso: - description: Cross reference URL pointing to additional copies of the license - items: - format: uri - maxLength: 2083 - minLength: 1 - type: string - title: Reference URLs - type: array - spdxUrl: - examples: - - https://spdx.org/licenses/Apache-2.0.html - format: uri - maxLength: 2083 - minLength: 1 - title: SPDX URL - type: string - url: - description: License URL - examples: - - http://www.apache.org/licenses/LICENSE-2.0 - format: uri - maxLength: 2083 - minLength: 1 - title: URL - type: string - required: - - licenseId - - name - - reference - - referenceNumber - - isDeprecatedLicenseId - - isOsiApproved - - seeAlso - - detailsUrl - - recommended - - url - - spdxUrl - title: LicenseMetadataModel - type: object - LimitedUserModel: - description: This is used when config options (expose_user_name and expose_user_email) - are in place. - properties: - email: - anyOf: - - type: string - - type: 'null' - title: Email - id: - description: Encoded ID of the user - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - username: - anyOf: - - type: string - - type: 'null' - title: Username - required: - - id - title: LimitedUserModel - type: object - Link: - properties: - name: - title: Name - type: string - required: - - name - title: Link - type: object - ListJstreeResponse: - default: [] - deprecated: true - items: {} - title: ListJstreeResponse - type: array - ListUriResponse: - default: [] - items: - discriminator: - mapping: - Directory: '#/components/schemas/RemoteDirectory' - File: '#/components/schemas/RemoteFile' - propertyName: class - oneOf: - - $ref: '#/components/schemas/RemoteFile' - - $ref: '#/components/schemas/RemoteDirectory' - title: ListUriResponse - type: array - MandatoryNotificationCategory: - const: broadcast - description: 'These notification categories cannot be opt-out by the user. - - - The user will always receive notifications from these categories.' - title: MandatoryNotificationCategory - type: string - MaterializeDatasetInstanceAPIRequest: - properties: - content: - description: 'Depending on the `source` it can be: - - - The encoded id of the source library dataset - - - The encoded id of the HDA - - ' - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Content - type: string - source: - allOf: - - $ref: '#/components/schemas/DatasetSourceType' - description: The source of the content. Can be other history element to - be copied or library elements. - title: Source - required: - - source - - content - title: MaterializeDatasetInstanceAPIRequest - type: object - MessageNotificationContent: - properties: - category: - const: message - default: message - title: Category - message: - description: The message of the notification (supports Markdown). - title: Message - type: string - subject: - description: The subject of the notification. - title: Subject - type: string - required: - - subject - - message - title: MessageNotificationContent - type: object - MetadataFile: - description: Metadata file associated with a dataset. - properties: - download_url: - description: The URL to download this item from the server. - title: Download URL - type: string - file_type: - description: TODO - title: File Type - type: string - required: - - file_type - - download_url - title: MetadataFile - type: object - Metric: - properties: - args: - description: A JSON string containing an array of extra data. - title: Arguments - type: string - level: - description: An integer representing the metric's log level. - title: Level - type: integer - namespace: - description: Label indicating the source of the metric. - title: Namespace - type: string - time: - description: The timestamp in ISO format. - examples: - - '2021-01-23T18:25:43.511Z' - title: Timestamp - type: string - required: - - namespace - - time - - level - - args - title: Metric - type: object - ModelStoreFormat: - description: Available types of model stores for export. - enum: - - tgz - - tar - - tar.gz - - bag.zip - - bag.tar - - bag.tgz - - rocrate.zip - - bco.json - title: ModelStoreFormat - type: string - NestedElement: - additionalProperties: false - properties: - MD5: - anyOf: - - type: string - - type: 'null' - title: Md5 - auto_decompress: - default: false - description: Decompress compressed data before sniffing? - title: Auto Decompress - type: boolean - collection_type: - anyOf: - - type: string - - type: 'null' - title: Collection Type - created_from_basename: - anyOf: - - type: string - - type: 'null' - title: Created From Basename - dbkey: - default: '?' - title: Dbkey - type: string - deferred: - default: false - title: Deferred - type: boolean - description: - anyOf: - - type: string - - type: 'null' - title: Description - elements: - items: - anyOf: - - discriminator: - mapping: - composite: '#/components/schemas/CompositeDataElement' - files: '#/components/schemas/FileDataElement' - ftp_import: '#/components/schemas/FtpImportElement' - pasted: '#/components/schemas/PastedDataElement' - path: '#/components/schemas/PathDataElement' - server_dir: '#/components/schemas/ServerDirElement' - url: '#/components/schemas/UrlDataElement' - propertyName: src - oneOf: - - $ref: '#/components/schemas/FileDataElement' - - $ref: '#/components/schemas/PastedDataElement' - - $ref: '#/components/schemas/UrlDataElement' - - $ref: '#/components/schemas/PathDataElement' - - $ref: '#/components/schemas/ServerDirElement' - - $ref: '#/components/schemas/FtpImportElement' - - $ref: '#/components/schemas/CompositeDataElement' - - $ref: '#/components/schemas/NestedElement' - title: Elements - type: array - elements_from: - anyOf: - - $ref: '#/components/schemas/ElementsFromType' - - type: 'null' - ext: - default: auto - title: Ext - type: string - extra_files: - anyOf: - - $ref: '#/components/schemas/ExtraFiles' - - type: 'null' - info: - anyOf: - - type: string - - type: 'null' - title: Info - name: - anyOf: - - type: string - - type: integer - - type: number - - type: boolean - - type: 'null' - title: Name - space_to_tab: - default: false - title: Space To Tab - type: boolean - tags: - anyOf: - - items: - type: string - type: array - - type: 'null' - title: Tags - to_posix_lines: - default: false - title: To Posix Lines - type: boolean - required: - - elements - title: NestedElement - type: object - NewSharedItemNotificationContent: - properties: - category: - const: new_shared_item - default: new_shared_item - title: Category - item_name: - description: The name of the shared item. - title: Item name - type: string - item_type: - description: The type of the shared item. - enum: - - history - - workflow - - visualization - - page - title: Item type - type: string - owner_name: - description: The name of the owner of the shared item. - title: Owner name - type: string - slug: - description: The slug of the shared item. Used for the link to the item. - title: Slug - type: string - required: - - item_type - - item_name - - owner_name - - slug - title: NewSharedItemNotificationContent - type: object - NotificationBroadcastUpdateRequest: - description: A notification update request specific for broadcasting. - properties: - content: - anyOf: - - $ref: '#/components/schemas/BroadcastNotificationContent' - - type: 'null' - description: The content of the broadcast notification. Broadcast notifications - are displayed prominently to all users and can contain action links to - redirect the user to a specific page. - title: Content - expiration_time: - anyOf: - - format: date-time - type: string - - type: 'null' - description: The time when the notification should expire. By default it - will expire after 6 months. Expired notifications will be permanently - deleted. - title: Expiration time - publication_time: - anyOf: - - format: date-time - type: string - - type: 'null' - description: The time when the notification should be published. Notifications - can be created and then scheduled to be published at a later time. - title: Publication time - source: - anyOf: - - type: string - - type: 'null' - description: The source of the notification. Represents the agent that created - the notification. - title: Source - variant: - anyOf: - - $ref: '#/components/schemas/NotificationVariant' - - type: 'null' - description: The variant of the notification. Used to express the importance - of the notification. - title: Variant - title: NotificationBroadcastUpdateRequest - type: object - NotificationCategorySettings: - description: The settings for a notification category. - properties: - channels: - allOf: - - $ref: '#/components/schemas/NotificationChannelSettings' - default: - push: true - description: The channels that the user wants to receive notifications from - for this category. - title: Channels - enabled: - default: true - description: Whether the user wants to receive notifications for this category. - title: Enabled - type: boolean - title: NotificationCategorySettings - type: object - NotificationChannelSettings: - description: The settings for each channel of a notification category. - properties: - push: - default: true - description: Whether the user wants to receive push notifications in the - browser for this category. - title: Push - type: boolean - title: NotificationChannelSettings - type: object - NotificationCreateData: - description: Basic common fields for all notification create requests. - properties: - category: - anyOf: - - $ref: '#/components/schemas/MandatoryNotificationCategory' - - $ref: '#/components/schemas/PersonalNotificationCategory' - description: The category of the notification. Represents the type of the - notification. E.g. 'message' or 'new_shared_item'. - title: Category - content: - description: The content of the notification. The structure depends on the - category. - discriminator: - mapping: - broadcast: '#/components/schemas/BroadcastNotificationContent' - message: '#/components/schemas/MessageNotificationContent' - new_shared_item: '#/components/schemas/NewSharedItemNotificationContent' - propertyName: category - oneOf: - - $ref: '#/components/schemas/MessageNotificationContent' - - $ref: '#/components/schemas/NewSharedItemNotificationContent' - - $ref: '#/components/schemas/BroadcastNotificationContent' - title: Content - expiration_time: - anyOf: - - format: date-time - type: string - - type: 'null' - description: The time when the notification should expire. By default it - will expire after 6 months. Expired notifications will be permanently - deleted. - title: Expiration time - publication_time: - anyOf: - - format: date-time - type: string - - type: 'null' - description: The time when the notification should be published. Notifications - can be created and then scheduled to be published at a later time. - title: Publication time - source: - description: The source of the notification. Represents the agent that created - the notification. E.g. 'galaxy' or 'admin'. - title: Source - type: string - variant: - allOf: - - $ref: '#/components/schemas/NotificationVariant' - description: The variant of the notification. Represents the intent or relevance - of the notification. E.g. 'info' or 'urgent'. - title: Variant - required: - - source - - category - - variant - - content - title: NotificationCreateData - type: object - NotificationCreateRequest: - description: Contains the recipients and the notification to create. - properties: - notification: - allOf: - - $ref: '#/components/schemas/NotificationCreateData' - description: The notification to create. The structure depends on the category. - title: Notification - recipients: - allOf: - - $ref: '#/components/schemas/NotificationRecipients' - description: The recipients of the notification. Can be a combination of - users, groups and roles. - title: Recipients - required: - - recipients - - notification - title: NotificationCreateRequest - type: object - NotificationCreatedResponse: - properties: - notification: - allOf: - - $ref: '#/components/schemas/NotificationResponse' - description: The notification that was created. The structure depends on - the category. - title: Notification - total_notifications_sent: - description: The total number of notifications that were sent to the recipients. - title: Total notifications sent - type: integer - required: - - total_notifications_sent - - notification - title: NotificationCreatedResponse - type: object - NotificationRecipients: - description: The recipients of a notification. Can be a combination of users, - groups and roles. - properties: - group_ids: - default: [] - description: The list of encoded group IDs of the groups that should receive - the notification. - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - title: Group IDs - type: array - role_ids: - default: [] - description: The list of encoded role IDs of the roles that should receive - the notification. - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - title: Role IDs - type: array - user_ids: - default: [] - description: The list of encoded user IDs of the users that should receive - the notification. - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - title: User IDs - type: array - title: NotificationRecipients - type: object - NotificationResponse: - description: Basic common fields for all notification responses. - properties: - category: - anyOf: - - $ref: '#/components/schemas/MandatoryNotificationCategory' - - $ref: '#/components/schemas/PersonalNotificationCategory' - description: The category of the notification. Represents the type of the - notification. E.g. 'message' or 'new_shared_item'. - title: Category - content: - description: The content of the notification. The structure depends on the - category. - discriminator: - mapping: - broadcast: '#/components/schemas/BroadcastNotificationContent' - message: '#/components/schemas/MessageNotificationContent' - new_shared_item: '#/components/schemas/NewSharedItemNotificationContent' - propertyName: category - oneOf: - - $ref: '#/components/schemas/MessageNotificationContent' - - $ref: '#/components/schemas/NewSharedItemNotificationContent' - - $ref: '#/components/schemas/BroadcastNotificationContent' - title: Content - create_time: - description: The time when the notification was created. - format: date-time - title: Create time - type: string - expiration_time: - anyOf: - - format: date-time - type: string - - type: 'null' - description: The time when the notification will expire. If not set, the - notification will never expire. Expired notifications will be permanently - deleted. - title: Expiration time - id: - description: The encoded ID of the notification. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - publication_time: - description: The time when the notification was published. Notifications - can be created and then published at a later time. - format: date-time - title: Publication time - type: string - source: - description: The source of the notification. Represents the agent that created - the notification. E.g. 'galaxy' or 'admin'. - title: Source - type: string - update_time: - description: The time when the notification was last updated. - format: date-time - title: Update time - type: string - variant: - allOf: - - $ref: '#/components/schemas/NotificationVariant' - description: The variant of the notification. Represents the intent or relevance - of the notification. E.g. 'info' or 'urgent'. - title: Variant - required: - - id - - source - - category - - variant - - create_time - - update_time - - publication_time - - content - title: NotificationResponse - type: object - NotificationStatusSummary: - description: A summary of the notification status for a user. Contains only - updates since a particular timestamp. - properties: - broadcasts: - description: The list of updated broadcasts. - items: - $ref: '#/components/schemas/BroadcastNotificationResponse' - title: Broadcasts - type: array - notifications: - description: The list of updated notifications for the user. - items: - $ref: '#/components/schemas/UserNotificationResponse' - title: Notifications - type: array - total_unread_count: - description: The total number of unread notifications for the user. - title: Total unread count - type: integer - required: - - total_unread_count - - notifications - - broadcasts - title: NotificationStatusSummary - type: object - NotificationVariant: - description: The notification variant communicates the intent or relevance of - the notification. - enum: - - info - - warning - - urgent - title: NotificationVariant - type: string - NotificationsBatchRequest: - properties: - notification_ids: - description: The list of encoded notification IDs of the notifications that - should be updated. - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - title: Notification IDs - type: array - required: - - notification_ids - title: NotificationsBatchRequest - type: object - NotificationsBatchUpdateResponse: - description: The response of a batch update request. - properties: - updated_count: - description: The number of notifications that were updated. - title: Updated count - type: integer - required: - - updated_count - title: NotificationsBatchUpdateResponse - type: object - ObjectExportTaskResponse: - properties: - create_time: - description: The time and date this item was created. - format: date-time - title: Create Time - type: string - export_metadata: - anyOf: - - $ref: '#/components/schemas/ExportObjectMetadata' - - type: 'null' - id: - description: The encoded database ID of the export request. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - preparing: - description: Whether the archive is currently being built or in preparation. - title: Preparing - type: boolean - ready: - description: Whether the export has completed successfully and the archive - is ready - title: Ready - type: boolean - task_uuid: - description: The identifier of the task processing the export. - format: uuid4 - title: Task ID - type: string - up_to_date: - description: False, if a new export archive should be generated. - title: Up to Date - type: boolean - required: - - id - - ready - - preparing - - up_to_date - - task_uuid - - create_time - title: ObjectExportTaskResponse - type: object - Organization: - properties: - name: - description: Name of the organization responsible for the service - examples: - - My organization - title: Name - type: string - url: - description: URL of the website of the organization (RFC 3986 format) - examples: - - https://example.com - format: uri - minLength: 1 - title: Url - type: string - required: - - name - - url - title: Organization - type: object - PageContentFormat: - enum: - - markdown - - html - title: PageContentFormat - type: string - PageDetails: - additionalProperties: true - properties: - content: - anyOf: - - type: string - - type: 'null' - default: '' - description: Raw text contents of the last page revision (type dependent - on content_format). - title: Content - content_format: - allOf: - - $ref: '#/components/schemas/PageContentFormat' - default: html - description: Either `markdown` or `html`. - title: Content format - create_time: - description: The time and date this item was created. - format: date-time - title: Create Time - type: string - deleted: - description: Whether this Page has been deleted. - title: Deleted - type: boolean - email_hash: - description: The encoded email of the user. - title: Encoded email - type: string - generate_time: - anyOf: - - type: string - - type: 'null' - description: The version of Galaxy this object was generated with. - title: Galaxy Version - generate_version: - anyOf: - - type: string - - type: 'null' - description: The version of Galaxy this object was generated with. - title: Galaxy Version - id: - description: Encoded ID of the Page. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - importable: - description: Whether this Page can be imported. - title: Importable - type: boolean - latest_revision_id: - description: The encoded ID of the last revision of this Page. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Latest revision ID - type: string - model_class: - const: Page - description: The name of the database model class. - title: Model class - type: string - published: - description: Whether this Page has been published. - title: Published - type: boolean - revision_ids: - description: The history with the encoded ID of each revision of the Page. - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - title: List of revisions - type: array - slug: - description: The title slug for the page URL, must be unique. - pattern: ^[a-z0-9\-]+$ - title: Identifier - type: string - tags: - $ref: '#/components/schemas/TagCollection' - title: - description: The name of the page. - title: Title - type: string - update_time: - description: The last time and date this item was updated. - format: date-time - title: Update Time - type: string - username: - description: The name of the user owning this Page. - title: Username - type: string - required: - - model_class - - title - - slug - - id - - username - - email_hash - - published - - importable - - deleted - - latest_revision_id - - revision_ids - - create_time - - update_time - - tags - title: PageDetails - type: object - PageSummary: - properties: - create_time: - description: The time and date this item was created. - format: date-time - title: Create Time - type: string - deleted: - description: Whether this Page has been deleted. - title: Deleted - type: boolean - email_hash: - description: The encoded email of the user. - title: Encoded email - type: string - id: - description: Encoded ID of the Page. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - importable: - description: Whether this Page can be imported. - title: Importable - type: boolean - latest_revision_id: - description: The encoded ID of the last revision of this Page. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Latest revision ID - type: string - model_class: - const: Page - description: The name of the database model class. - title: Model class - type: string - published: - description: Whether this Page has been published. - title: Published - type: boolean - revision_ids: - description: The history with the encoded ID of each revision of the Page. - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - title: List of revisions - type: array - slug: - description: The title slug for the page URL, must be unique. - pattern: ^[a-z0-9\-]+$ - title: Identifier - type: string - tags: - $ref: '#/components/schemas/TagCollection' - title: - description: The name of the page. - title: Title - type: string - update_time: - description: The last time and date this item was updated. - format: date-time - title: Update Time - type: string - username: - description: The name of the user owning this Page. - title: Username - type: string - required: - - model_class - - title - - slug - - id - - username - - email_hash - - published - - importable - - deleted - - latest_revision_id - - revision_ids - - create_time - - update_time - - tags - title: PageSummary - type: object - PageSummaryList: - default: [] - items: - $ref: '#/components/schemas/PageSummary' - title: PageSummaryList - type: array - PastedDataElement: - additionalProperties: false - properties: - MD5: - anyOf: - - type: string - - type: 'null' - title: Md5 - auto_decompress: - default: false - description: Decompress compressed data before sniffing? - title: Auto Decompress - type: boolean - collection_type: - anyOf: - - type: string - - type: 'null' - title: Collection Type - created_from_basename: - anyOf: - - type: string - - type: 'null' - title: Created From Basename - dbkey: - default: '?' - title: Dbkey - type: string - deferred: - default: false - title: Deferred - type: boolean - description: - anyOf: - - type: string - - type: 'null' - title: Description - elements_from: - anyOf: - - $ref: '#/components/schemas/ElementsFromType' - - type: 'null' - ext: - default: auto - title: Ext - type: string - extra_files: - anyOf: - - $ref: '#/components/schemas/ExtraFiles' - - type: 'null' - info: - anyOf: - - type: string - - type: 'null' - title: Info - name: - anyOf: - - type: string - - type: integer - - type: number - - type: boolean - - type: 'null' - title: Name - paste_content: - anyOf: - - type: string - - type: integer - - type: number - - type: boolean - description: Content to upload - title: Paste Content - space_to_tab: - default: false - title: Space To Tab - type: boolean - src: - const: pasted - title: Src - tags: - anyOf: - - items: - type: string - type: array - - type: 'null' - title: Tags - to_posix_lines: - default: false - title: To Posix Lines - type: boolean - required: - - src - - paste_content - title: PastedDataElement - type: object - PathDataElement: - additionalProperties: false - properties: - MD5: - anyOf: - - type: string - - type: 'null' - title: Md5 - auto_decompress: - default: false - description: Decompress compressed data before sniffing? - title: Auto Decompress - type: boolean - collection_type: - anyOf: - - type: string - - type: 'null' - title: Collection Type - created_from_basename: - anyOf: - - type: string - - type: 'null' - title: Created From Basename - dbkey: - default: '?' - title: Dbkey - type: string - deferred: - default: false - title: Deferred - type: boolean - description: - anyOf: - - type: string - - type: 'null' - title: Description - elements_from: - anyOf: - - $ref: '#/components/schemas/ElementsFromType' - - type: 'null' - ext: - default: auto - title: Ext - type: string - extra_files: - anyOf: - - $ref: '#/components/schemas/ExtraFiles' - - type: 'null' - info: - anyOf: - - type: string - - type: 'null' - title: Info - link_data_only: - anyOf: - - type: boolean - - type: 'null' - title: Link Data Only - name: - anyOf: - - type: string - - type: integer - - type: number - - type: boolean - - type: 'null' - title: Name - path: - title: Path - type: string - space_to_tab: - default: false - title: Space To Tab - type: boolean - src: - const: path - title: Src - tags: - anyOf: - - items: - type: string - type: array - - type: 'null' - title: Tags - to_posix_lines: - default: false - title: To Posix Lines - type: boolean - required: - - src - - path - title: PathDataElement - type: object - PersonalNotificationCategory: - description: 'These notification categories can be opt-out by the user and will - be - - displayed in the notification preferences.' - enum: - - message - - new_shared_item - title: PersonalNotificationCategory - type: string - PluginKind: - description: Enum to distinguish between different kinds or categories of plugins. - enum: - - rfs - - drs - - rdm - - stock - title: PluginKind - type: string - PrepareStoreDownloadPayload: - properties: - bco_merge_history_metadata: - default: false - description: When reading tags/annotations to generate BCO object include - history metadata. - title: Bco Merge History Metadata - type: boolean - bco_override_algorithmic_error: - anyOf: - - additionalProperties: - type: string - type: object - - type: 'null' - description: Override algorithmic error for 'error domain' when generating - BioCompute object. - title: Bco Override Algorithmic Error - bco_override_empirical_error: - anyOf: - - additionalProperties: - type: string - type: object - - type: 'null' - description: Override empirical error for 'error domain' when generating - BioCompute object. - title: Bco Override Empirical Error - bco_override_environment_variables: - anyOf: - - additionalProperties: - type: string - type: object - - type: 'null' - description: Override environment variables for 'execution_domain' when - generating BioCompute object. - title: Bco Override Environment Variables - bco_override_xref: - anyOf: - - items: - $ref: '#/components/schemas/XrefItem' - type: array - - type: 'null' - description: Override xref for 'description domain' when generating BioCompute - object. - title: Bco Override Xref - include_deleted: - default: false - description: Include file contents for deleted datasets (if include_files - is True). - title: Include deleted - type: boolean - include_files: - default: true - description: include materialized files in export when available - title: Include Files - type: boolean - include_hidden: - default: false - description: Include file contents for hidden datasets (if include_files - is True). - title: Include hidden - type: boolean - model_store_format: - allOf: - - $ref: '#/components/schemas/ModelStoreFormat' - default: tar.gz - description: format of model store to export - title: PrepareStoreDownloadPayload - type: object - QuotaDetails: - properties: - bytes: - description: The amount, expressed in bytes, of this Quota. - title: Bytes - type: integer - default: - default: [] - description: A list indicating which types of default user quotas, if any, - are associated with this quota. - items: - $ref: '#/components/schemas/DefaultQuota' - title: Default - type: array - description: - description: Detailed text description for this Quota. - title: Description - type: string - display_amount: - description: Human-readable representation of the `amount` field. - title: Display Amount - type: string - groups: - default: [] - description: A list of specific groups of users associated with this quota. - items: - $ref: '#/components/schemas/GroupQuota' - title: Groups - type: array - id: - description: The `encoded identifier` of the quota. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - model_class: - const: Quota - description: The name of the database model class. - title: Model class - type: string - name: - description: The name of the quota. This must be unique within a Galaxy - instance. - title: Name - type: string - operation: - allOf: - - $ref: '#/components/schemas/QuotaOperation' - default: '=' - description: 'Quotas can have one of three `operations`:- `=` : The quota - is exactly the amount specified- `+` : The amount specified will be added - to the amounts of the user''s other associated quota definitions- `-` - : The amount specified will be subtracted from the amounts of the user''s - other associated quota definitions' - title: Operation - quota_source_label: - anyOf: - - type: string - - type: 'null' - description: Quota source label - title: Quota Source Label - users: - default: [] - description: A list of specific users associated with this quota. - items: - $ref: '#/components/schemas/UserQuota' - title: Users - type: array - required: - - model_class - - id - - name - - description - - bytes - - display_amount - title: QuotaDetails - type: object - QuotaModel: - properties: - enabled: - title: Enabled - type: boolean - source: - anyOf: - - type: string - - type: 'null' - title: Source - required: - - enabled - title: QuotaModel - type: object - QuotaOperation: - enum: - - '=' - - + - - '-' - title: QuotaOperation - type: string - QuotaSummary: - description: Contains basic information about a Quota - properties: - id: - description: The `encoded identifier` of the quota. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - model_class: - const: Quota - description: The name of the database model class. - title: Model class - type: string - name: - description: The name of the quota. This must be unique within a Galaxy - instance. - title: Name - type: string - quota_source_label: - anyOf: - - type: string - - type: 'null' - description: Quota source label - title: Quota Source Label - url: - deprecated: true - description: The relative URL to get this particular Quota details from - the rest API. - title: URL - type: string - required: - - model_class - - id - - name - - url - title: QuotaSummary - type: object - QuotaSummaryList: - default: [] - items: - $ref: '#/components/schemas/QuotaSummary' - title: QuotaSummaryList - type: array - ReloadFeedback: - properties: - failed: - items: - anyOf: - - type: string - - type: 'null' - title: Failed - type: array - message: - title: Message - type: string - reloaded: - items: - anyOf: - - type: string - - type: 'null' - title: Reloaded - type: array - required: - - message - - reloaded - - failed - title: ReloadFeedback - type: object - RemoteDirectory: - properties: - class: - const: Directory - title: Class - name: - description: The name of the entry. - title: Name - type: string - path: - description: The path of the entry. - title: Path - type: string - uri: - description: The URI of the entry. - title: URI - type: string - required: - - name - - uri - - path - - class - title: RemoteDirectory - type: object - RemoteFile: - properties: - class: - const: File - title: Class - ctime: - description: The creation time of the file. - title: Creation time - type: string - name: - description: The name of the entry. - title: Name - type: string - path: - description: The path of the entry. - title: Path - type: string - size: - description: The size of the file in bytes. - title: Size - type: integer - uri: - description: The URI of the entry. - title: URI - type: string - required: - - name - - uri - - path - - class - - size - - ctime - title: RemoteFile - type: object - RemoteFilesDisableMode: - enum: - - folders - - files - title: RemoteFilesDisableMode - type: string - RemoteFilesFormat: - enum: - - flat - - jstree - - uri - title: RemoteFilesFormat - type: string - RemoteUserCreationPayload: - properties: - remote_user_email: - description: Email of the user - title: Email - type: string - required: - - remote_user_email - title: RemoteUserCreationPayload - type: object - ReportJobErrorPayload: - properties: - dataset_id: - description: The History Dataset Association ID related to the error. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: History Dataset Association ID - type: string - email: - anyOf: - - type: string - - type: 'null' - description: Email address for communication with the user. Only required - for anonymous users. - title: Email - message: - anyOf: - - type: string - - type: 'null' - description: The optional message sent with the error report. - title: Message - required: - - dataset_id - title: ReportJobErrorPayload - type: object - RequestDataType: - description: Particular pieces of information that can be requested for a dataset. - enum: - - state - - converted_datasets_state - - data - - features - - raw_data - - track_config - - genome_data - - in_use_state - title: RequestDataType - type: string - Requirement: - description: Available types of job sources (model classes) that produce dataset - collections. - enum: - - logged_in - - new_history - - admin - title: Requirement - type: string - RoleDefinitionModel: - properties: - description: - description: Description of the role - title: Description - type: string - group_ids: - anyOf: - - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - type: array - - type: 'null' - default: [] - title: Group IDs - name: - description: Name of the role - title: Name - type: string - user_ids: - anyOf: - - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - type: array - - type: 'null' - default: [] - title: User IDs - required: - - name - - description - title: RoleDefinitionModel - type: object - RoleListResponse: - items: - $ref: '#/components/schemas/RoleModelResponse' - title: RoleListResponse - type: array - RoleModelResponse: - properties: - description: - anyOf: - - description: Description of the role - title: Description - type: string - - type: 'null' - title: Description - id: - description: Encoded ID of the role - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - model_class: - const: Role - description: The name of the database model class. - title: Model class - type: string - name: - description: Name of the role - title: Name - type: string - type: - description: Type or category of the role - title: Type - type: string - url: - deprecated: true - description: The relative URL to access this item. - title: URL - type: string - required: - - model_class - - id - - name - - type - - description - - url - title: RoleModelResponse - type: object - RootModel_Dict_str__int__: - additionalProperties: - type: integer - title: RootModel[Dict[str, int]] - type: object - SearchJobsPayload: - additionalProperties: true - properties: - inputs: - description: The inputs of the job. - title: Inputs - type: object - state: - anyOf: - - $ref: '#/components/schemas/JobState' - - type: 'null' - description: Current state of the job. - title: State - tool_id: - description: The tool ID related to the job. - title: Tool ID - type: string - required: - - tool_id - - inputs - title: SearchJobsPayload - type: object - ServerDirElement: - additionalProperties: false - properties: - MD5: - anyOf: - - type: string - - type: 'null' - title: Md5 - auto_decompress: - default: false - description: Decompress compressed data before sniffing? - title: Auto Decompress - type: boolean - collection_type: - anyOf: - - type: string - - type: 'null' - title: Collection Type - created_from_basename: - anyOf: - - type: string - - type: 'null' - title: Created From Basename - dbkey: - default: '?' - title: Dbkey - type: string - deferred: - default: false - title: Deferred - type: boolean - description: - anyOf: - - type: string - - type: 'null' - title: Description - elements_from: - anyOf: - - $ref: '#/components/schemas/ElementsFromType' - - type: 'null' - ext: - default: auto - title: Ext - type: string - extra_files: - anyOf: - - $ref: '#/components/schemas/ExtraFiles' - - type: 'null' - info: - anyOf: - - type: string - - type: 'null' - title: Info - link_data_only: - anyOf: - - type: boolean - - type: 'null' - title: Link Data Only - name: - anyOf: - - type: string - - type: integer - - type: number - - type: boolean - - type: 'null' - title: Name - server_dir: - title: Server Dir - type: string - space_to_tab: - default: false - title: Space To Tab - type: boolean - src: - const: server_dir - title: Src - tags: - anyOf: - - items: - type: string - type: array - - type: 'null' - title: Tags - to_posix_lines: - default: false - title: To Posix Lines - type: boolean - required: - - src - - server_dir - title: ServerDirElement - type: object - Service: - properties: - contactUrl: - anyOf: - - format: uri - minLength: 1 - type: string - - type: 'null' - description: URL of the contact for the provider of this service, e.g. a - link to a contact form (RFC 3986 format), or an email (RFC 2368 format). - examples: - - mailto:support@example.com - title: Contacturl - createdAt: - anyOf: - - format: date-time - type: string - - type: 'null' - description: Timestamp describing when the service was first deployed and - available (RFC 3339 format) - examples: - - '2019-06-04T12:58:19Z' - title: Createdat - description: - anyOf: - - type: string - - type: 'null' - description: Description of the service. Should be human readable and provide - information about the service. - examples: - - This service provides... - title: Description - documentationUrl: - anyOf: - - format: uri - minLength: 1 - type: string - - type: 'null' - description: URL of the documentation of this service (RFC 3986 format). - This should help someone learn how to use your service, including any - specifics required to access data, e.g. authentication. - examples: - - https://docs.myservice.example.com - title: Documentationurl - environment: - anyOf: - - type: string - - type: 'null' - description: Environment the service is running in. Use this to distinguish - between production, development and testing/staging deployments. Suggested - values are prod, test, dev, staging. However this is advised and not enforced. - examples: - - test - title: Environment - id: - description: Unique ID of this service. Reverse domain name notation is - recommended, though not required. The identifier should attempt to be - globally unique so it can be used in downstream aggregator services e.g. - Service Registry. - examples: - - org.ga4gh.myservice - title: Id - type: string - name: - description: Name of this service. Should be human readable. - examples: - - My project - title: Name - type: string - organization: - allOf: - - $ref: '#/components/schemas/Organization' - description: Organization providing the service - type: - $ref: '#/components/schemas/ServiceType' - updatedAt: - anyOf: - - format: date-time - type: string - - type: 'null' - description: Timestamp describing when the service was last updated (RFC - 3339 format) - examples: - - '2019-06-04T12:58:19Z' - title: Updatedat - version: - description: Version of the service being described. Semantic versioning - is recommended, but other identifiers, such as dates or commit hashes, - are also allowed. The version should be changed whenever the service is - updated. - examples: - - 1.0.0 - title: Version - type: string - required: - - id - - name - - type - - organization - - version - title: Service - type: object - ServiceType: - properties: - artifact: - description: Name of the API or GA4GH specification implemented. Official - GA4GH types should be assigned as part of standards approval process. - Custom artifacts are supported. - examples: - - beacon - title: Artifact - type: string - group: - description: Namespace in reverse domain name format. Use `org.ga4gh` for - implementations compliant with official GA4GH specifications. For services - with custom APIs not standardized by GA4GH, or implementations diverging - from official GA4GH specifications, use a different namespace (e.g. your - organization's reverse domain name). - examples: - - org.ga4gh - title: Group - type: string - version: - description: Version of the API or specification. GA4GH specifications use - semantic versioning. - examples: - - 1.0.0 - title: Version - type: string - required: - - group - - artifact - - version - title: ServiceType - type: object - SetSlugPayload: - properties: - new_slug: - description: The slug that will be used to access this shared item. - title: New Slug - type: string - required: - - new_slug - title: SetSlugPayload - type: object - ShareHistoryExtra: - properties: - accessible_count: - default: 0 - description: The number of datasets in the history that are public or accessible - by all the target users. - title: Accessible Count - type: integer - can_change: - default: [] - description: A collection of datasets that are not accessible by one or - more of the target users and that can be made accessible for others by - the user sharing the history. - items: - $ref: '#/components/schemas/HDABasicInfo' - title: Can Change - type: array - can_share: - default: false - description: Indicates whether the resource can be directly shared or requires - further actions. - title: Can Share - type: boolean - cannot_change: - default: [] - description: A collection of datasets that are not accessible by one or - more of the target users and that cannot be made accessible for others - by the user sharing the history. - items: - $ref: '#/components/schemas/HDABasicInfo' - title: Cannot Change - type: array - title: ShareHistoryExtra - type: object - ShareHistoryWithStatus: - properties: - email_hash: - anyOf: - - type: string - - type: 'null' - description: Encoded owner email. - title: Encoded Email - errors: - default: [] - description: Collection of messages indicating that the resource was not - shared with some (or all users) due to an error. - items: - type: string - title: Errors - type: array - extra: - allOf: - - $ref: '#/components/schemas/ShareHistoryExtra' - description: Optional extra information about this shareable resource that - may be of interest. The contents of this field depend on the particular - resource. - title: Extra - id: - description: The encoded ID of the resource to be shared. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - importable: - description: Whether this resource can be published using a link. - title: Importable - type: boolean - published: - description: Whether this resource is currently published. - title: Published - type: boolean - title: - description: The title or name of the resource. - title: Title - type: string - username: - anyOf: - - type: string - - type: 'null' - description: The owner's username. - title: Username - username_and_slug: - anyOf: - - type: string - - type: 'null' - description: The relative URL in the form of /u/{username}/{resource_single_char}/{slug} - title: Username and slug - users_shared_with: - default: [] - description: The list of encoded ids for users the resource has been shared. - items: - $ref: '#/components/schemas/UserEmail' - title: Users shared with - type: array - required: - - id - - title - - importable - - published - - extra - title: ShareHistoryWithStatus - type: object - ShareWithExtra: - properties: - can_share: - default: false - description: Indicates whether the resource can be directly shared or requires - further actions. - title: Can Share - type: boolean - title: ShareWithExtra - type: object - ShareWithPayload: - properties: - share_option: - anyOf: - - $ref: '#/components/schemas/SharingOptions' - - type: 'null' - description: "User choice for sharing resources which its contents may be\ - \ restricted:\n - None: The user did not choose anything yet or no option\ - \ is needed.\n - make_public: The contents of the resource will be made\ - \ publicly accessible.\n - make_accessible_to_shared: This will automatically\ - \ create a new `sharing role` allowing protected contents to be accessed\ - \ only by the desired users.\n - no_changes: This won't change the current\ - \ permissions for the contents. The user which this resource will be shared\ - \ may not be able to access all its contents.\n" - title: Share Option - user_ids: - description: A collection of encoded IDs (or email addresses) of users that - this resource will be shared with. - items: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: string - title: User Identifiers - type: array - required: - - user_ids - title: ShareWithPayload - type: object - ShareWithStatus: - properties: - email_hash: - anyOf: - - type: string - - type: 'null' - description: Encoded owner email. - title: Encoded Email - errors: - default: [] - description: Collection of messages indicating that the resource was not - shared with some (or all users) due to an error. - items: - type: string - title: Errors - type: array - extra: - anyOf: - - $ref: '#/components/schemas/ShareWithExtra' - - type: 'null' - description: Optional extra information about this shareable resource that - may be of interest. The contents of this field depend on the particular - resource. - title: Extra - id: - description: The encoded ID of the resource to be shared. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - importable: - description: Whether this resource can be published using a link. - title: Importable - type: boolean - published: - description: Whether this resource is currently published. - title: Published - type: boolean - title: - description: The title or name of the resource. - title: Title - type: string - username: - anyOf: - - type: string - - type: 'null' - description: The owner's username. - title: Username - username_and_slug: - anyOf: - - type: string - - type: 'null' - description: The relative URL in the form of /u/{username}/{resource_single_char}/{slug} - title: Username and slug - users_shared_with: - default: [] - description: The list of encoded ids for users the resource has been shared. - items: - $ref: '#/components/schemas/UserEmail' - title: Users shared with - type: array - required: - - id - - title - - importable - - published - title: ShareWithStatus - type: object - SharingOptions: - description: Options for sharing resources that may have restricted access to - all or part of their contents. - enum: - - make_public - - make_accessible_to_shared - - no_changes - title: SharingOptions - type: string - SharingStatus: - properties: - email_hash: - anyOf: - - type: string - - type: 'null' - description: Encoded owner email. - title: Encoded Email - id: - description: The encoded ID of the resource to be shared. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - importable: - description: Whether this resource can be published using a link. - title: Importable - type: boolean - published: - description: Whether this resource is currently published. - title: Published - type: boolean - title: - description: The title or name of the resource. - title: Title - type: string - username: - anyOf: - - type: string - - type: 'null' - description: The owner's username. - title: Username - username_and_slug: - anyOf: - - type: string - - type: 'null' - description: The relative URL in the form of /u/{username}/{resource_single_char}/{slug} - title: Username and slug - users_shared_with: - default: [] - description: The list of encoded ids for users the resource has been shared. - items: - $ref: '#/components/schemas/UserEmail' - title: Users shared with - type: array - required: - - id - - title - - importable - - published - title: SharingStatus - type: object - ShortTermStoreExportPayload: - properties: - duration: - anyOf: - - type: integer - - type: number - - type: 'null' - title: Duration - include_deleted: - default: false - description: Include file contents for deleted datasets (if include_files - is True). - title: Include deleted - type: boolean - include_files: - default: true - description: include materialized files in export when available - title: Include Files - type: boolean - include_hidden: - default: false - description: Include file contents for hidden datasets (if include_files - is True). - title: Include hidden - type: boolean - model_store_format: - allOf: - - $ref: '#/components/schemas/ModelStoreFormat' - default: tar.gz - description: format of model store to export - short_term_storage_request_id: - format: uuid - title: Short Term Storage Request Id - type: string - required: - - short_term_storage_request_id - title: ShortTermStoreExportPayload - type: object - ShowFullJobResponse: - properties: - command_line: - anyOf: - - type: string - - type: 'null' - description: The command line produced by the job. Users can see this value - if allowed in the configuration, administrator can always see this value. - title: Command Line - command_version: - anyOf: - - type: string - - type: 'null' - description: Tool version indicated during job execution. - title: Command Version - copied_from_job_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: Reference to cached job if job execution was cached. - title: Copied from Job-ID - create_time: - description: The time and date this item was created. - format: date-time - title: Create Time - type: string - dependencies: - anyOf: - - items: {} - type: array - - type: 'null' - description: The dependencies of the job. - title: Job dependencies - exit_code: - anyOf: - - type: integer - - type: 'null' - description: The exit code returned by the tool. Can be unset if the job - is not completed yet. - title: Exit Code - external_id: - anyOf: - - type: string - - type: 'null' - description: The job id used by the external job runner (Condor, Pulsar, - etc.). Only administrator can see this value. - title: External ID - galaxy_version: - anyOf: - - type: string - - type: 'null' - description: The (major) version of Galaxy used to create this job. - examples: - - '21.05' - title: Galaxy Version - handler: - anyOf: - - type: string - - type: 'null' - description: The job handler process assigned to handle this job. Only administrator - can see this value. - title: Job Handler - history_id: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - - type: 'null' - description: The encoded ID of the history associated with this item. - title: History ID - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Job ID - type: string - inputs: - additionalProperties: - $ref: '#/components/schemas/EncodedDatasetJobInfo' - default: {} - description: Dictionary mapping all the tool inputs (by name) to the corresponding - data references. - title: Inputs - type: object - job_messages: - anyOf: - - items: {} - type: array - - type: 'null' - description: List with additional information and possible reasons for a - failed job. - title: Job Messages - job_metrics: - anyOf: - - $ref: '#/components/schemas/JobMetricCollection' - - type: 'null' - description: Collections of metrics provided by `JobInstrumenter` plugins - on a particular job. Only administrators can see these metrics. - title: Job Metrics - job_runner_name: - anyOf: - - type: string - - type: 'null' - description: Name of the job runner plugin that handles this job. Only administrator - can see this value. - title: Job Runner Name - job_stderr: - anyOf: - - type: string - - type: 'null' - description: The captured standard error of the job execution. - title: Job Standard Error - job_stdout: - anyOf: - - type: string - - type: 'null' - description: The captured standard output of the job execution. - title: Job Standard Output - model_class: - const: Job - description: The name of the database model class. - title: Model class - type: string - output_collections: - additionalProperties: - $ref: '#/components/schemas/EncodedHdcaSourceId' - default: {} - description: '' - title: Output collections - type: object - outputs: - additionalProperties: - $ref: '#/components/schemas/EncodedDatasetJobInfo' - default: {} - description: Dictionary mapping all the tool outputs (by name) to the corresponding - data references. - title: Outputs - type: object - params: - description: Object containing all the parameters of the tool associated - with this job. The specific parameters depend on the tool itself. - title: Parameters - state: - allOf: - - $ref: '#/components/schemas/JobState' - description: Current state of the job. - title: State - stderr: - anyOf: - - type: string - - type: 'null' - description: Combined tool and job standard error streams. - title: Standard Error - stdout: - anyOf: - - type: string - - type: 'null' - description: Combined tool and job standard output streams. - title: Standard Output - tool_id: - description: Identifier of the tool that generated this job. - title: Tool ID - type: string - tool_stderr: - anyOf: - - type: string - - type: 'null' - description: The captured standard error of the tool executed by the job. - title: Tool Standard Error - tool_stdout: - anyOf: - - type: string - - type: 'null' - description: The captured standard output of the tool executed by the job. - title: Tool Standard Output - update_time: - description: The last time and date this item was updated. - format: date-time - title: Update Time - type: string - user_email: - anyOf: - - type: string - - type: 'null' - description: The email of the user that owns this job. Only the owner of - the job and administrators can see this value. - title: User Email - required: - - model_class - - id - - tool_id - - state - - create_time - - update_time - - params - title: ShowFullJobResponse - type: object - Src: - enum: - - url - - pasted - - files - - path - - composite - - ftp_import - - server_dir - title: Src - type: string - StorageItemCleanupError: - properties: - error: - title: Error - type: string - item_id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Item Id - type: string - required: - - item_id - - error - title: StorageItemCleanupError - type: object - StorageItemsCleanupResult: - properties: - errors: - items: - $ref: '#/components/schemas/StorageItemCleanupError' - title: Errors - type: array - success_item_count: - title: Success Item Count - type: integer - total_free_bytes: - title: Total Free Bytes - type: integer - total_item_count: - title: Total Item Count - type: integer - required: - - total_item_count - - success_item_count - - total_free_bytes - - errors - title: StorageItemsCleanupResult - type: object - StoreExportPayload: - properties: - include_deleted: - default: false - description: Include file contents for deleted datasets (if include_files - is True). - title: Include deleted - type: boolean - include_files: - default: true - description: include materialized files in export when available - title: Include Files - type: boolean - include_hidden: - default: false - description: Include file contents for hidden datasets (if include_files - is True). - title: Include hidden - type: boolean - model_store_format: - allOf: - - $ref: '#/components/schemas/ModelStoreFormat' - default: tar.gz - description: format of model store to export - title: StoreExportPayload - type: object - StoredItem: - properties: - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Id - type: string - name: - title: Name - type: string - size: - title: Size - type: integer - type: - anyOf: - - const: history - - const: dataset - title: Type - update_time: - description: The last time and date this item was updated. - format: date-time - title: Update Time - type: string - required: - - id - - name - - type - - size - - update_time - title: StoredItem - type: object - StoredItemOrderBy: - description: Available options for sorting Stored Items results. - enum: - - name-asc - - name-dsc - - size-asc - - size-dsc - - update_time-asc - - update_time-dsc - title: StoredItemOrderBy - type: string - SuitableConverter: - properties: - name: - description: The name of the converter. - title: Name - type: string - original_type: - description: The type to convert from. - title: Original Type - type: string - target_type: - description: The type to convert to. - title: Target Type - type: string - tool_id: - description: The ID of the tool that can perform the type conversion. - title: Tool Id - type: string - required: - - tool_id - - name - - target_type - - original_type - title: SuitableConverter - type: object - SuitableConverters: - description: Collection of converters that can be used on a particular dataset - collection. - items: - $ref: '#/components/schemas/SuitableConverter' - title: SuitableConverters - type: array - SupportedType: - enum: - - None - - BasicAuth - - BearerAuth - - PassportAuth - title: SupportedType - type: string - TagCollection: - description: Represents the collection of tags associated with an item. - items: - pattern: ^([^\s.:])+(.[^\s.:]+)*(:[^\s.:]+)?$ - type: string - title: TagCollection - type: array - TagOperationParams: - properties: - tags: - items: - type: string - title: Tags - type: array - type: - anyOf: - - const: add_tags - - const: remove_tags - title: Type - required: - - type - - tags - title: TagOperationParams - type: object - TaggableItemClass: - enum: - - History - - HistoryDatasetAssociation - - HistoryDatasetCollectionAssociation - - LibraryDatasetDatasetAssociation - - Page - - StoredWorkflow - - Visualization - title: TaggableItemClass - type: string - TaskState: - description: Enum representing the possible states of a task. - enum: - - PENDING - - STARTED - - RETRY - - FAILURE - - SUCCESS - title: TaskState - type: string - ToolDataDetails: - properties: - columns: - description: A list of column names - examples: - - value - - dbkey - - name - - path - items: - type: string - title: Columns - type: array - fields: - default: [] - description: '' - items: - items: - type: string - type: array - title: Fields - type: array - model_class: - description: The name of class modelling this tool data - examples: - - TabularToolDataTable - title: Model class - type: string - name: - description: The name of this tool data entry - examples: - - all_fasta - title: Name - type: string - required: - - name - - model_class - - columns - title: ToolDataDetails - type: object - ToolDataEntry: - properties: - model_class: - description: The name of class modelling this tool data - examples: - - TabularToolDataTable - title: Model class - type: string - name: - description: The name of this tool data entry - examples: - - all_fasta - title: Name - type: string - required: - - name - - model_class - title: ToolDataEntry - type: object - ToolDataEntryList: - items: - $ref: '#/components/schemas/ToolDataEntry' - title: ToolDataEntryList - type: array - ToolDataField: - properties: - base_dir: - description: A list of directories where the data files are stored - items: - type: string - title: Base directories - type: array - fields: - additionalProperties: - type: string - description: '' - title: Fields - type: object - files: - additionalProperties: - type: integer - description: A dictionary of file names and their size in bytes - examples: - - file.txt: 136 - title: Files - type: object - fingerprint: - description: SHA1 Hash - examples: - - 22b45237a85c2b3f474bf66888c534387ffe0ced - title: Fingerprint - type: string - model_class: - description: The name of class modelling this tool data field - examples: - - TabularToolDataField - title: Model class - type: string - name: - description: The name of the field - title: Name - type: string - required: - - name - - model_class - - fields - - base_dir - - files - - fingerprint - title: ToolDataField - type: object - ToolDataItem: - properties: - values: - description: A `\t` (TAB) separated list of column __contents__. You must - specify a value for each of the columns of the data table. - examples: - - "value\tdbkey\tname\tpath" - title: Values - type: string - required: - - values - title: ToolDataItem - type: object - Tour: - properties: - description: - description: Tour description - title: Description - type: string - id: - description: Tour identifier - title: Identifier - type: string - name: - description: Name of tour - title: Name - type: string - requirements: - description: Requirements to run the tour. - items: - $ref: '#/components/schemas/Requirement' - title: Requirements - type: array - tags: - description: Topic topic tags - items: - type: string - title: Tags - type: array - required: - - name - - description - - tags - - requirements - - id - title: Tour - type: object - TourDetails: - properties: - description: - description: Tour description - title: Description - type: string - name: - description: Name of tour - title: Name - type: string - requirements: - description: Requirements to run the tour. - items: - $ref: '#/components/schemas/Requirement' - title: Requirements - type: array - steps: - description: Tour steps - items: - $ref: '#/components/schemas/TourStep' - title: Steps - type: array - tags: - description: Topic topic tags - items: - type: string - title: Tags - type: array - title_default: - anyOf: - - type: string - - type: 'null' - description: Default title for each step - title: Default title - required: - - name - - description - - tags - - requirements - - steps - title: TourDetails - type: object - TourList: - default: [] - items: - $ref: '#/components/schemas/Tour' - title: TourList - type: array - TourStep: - properties: - content: - anyOf: - - type: string - - type: 'null' - description: Text shown to the user - title: Content - element: - anyOf: - - type: string - - type: 'null' - description: CSS selector for the element to be described/clicked - title: Element - placement: - anyOf: - - type: string - - type: 'null' - description: Placement of the text box relative to the selected element - title: Placement - postclick: - anyOf: - - type: boolean - - items: - type: string - type: array - - type: 'null' - description: Elements that receive a click() event after the step is shown - title: Post-click - preclick: - anyOf: - - type: boolean - - items: - type: string - type: array - - type: 'null' - description: Elements that receive a click() event before the step is shown - title: Pre-click - textinsert: - anyOf: - - type: string - - type: 'null' - description: Text to insert if element is a text box (e.g. tool search or - upload) - title: Text-insert - title: - anyOf: - - type: string - - type: 'null' - description: Title displayed in the header of the step container - title: Title - title: TourStep - type: object - UndeleteHistoriesPayload: - properties: - ids: - description: List of history IDs to be undeleted. - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - title: IDs - type: array - required: - - ids - title: UndeleteHistoriesPayload - type: object - UpdateCollectionAttributePayload: - additionalProperties: false - description: Contains attributes that can be updated for all elements in a dataset - collection. - properties: - dbkey: - description: TODO - title: Dbkey - type: string - required: - - dbkey - title: UpdateCollectionAttributePayload - type: object - UpdateContentItem: - additionalProperties: true - description: Used for updating a particular history item. All fields are optional. - properties: - history_content_type: - allOf: - - $ref: '#/components/schemas/HistoryContentType' - description: The type of this item. - title: Content Type - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Id - type: string - required: - - history_content_type - - id - title: UpdateContentItem - type: object - UpdateHistoryContentsBatchPayload: - additionalProperties: true - description: Contains property values that will be updated for all the history - `items` provided. - example: - items: - - history_content_type: dataset - id: string - visible: false - properties: - items: - description: A list of content items to update with the changes. - items: - $ref: '#/components/schemas/UpdateContentItem' - title: Items - type: array - required: - - items - title: UpdateHistoryContentsBatchPayload - type: object - UpdateHistoryContentsPayload: - additionalProperties: true - description: Can contain arbitrary/dynamic fields that will be updated for a - particular history item. - example: - annotation: Test - visible: false - properties: - annotation: - anyOf: - - type: string - - type: 'null' - description: A user-defined annotation for this item. - title: Annotation - deleted: - anyOf: - - type: boolean - - type: 'null' - description: Whether this item is marked as deleted. - title: Deleted - name: - anyOf: - - type: string - - type: 'null' - description: The new name of the item. - title: Name - tags: - anyOf: - - $ref: '#/components/schemas/TagCollection' - - type: 'null' - description: A list of tags to add to this item. - title: Tags - visible: - anyOf: - - type: boolean - - type: 'null' - description: Whether this item is visible in the history. - title: Visible - title: UpdateHistoryContentsPayload - type: object - UpdateLibraryFolderPayload: - properties: - description: - anyOf: - - type: string - - type: 'null' - description: The new description of the library folder. - title: Description - name: - anyOf: - - type: string - - type: 'null' - description: The new name of the library folder. - title: Name - title: UpdateLibraryFolderPayload - type: object - UpdateLibraryPayload: - properties: - description: - anyOf: - - type: string - - type: 'null' - description: A detailed description of the Library. Leave unset to keep - the existing. - title: Description - name: - anyOf: - - type: string - - type: 'null' - description: The new name of the Library. Leave unset to keep the existing. - title: Name - synopsis: - anyOf: - - type: string - - type: 'null' - description: A short text describing the contents of the Library. Leave - unset to keep the existing. - title: Synopsis - title: UpdateLibraryPayload - type: object - UpdateObjectStoreIdPayload: - properties: - object_store_id: - description: Object store ID to update to, it must be an object store with - the same device ID as the target dataset currently. - title: Object Store Id - type: string - required: - - object_store_id - title: UpdateObjectStoreIdPayload - type: object - UpdateQuotaParams: - properties: - amount: - anyOf: - - type: string - - type: 'null' - description: Quota size (E.g. ``10000MB``, ``99 gb``, ``0.2T``, ``unlimited``) - title: Amount - default: - anyOf: - - $ref: '#/components/schemas/DefaultQuotaValues' - - type: 'null' - description: Whether or not this is a default quota. Valid values are ``no``, - ``unregistered``, ``registered``. Calling this method with ``default="no"`` - on a non-default quota will throw an error. Not passing this parameter - is equivalent to passing ``no``. - title: Default - description: - anyOf: - - type: string - - type: 'null' - description: Detailed text description for this Quota. - title: Description - in_groups: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: A list of group IDs or names to associate with this quota. - title: Groups - in_users: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: A list of user IDs or user emails to associate with this quota. - title: Users - name: - anyOf: - - type: string - - type: 'null' - description: The new name of the quota. This must be unique within a Galaxy - instance. - title: Name - operation: - allOf: - - $ref: '#/components/schemas/QuotaOperation' - default: '=' - description: One of (``+``, ``-``, ``=``). If you wish to change this value, - you must also provide the ``amount``, otherwise it will not take effect. - title: Operation - title: UpdateQuotaParams - type: object - UpdateUserNotificationPreferencesRequest: - description: Contains the new notification preferences of a user. - examples: - - preferences: - message: - channels: - push: true - enabled: true - new_shared_item: - channels: - push: true - enabled: true - properties: - preferences: - additionalProperties: - $ref: '#/components/schemas/NotificationCategorySettings' - description: The new notification preferences of the user. - title: Preferences - type: object - required: - - preferences - title: UpdateUserNotificationPreferencesRequest - type: object - UrlDataElement: - additionalProperties: false - properties: - MD5: - anyOf: - - type: string - - type: 'null' - title: Md5 - auto_decompress: - default: false - description: Decompress compressed data before sniffing? - title: Auto Decompress - type: boolean - collection_type: - anyOf: - - type: string - - type: 'null' - title: Collection Type - created_from_basename: - anyOf: - - type: string - - type: 'null' - title: Created From Basename - dbkey: - default: '?' - title: Dbkey - type: string - deferred: - default: false - title: Deferred - type: boolean - description: - anyOf: - - type: string - - type: 'null' - title: Description - elements_from: - anyOf: - - $ref: '#/components/schemas/ElementsFromType' - - type: 'null' - ext: - default: auto - title: Ext - type: string - extra_files: - anyOf: - - $ref: '#/components/schemas/ExtraFiles' - - type: 'null' - info: - anyOf: - - type: string - - type: 'null' - title: Info - name: - anyOf: - - type: string - - type: integer - - type: number - - type: boolean - - type: 'null' - title: Name - space_to_tab: - default: false - title: Space To Tab - type: boolean - src: - const: url - title: Src - tags: - anyOf: - - items: - type: string - type: array - - type: 'null' - title: Tags - to_posix_lines: - default: false - title: To Posix Lines - type: boolean - url: - description: URL to upload - title: Url - type: string - required: - - src - - url - title: UrlDataElement - type: object - UserBeaconSetting: - properties: - enabled: - description: True if beacon sharing is enabled - title: Enabled - type: boolean - required: - - enabled - title: UserBeaconSetting - type: object - UserCreationPayload: - properties: - email: - description: Email of the user - title: Email - type: string - password: - description: The password of the user. - title: user_password - type: string - username: - description: The name of the user. - title: user_name - type: string - required: - - password - - email - - username - title: UserCreationPayload - type: object - UserDeletionPayload: - properties: - purge: - description: Purge the user - title: Purge user - type: boolean - required: - - purge - title: UserDeletionPayload - type: object - UserEmail: - properties: - email: - description: The email of the user. - title: Email - type: string - id: - description: The encoded ID of the user. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: User ID - type: string - required: - - id - - email - title: UserEmail - type: object - UserModel: - description: User in a transaction context. - properties: - active: - description: User is active - title: Active - type: boolean - deleted: - description: ' User is deleted' - title: Deleted - type: boolean - email: - description: Email of the user - title: Email - type: string - id: - description: Encoded ID of the user - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - last_password_change: - anyOf: - - format: date-time - type: string - - type: 'null' - description: '' - title: Last password change - model_class: - const: User - description: The name of the database model class. - title: Model class - type: string - username: - description: The name of the user. - title: user_name - type: string - required: - - model_class - - id - - username - - email - - deleted - - active - - last_password_change - title: UserModel - type: object - UserNotificationListResponse: - description: A list of user notifications. - items: - $ref: '#/components/schemas/UserNotificationResponse' - title: UserNotificationListResponse - type: array - UserNotificationPreferences: - description: Contains the full notification preferences of a user. - examples: - - preferences: - message: - channels: - push: true - enabled: true - new_shared_item: - channels: - push: true - enabled: true - properties: - preferences: - additionalProperties: - $ref: '#/components/schemas/NotificationCategorySettings' - description: The notification preferences of the user. - title: Preferences - type: object - required: - - preferences - title: UserNotificationPreferences - type: object - UserNotificationResponse: - description: A notification response specific to the user. - properties: - category: - allOf: - - $ref: '#/components/schemas/PersonalNotificationCategory' - description: The category of the notification. Represents the type of the - notification. E.g. 'message' or 'new_shared_item'. - title: Category - content: - description: The content of the notification. The structure depends on the - category. - discriminator: - mapping: - broadcast: '#/components/schemas/BroadcastNotificationContent' - message: '#/components/schemas/MessageNotificationContent' - new_shared_item: '#/components/schemas/NewSharedItemNotificationContent' - propertyName: category - oneOf: - - $ref: '#/components/schemas/MessageNotificationContent' - - $ref: '#/components/schemas/NewSharedItemNotificationContent' - - $ref: '#/components/schemas/BroadcastNotificationContent' - title: Content - create_time: - description: The time when the notification was created. - format: date-time - title: Create time - type: string - deleted: - description: Whether the notification is marked as deleted by the user. - Deleted notifications don't show up in the notification list. - title: Deleted - type: boolean - expiration_time: - anyOf: - - format: date-time - type: string - - type: 'null' - description: The time when the notification will expire. If not set, the - notification will never expire. Expired notifications will be permanently - deleted. - title: Expiration time - id: - description: The encoded ID of the notification. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - publication_time: - description: The time when the notification was published. Notifications - can be created and then published at a later time. - format: date-time - title: Publication time - type: string - seen_time: - anyOf: - - format: date-time - type: string - - type: 'null' - description: The time when the notification was seen by the user. If not - set, the notification was not seen yet. - title: Seen time - source: - description: The source of the notification. Represents the agent that created - the notification. E.g. 'galaxy' or 'admin'. - title: Source - type: string - update_time: - description: The time when the notification was last updated. - format: date-time - title: Update time - type: string - variant: - allOf: - - $ref: '#/components/schemas/NotificationVariant' - description: The variant of the notification. Represents the intent or relevance - of the notification. E.g. 'info' or 'urgent'. - title: Variant - required: - - id - - source - - category - - variant - - create_time - - update_time - - publication_time - - content - - deleted - title: UserNotificationResponse - type: object - UserNotificationUpdateRequest: - description: A notification update request specific to the user. - properties: - deleted: - anyOf: - - type: boolean - - type: 'null' - description: Whether the notification should be marked as deleted by the - user. If not set, the notification will not be changed. - title: Deleted - seen: - anyOf: - - type: boolean - - type: 'null' - description: Whether the notification should be marked as seen by the user. - If not set, the notification will not be changed. - title: Seen - title: UserNotificationUpdateRequest - type: object - UserNotificationsBatchUpdateRequest: - description: A batch update request specific for user notifications. - properties: - changes: - allOf: - - $ref: '#/components/schemas/UserNotificationUpdateRequest' - description: The changes that should be applied to the notifications. Only - the fields that are set will be changed. - title: Changes - notification_ids: - description: The list of encoded notification IDs of the notifications that - should be updated. - items: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - type: string - title: Notification IDs - type: array - required: - - notification_ids - - changes - title: UserNotificationsBatchUpdateRequest - type: object - UserQuota: - properties: - model_class: - const: UserQuotaAssociation - description: The name of the database model class. - title: Model class - type: string - user: - allOf: - - $ref: '#/components/schemas/UserModel' - description: Information about a user associated with a quota. - title: User - required: - - model_class - - user - title: UserQuota - type: object - UserQuotaUsage: - properties: - quota: - anyOf: - - type: string - - type: 'null' - title: Quota - quota_bytes: - anyOf: - - type: integer - - type: 'null' - title: Quota Bytes - quota_percent: - anyOf: - - type: number - - type: 'null' - title: Quota Percent - quota_source_label: - anyOf: - - type: string - - type: 'null' - title: Quota Source Label - total_disk_usage: - title: Total Disk Usage - type: number - required: - - total_disk_usage - title: UserQuotaUsage - type: object - ValidationError: - properties: - loc: - items: - anyOf: - - type: string - - type: integer - title: Location - type: array - msg: - title: Message - type: string - type: - title: Error Type - type: string - required: - - loc - - msg - - type - title: ValidationError - type: object - Visualization: - properties: {} - title: Visualization - type: object - VisualizationSummary: - additionalProperties: true - properties: - annotation: - anyOf: - - type: string - - type: 'null' - description: The annotation of this Visualization. - title: Annotation - create_time: - anyOf: - - format: date-time - type: string - - type: 'null' - description: The time and date this item was created. - title: Create Time - dbkey: - anyOf: - - type: string - - type: 'null' - description: The database key of the visualization. - title: DbKey - deleted: - description: Whether this Visualization has been deleted. - title: Deleted - type: boolean - id: - description: Encoded ID of the Visualization. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - importable: - description: Whether this Visualization can be imported. - title: Importable - type: boolean - published: - description: Whether this Visualization has been published. - title: Published - type: boolean - tags: - anyOf: - - $ref: '#/components/schemas/TagCollection' - - type: 'null' - description: A list of tags to add to this item. - title: Tags - title: - description: The name of the visualization. - title: Title - type: string - type: - description: The type of the visualization. - title: Type - type: string - update_time: - anyOf: - - format: date-time - type: string - - type: 'null' - description: The last time and date this item was updated. - title: Update Time - username: - description: The name of the user owning this Visualization. - title: Username - type: string - required: - - id - - deleted - - importable - - published - - tags - - title - - type - - username - - create_time - - update_time - title: VisualizationSummary - type: object - VisualizationSummaryList: - default: [] - items: - $ref: '#/components/schemas/VisualizationSummary' - title: VisualizationSummaryList - type: array - WorkflowInvocationCollectionView: - properties: - create_time: - description: The time and date this item was created. - format: date-time - title: Create Time - type: string - history_id: - description: The encoded ID of the history associated with the invocation. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: History ID - type: string - id: - description: The encoded ID of the workflow invocation. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - model_class: - const: WorkflowInvocation - description: The name of the database model class. - title: Model class - type: string - state: - allOf: - - $ref: '#/components/schemas/InvocationState' - description: State of workflow invocation. - title: Invocation state - update_time: - description: The last time and date this item was updated. - format: date-time - title: Update Time - type: string - uuid: - anyOf: - - format: uuid4 - type: string - - format: uuid1 - type: string - - type: 'null' - description: Universal unique identifier of the workflow invocation. - title: UUID - workflow_id: - description: The encoded Workflow ID associated with the invocation. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Workflow ID - type: string - required: - - model_class - - id - - create_time - - update_time - - workflow_id - - history_id - - state - title: WorkflowInvocationCollectionView - type: object - WorkflowInvocationElementView: - properties: - create_time: - description: The time and date this item was created. - format: date-time - title: Create Time - type: string - history_id: - description: The encoded ID of the history associated with the invocation. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: History ID - type: string - id: - description: The encoded ID of the workflow invocation. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: ID - type: string - input_step_parameters: - additionalProperties: - $ref: '#/components/schemas/InvocationInputParameter' - description: Input step parameters of the workflow invocation. - title: Input step parameters - type: object - inputs: - additionalProperties: - $ref: '#/components/schemas/InvocationInput' - description: Input datasets/dataset collections of the workflow invocation. - title: Inputs - type: object - messages: - description: A list of messages about why the invocation did not succeed. - items: - discriminator: - mapping: - cancelled_on_review: '#/components/schemas/InvocationCancellationReviewFailedResponse' - collection_failed: '#/components/schemas/InvocationFailureCollectionFailedResponse' - dataset_failed: '#/components/schemas/InvocationFailureDatasetFailedResponse' - expression_evaluation_failed: '#/components/schemas/InvocationFailureExpressionEvaluationFailedResponse' - history_deleted: '#/components/schemas/InvocationCancellationHistoryDeletedResponse' - job_failed: '#/components/schemas/InvocationFailureJobFailedResponse' - output_not_found: '#/components/schemas/InvocationFailureOutputNotFoundResponse' - unexpected_failure: '#/components/schemas/InvocationUnexpectedFailureResponse' - user_request: '#/components/schemas/InvocationCancellationUserRequestResponse' - when_not_boolean: '#/components/schemas/InvocationFailureWhenNotBooleanResponse' - workflow_output_not_found: '#/components/schemas/InvocationEvaluationWarningWorkflowOutputNotFoundResponse' - propertyName: reason - oneOf: - - $ref: '#/components/schemas/InvocationCancellationReviewFailedResponse' - - $ref: '#/components/schemas/InvocationCancellationHistoryDeletedResponse' - - $ref: '#/components/schemas/InvocationCancellationUserRequestResponse' - - $ref: '#/components/schemas/InvocationFailureDatasetFailedResponse' - - $ref: '#/components/schemas/InvocationFailureCollectionFailedResponse' - - $ref: '#/components/schemas/InvocationFailureJobFailedResponse' - - $ref: '#/components/schemas/InvocationFailureOutputNotFoundResponse' - - $ref: '#/components/schemas/InvocationFailureExpressionEvaluationFailedResponse' - - $ref: '#/components/schemas/InvocationFailureWhenNotBooleanResponse' - - $ref: '#/components/schemas/InvocationUnexpectedFailureResponse' - - $ref: '#/components/schemas/InvocationEvaluationWarningWorkflowOutputNotFoundResponse' - title: Messages - type: array - model_class: - const: WorkflowInvocation - description: The name of the database model class. - title: Model class - type: string - output_collections: - additionalProperties: - $ref: '#/components/schemas/InvocationOutputCollection' - description: Output dataset collections of the workflow invocation. - title: Output collections - type: object - output_values: - description: Output values of the workflow invocation. - title: Output values - type: object - outputs: - additionalProperties: - $ref: '#/components/schemas/InvocationOutput' - description: Output datasets of the workflow invocation. - title: Outputs - type: object - state: - allOf: - - $ref: '#/components/schemas/InvocationState' - description: State of workflow invocation. - title: Invocation state - steps: - description: Steps of the workflow invocation. - items: - $ref: '#/components/schemas/InvocationStep' - title: Steps - type: array - update_time: - description: The last time and date this item was updated. - format: date-time - title: Update Time - type: string - uuid: - anyOf: - - format: uuid4 - type: string - - format: uuid1 - type: string - - type: 'null' - description: Universal unique identifier of the workflow invocation. - title: UUID - workflow_id: - description: The encoded Workflow ID associated with the invocation. - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Workflow ID - type: string - required: - - model_class - - id - - create_time - - update_time - - workflow_id - - history_id - - state - - steps - - inputs - - input_step_parameters - - outputs - - output_collections - - output_values - - messages - title: WorkflowInvocationElementView - type: object - WorkflowInvocationResponse: - anyOf: - - $ref: '#/components/schemas/WorkflowInvocationElementView' - - $ref: '#/components/schemas/WorkflowInvocationCollectionView' - title: WorkflowInvocationResponse - WorkflowInvocationStateSummary: - properties: - id: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Id - type: string - model: - const: WorkflowInvocation - description: The name of the database model class. - title: Model class - type: string - populated_state: - allOf: - - $ref: '#/components/schemas/DatasetCollectionPopulatedState' - description: 'Indicates the general state of the elements in the dataset - collection:- ''new'': new dataset collection, unpopulated elements.- ''ok'': - collection elements populated (HDAs may or may not have errors).- ''failed'': - some problem populating, won''t be populated.' - title: Populated State - states: - additionalProperties: - type: integer - default: {} - description: A dictionary of job states and the number of jobs in that state. - title: States - type: object - required: - - id - - populated_state - - model - title: WorkflowInvocationStateSummary - type: object - WriteInvocationStoreToPayload: - properties: - bco_merge_history_metadata: - default: false - description: When reading tags/annotations to generate BCO object include - history metadata. - title: Bco Merge History Metadata - type: boolean - bco_override_algorithmic_error: - anyOf: - - additionalProperties: - type: string - type: object - - type: 'null' - description: Override algorithmic error for 'error domain' when generating - BioCompute object. - title: Bco Override Algorithmic Error - bco_override_empirical_error: - anyOf: - - additionalProperties: - type: string - type: object - - type: 'null' - description: Override empirical error for 'error domain' when generating - BioCompute object. - title: Bco Override Empirical Error - bco_override_environment_variables: - anyOf: - - additionalProperties: - type: string - type: object - - type: 'null' - description: Override environment variables for 'execution_domain' when - generating BioCompute object. - title: Bco Override Environment Variables - bco_override_xref: - anyOf: - - items: - $ref: '#/components/schemas/XrefItem' - type: array - - type: 'null' - description: Override xref for 'description domain' when generating BioCompute - object. - title: Bco Override Xref - include_deleted: - default: false - description: Include file contents for deleted datasets (if include_files - is True). - title: Include deleted - type: boolean - include_files: - default: true - description: include materialized files in export when available - title: Include Files - type: boolean - include_hidden: - default: false - description: Include file contents for hidden datasets (if include_files - is True). - title: Include hidden - type: boolean - model_store_format: - allOf: - - $ref: '#/components/schemas/ModelStoreFormat' - default: tar.gz - description: format of model store to export - target_uri: - description: Galaxy Files URI to write mode store content to. - title: Target URI - type: string - required: - - target_uri - title: WriteInvocationStoreToPayload - type: object - WriteStoreToPayload: - properties: - include_deleted: - default: false - description: Include file contents for deleted datasets (if include_files - is True). - title: Include deleted - type: boolean - include_files: - default: true - description: include materialized files in export when available - title: Include Files - type: boolean - include_hidden: - default: false - description: Include file contents for hidden datasets (if include_files - is True). - title: Include hidden - type: boolean - model_store_format: - allOf: - - $ref: '#/components/schemas/ModelStoreFormat' - default: tar.gz - description: format of model store to export - target_uri: - description: Galaxy Files URI to write mode store content to. - title: Target URI - type: string - required: - - target_uri - title: WriteStoreToPayload - type: object - XrefItem: - properties: - access_time: - description: Date and time the external reference was accessed - format: date-time - title: Access Time - type: string - ids: - description: List of reference identifiers - items: - type: string - title: Ids - type: array - name: - description: Name of external reference - examples: - - PubChem-compound - title: Name - type: string - namespace: - description: External resource vendor prefix - examples: - - pubchem.compound - title: Namespace - type: string - required: - - namespace - - name - - ids - - access_time - title: XrefItem - type: object - securitySchemes: - APIKeyCookie: - in: cookie - name: galaxysession - type: apiKey - APIKeyHeader: - in: header - name: x-api-key - type: apiKey - APIKeyQuery: - in: query - name: key - type: apiKey - HTTPBearer: - scheme: bearer - type: http -info: - license: - name: MIT - url: https://github.com/galaxyproject/galaxy/blob/dev/LICENSE.txt - title: Galaxy API - version: 0.1.0 -openapi: 3.1.0 -paths: - /api/authenticate/baseauth: - get: - operationId: get_api_key_api_authenticate_baseauth_get - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/APIKeyResponse' - description: Successful Response - summary: Returns returns an API key for authenticated user based on BaseAuth - headers. - tags: - - authenticate - - authenticate - /api/cloud/storage/get: - post: - deprecated: true - operationId: get_api_cloud_storage_get_post - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/CloudObjects' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DatasetSummaryList' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Gets given objects from a given cloud-based bucket to a Galaxy history. - tags: - - cloud - - cloud - /api/cloud/storage/send: - post: - deprecated: true - operationId: send_api_cloud_storage_send_post - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/CloudDatasets' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/CloudDatasetsResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Sends given dataset(s) in a given history to a given cloud-based bucket. - tags: - - cloud - - cloud - /api/configuration: - get: - description: 'Return an object containing exposable configuration settings. - - - A more complete list is returned if the user is an admin. - - Pass in `view` and a comma-seperated list of keys to control which - - configuration settings are returned.' - operationId: index_api_configuration_get - parameters: - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - title: Response Index Api Configuration Get - type: object - description: Object containing exposable configuration settings - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return an object containing exposable configuration settings - tags: - - configuration - - configuration - /api/configuration/decode/{encoded_id}: - get: - description: Decode a given id. - operationId: decode_id_api_configuration_decode__encoded_id__get - parameters: - - description: Encoded id to be decoded - in: path - name: encoded_id - required: true - schema: - description: Encoded id to be decoded - title: Encoded id - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - additionalProperties: - type: integer - title: Response Decode Id Api Configuration Decode Encoded Id Get - type: object - description: Decoded id - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Decode a given id - tags: - - configuration - - configuration - /api/configuration/dynamic_tool_confs: - get: - description: Return dynamic tool configuration files. - operationId: dynamic_tool_confs_api_configuration_dynamic_tool_confs_get - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - additionalProperties: - type: string - type: object - title: Response Dynamic Tool Confs Api Configuration Dynamic Tool - Confs Get - type: array - description: Dynamic tool configuration files - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return dynamic tool configuration files - tags: - - configuration - - configuration - /api/configuration/encode/{decoded_id}: - get: - description: Decode a given id. - operationId: encode_id_api_configuration_encode__decoded_id__get - parameters: - - description: Decoded id to be encoded - in: path - name: decoded_id - required: true - schema: - description: Decoded id to be encoded - title: Decoded id - type: integer - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - additionalProperties: - type: string - title: Response Encode Id Api Configuration Encode Decoded Id Get - type: object - description: Encoded id - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Encode a given id - tags: - - configuration - - configuration - /api/configuration/tool_lineages: - get: - description: Return tool lineages for tools that have them. - operationId: tool_lineages_api_configuration_tool_lineages_get - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - additionalProperties: - type: object - type: object - title: Response Tool Lineages Api Configuration Tool Lineages Get - type: array - description: Tool lineages for tools that have them - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return tool lineages for tools that have them - tags: - - configuration - - configuration - /api/configuration/toolbox: - put: - description: Reload the Galaxy toolbox (but not individual tools). - operationId: reload_toolbox_api_configuration_toolbox_put - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Reload the Galaxy toolbox (but not individual tools) - tags: - - configuration - - configuration - /api/dataset_collection_element/{dce_id}: - get: - operationId: content_api_dataset_collection_element__dce_id__get - parameters: - - description: The encoded ID of the dataset collection element. - in: path - name: dce_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DCESummary' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Content - tags: - - dataset collections - - dataset collections - /api/dataset_collections: - post: - operationId: create_api_dataset_collections_post - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/CreateNewCollectionPayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/HDCADetailed' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Create a new dataset collection instance. - tags: - - dataset collections - - dataset collections - /api/dataset_collections/{hdca_id}/contents/{parent_id}: - get: - operationId: contents_dataset_collection_api_dataset_collections__hdca_id__contents__parent_id__get - parameters: - - description: The ID of the `HDCA`. - in: path - name: hdca_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: Parent collection ID describing what collection the contents - belongs to. - in: path - name: parent_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The type of collection instance. Either `history` (default) or - `library`. - in: query - name: instance_type - required: false - schema: - default: history - description: The type of collection instance. Either `history` (default) - or `library`. - enum: - - history - - library - title: Instance Type - type: string - - description: The maximum number of content elements to return. - in: query - name: limit - required: false - schema: - anyOf: - - type: integer - - type: 'null' - description: The maximum number of content elements to return. - title: Limit - - description: The number of content elements that will be skipped before returning. - in: query - name: offset - required: false - schema: - anyOf: - - type: integer - - type: 'null' - description: The number of content elements that will be skipped before - returning. - title: Offset - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DatasetCollectionContentElements' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns direct child contents of indicated dataset collection parent - ID. - tags: - - dataset collections - - dataset collections - /api/dataset_collections/{id}: - get: - operationId: show_api_dataset_collections__id__get - parameters: - - description: The ID of the `HDCA`. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The type of collection instance. Either `history` (default) or - `library`. - in: query - name: instance_type - required: false - schema: - default: history - description: The type of collection instance. Either `history` (default) - or `library`. - enum: - - history - - library - title: Instance Type - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/HDCADetailed' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns detailed information about the given collection. - tags: - - dataset collections - - dataset collections - /api/dataset_collections/{id}/attributes: - get: - operationId: attributes_api_dataset_collections__id__attributes_get - parameters: - - description: The ID of the `HDCA`. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The type of collection instance. Either `history` (default) or - `library`. - in: query - name: instance_type - required: false - schema: - default: history - description: The type of collection instance. Either `history` (default) - or `library`. - enum: - - history - - library - title: Instance Type - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DatasetCollectionAttributesResult' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns `dbkey`/`extension` attributes for all the collection elements. - tags: - - dataset collections - - dataset collections - /api/dataset_collections/{id}/copy: - post: - operationId: copy_api_dataset_collections__id__copy_post - parameters: - - description: The ID of the `HDCA`. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/UpdateCollectionAttributePayload' - required: true - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Copy the given collection datasets to a new collection using a new - `dbkey` attribute. - tags: - - dataset collections - - dataset collections - /api/dataset_collections/{id}/download: - get: - description: 'Download the content of a history dataset collection as a `zip` - archive - - while maintaining approximate collection structure.' - operationId: dataset_collections__download - parameters: - - description: The ID of the `HDCA`. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Download the content of a dataset collection as a `zip` archive. - tags: - - histories - - histories - - dataset collections - /api/dataset_collections/{id}/prepare_download: - post: - description: 'The history dataset collection will be written as a `zip` archive - to the - - returned short term storage object. Progress tracking this file''s creation - - can be tracked with the short_term_storage API.' - operationId: prepare_collection_download_api_dataset_collections__id__prepare_download_post - parameters: - - description: The ID of the `HDCA`. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/AsyncFile' - description: Short term storage reference for async monitoring of this download. - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - '501': - description: Required asynchronous tasks required for this operation not - available. - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Prepare an short term storage object that the collection will be downloaded - to. - tags: - - histories - - histories - - dataset collections - /api/dataset_collections/{id}/suitable_converters: - get: - operationId: suitable_converters_api_dataset_collections__id__suitable_converters_get - parameters: - - description: The ID of the `HDCA`. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The type of collection instance. Either `history` (default) or - `library`. - in: query - name: instance_type - required: false - schema: - default: history - description: The type of collection instance. Either `history` (default) - or `library`. - enum: - - history - - library - title: Instance Type - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/SuitableConverters' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns a list of applicable converters for all datatypes in the given - collection. - tags: - - dataset collections - - dataset collections - /api/datasets: - delete: - description: 'Deletes or purges a batch of datasets. - - **Warning**: only the ownership of the datasets (and upload state for HDAs) - is checked, - - no other checks or restrictions are made.' - operationId: delete_batch_api_datasets_delete - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/DeleteDatasetBatchPayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DeleteDatasetBatchResult' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Deletes or purges a batch of datasets. - tags: - - datasets - - datasets - get: - operationId: index_api_datasets_get - parameters: - - description: Optional identifier of a History. Use it to restrict the search - within a particular History. - in: query - name: history_id - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: Optional identifier of a History. Use it to restrict the search - within a particular History. - title: History Id - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: Generally a property name to filter by followed by an (often - optional) hyphen and operator string. - in: query - name: q - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: Generally a property name to filter by followed by an (often - optional) hyphen and operator string. - examples: - - create_time-gt - title: Filter Query - - description: The value to filter by. - in: query - name: qv - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: The value to filter by. - examples: - - '2015-01-29' - title: Filter Value - - description: Starts at the beginning skip the first ( offset - 1 ) items and - begin returning at the Nth item - in: query - name: offset - required: false - schema: - anyOf: - - minimum: 0 - type: integer - - type: 'null' - default: 0 - description: Starts at the beginning skip the first ( offset - 1 ) items - and begin returning at the Nth item - title: Offset - - description: The maximum number of items to return. - in: query - name: limit - required: false - schema: - anyOf: - - minimum: 1 - type: integer - - type: 'null' - description: The maximum number of items to return. - title: Limit - - description: String containing one of the valid ordering attributes followed - (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. - Orders can be stacked as a comma-separated list of values. - in: query - name: order - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: String containing one of the valid ordering attributes followed - (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. - Orders can be stacked as a comma-separated list of values. - title: Order - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - anyOf: - - $ref: '#/components/schemas/HDADetailed' - - $ref: '#/components/schemas/HDASummary' - - $ref: '#/components/schemas/HDCADetailed' - - $ref: '#/components/schemas/HDCASummary' - - $ref: '#/components/schemas/CustomHistoryItem' - title: Response Index Api Datasets Get - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Search datasets or collections using a query system. - tags: - - datasets - - datasets - /api/datasets/{dataset_id}: - get: - description: '**Note**: Due to the multipurpose nature of this endpoint, which - can receive a wild variety of parameters - - and return different kinds of responses, the documentation here will be limited. - - To get more information please check the source code.' - operationId: show_api_datasets__dataset_id__get - parameters: - - description: The ID of the History Dataset. - in: path - name: dataset_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The type of information about the dataset to be requested. - in: query - name: hda_ldda - required: false - schema: - allOf: - - $ref: '#/components/schemas/DatasetSourceType' - default: hda - description: The type of information about the dataset to be requested. - title: Hda Ldda - - description: The type of information about the dataset to be requested. Each - of these values may require additional parameters in the request and may - return different responses. - in: query - name: data_type - required: false - schema: - anyOf: - - $ref: '#/components/schemas/RequestDataType' - - type: 'null' - description: The type of information about the dataset to be requested. - Each of these values may require additional parameters in the request - and may return different responses. - title: Data Type - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Displays information about and/or content of a dataset. - tags: - - datasets - - datasets - /api/datasets/{dataset_id}/content/{content_type}: - get: - operationId: get_structured_content_api_datasets__dataset_id__content__content_type__get - parameters: - - description: The ID of the History Dataset. - in: path - name: dataset_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - in: path - name: content_type - required: true - schema: - $ref: '#/components/schemas/DatasetContentType' - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Retrieve information about the content of a dataset. - tags: - - datasets - - datasets - /api/datasets/{dataset_id}/converted: - get: - description: 'Return a map of ` : ` containing - all the *existing* converted datasets.' - operationId: converted_api_datasets__dataset_id__converted_get - parameters: - - description: The ID of the History Dataset. - in: path - name: dataset_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ConvertedDatasetsMap' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return a a map with all the existing converted datasets associated - with this instance. - tags: - - datasets - - datasets - /api/datasets/{dataset_id}/converted/{ext}: - get: - description: 'Return information about datasets made by converting this dataset - to a new format. - - - If there is no existing converted dataset for the format in `ext`, one will - be created. - - - **Note**: `view` and `keys` are also available to control the serialization - of the dataset.' - operationId: converted_ext_api_datasets__dataset_id__converted__ext__get - parameters: - - description: The ID of the History Dataset. - in: path - name: dataset_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: File extension of the new format to convert this dataset to. - in: path - name: ext - required: true - schema: - description: File extension of the new format to convert this dataset to. - title: Ext - type: string - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/HDADetailed' - - $ref: '#/components/schemas/HDASummary' - title: Response Converted Ext Api Datasets Dataset Id Converted Ext Get - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return information about datasets made by converting this dataset to - a new format. - tags: - - datasets - - datasets - /api/datasets/{dataset_id}/extra_files: - get: - operationId: extra_files_api_datasets__dataset_id__extra_files_get - parameters: - - description: The encoded database identifier of the dataset. - in: path - name: dataset_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DatasetExtraFiles' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get the list of extra files/directories associated with a dataset. - tags: - - datasets - - datasets - /api/datasets/{dataset_id}/get_content_as_text: - get: - operationId: get_content_as_text_api_datasets__dataset_id__get_content_as_text_get - parameters: - - description: The ID of the History Dataset. - in: path - name: dataset_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DatasetTextContentDetails' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns dataset content as Text. - tags: - - datasets - - datasets - /api/datasets/{dataset_id}/hash: - put: - operationId: compute_hash_api_datasets__dataset_id__hash_put - parameters: - - description: The ID of the History Dataset. - in: path - name: dataset_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: Whether this dataset belongs to a history (HDA) or a library - (LDDA). - in: query - name: hda_ldda - required: false - schema: - allOf: - - $ref: '#/components/schemas/DatasetSourceType' - default: hda - description: Whether this dataset belongs to a history (HDA) or a library - (LDDA). - title: Hda Ldda - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/ComputeDatasetHashPayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/AsyncTaskResultSummary' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Compute dataset hash for dataset and update model - tags: - - datasets - - datasets - /api/datasets/{dataset_id}/inheritance_chain: - get: - operationId: show_inheritance_chain_api_datasets__dataset_id__inheritance_chain_get - parameters: - - description: The ID of the History Dataset. - in: path - name: dataset_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: Whether this dataset belongs to a history (HDA) or a library - (LDDA). - in: query - name: hda_ldda - required: false - schema: - allOf: - - $ref: '#/components/schemas/DatasetSourceType' - default: hda - description: Whether this dataset belongs to a history (HDA) or a library - (LDDA). - title: Hda Ldda - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DatasetInheritanceChain' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: For internal use, this endpoint may change without warning. - tags: - - datasets - - datasets - /api/datasets/{dataset_id}/metrics: - get: - deprecated: true - operationId: get_metrics_api_datasets__dataset_id__metrics_get - parameters: - - description: The ID of the dataset - in: path - name: dataset_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: Whether this dataset belongs to a history (HDA) or a library - (LDDA). - in: query - name: hda_ldda - required: false - schema: - allOf: - - $ref: '#/components/schemas/DatasetSourceType' - default: hda - description: Whether this dataset belongs to a history (HDA) or a library - (LDDA). - title: HDA or LDDA - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - anyOf: - - $ref: '#/components/schemas/JobMetric' - - type: 'null' - title: Response Get Metrics Api Datasets Dataset Id Metrics Get - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return job metrics for specified job. - tags: - - jobs - - jobs - /api/datasets/{dataset_id}/object_store_id: - put: - operationId: datasets__update_object_store_id - parameters: - - description: The ID of the History Dataset. - in: path - name: dataset_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/UpdateObjectStoreIdPayload' - required: true - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Update an object store ID for a dataset you own. - tags: - - datasets - - datasets - /api/datasets/{dataset_id}/parameters_display: - get: - deprecated: true - description: 'Resolve parameters as a list for nested display. - - This API endpoint is unstable and tied heavily to Galaxy''s JS client code, - - this endpoint will change frequently.' - operationId: resolve_parameters_display_api_datasets__dataset_id__parameters_display_get - parameters: - - description: The ID of the dataset - in: path - name: dataset_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: Whether this dataset belongs to a history (HDA) or a library - (LDDA). - in: query - name: hda_ldda - required: false - schema: - allOf: - - $ref: '#/components/schemas/DatasetSourceType' - default: hda - description: Whether this dataset belongs to a history (HDA) or a library - (LDDA). - title: HDA or LDDA - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/JobDisplayParametersSummary' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Resolve parameters as a list for nested display. - tags: - - jobs - - jobs - /api/datasets/{dataset_id}/permissions: - put: - description: Set permissions of the given history dataset to the given role - ids. - operationId: update_permissions_api_datasets__dataset_id__permissions_put - parameters: - - description: The ID of the History Dataset. - in: path - name: dataset_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - examples: - - access_ids[]: [] - action: set_permissions - manage_ids[]: [] - modify_ids[]: [] - title: Payload - type: object - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DatasetAssociationRoles' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Set permissions of the given history dataset to the given role ids. - tags: - - datasets - - datasets - /api/datasets/{dataset_id}/storage: - get: - operationId: show_storage_api_datasets__dataset_id__storage_get - parameters: - - description: The ID of the History Dataset. - in: path - name: dataset_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: Whether this dataset belongs to a history (HDA) or a library - (LDDA). - in: query - name: hda_ldda - required: false - schema: - allOf: - - $ref: '#/components/schemas/DatasetSourceType' - default: hda - description: Whether this dataset belongs to a history (HDA) or a library - (LDDA). - title: Hda Ldda - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DatasetStorageDetails' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Display user-facing storage details related to the objectstore a dataset - resides in. - tags: - - datasets - - datasets - /api/datasets/{history_content_id}/display: - get: - description: Streams the dataset for download or the contents preview to be - displayed in a browser. - operationId: display_api_datasets__history_content_id__display_get - parameters: - - description: The ID of the History Dataset. - in: path - name: history_content_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: Whether to get preview contents to be directly displayed on the - web. If preview is False (default) the contents will be downloaded instead. - in: query - name: preview - required: false - schema: - default: false - description: Whether to get preview contents to be directly displayed on - the web. If preview is False (default) the contents will be downloaded - instead. - title: Preview - type: boolean - - description: If non-null, get the specified filename from the extra files - for this dataset. - in: query - name: filename - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: If non-null, get the specified filename from the extra files - for this dataset. - title: Filename - - description: The file extension when downloading the display data. Use the - value `data` to let the server infer it from the data type. - in: query - name: to_ext - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: The file extension when downloading the display data. Use the - value `data` to let the server infer it from the data type. - title: To Ext - - description: The query parameter 'raw' should be considered experimental and - may be dropped at some point in the future without warning. Generally, data - should be processed by its datatype prior to display. - in: query - name: raw - required: false - schema: - default: false - description: The query parameter 'raw' should be considered experimental - and may be dropped at some point in the future without warning. Generally, - data should be processed by its datatype prior to display. - title: Raw - type: boolean - - description: Set this for datatypes that allow chunked display through the - display_data method to enable chunking. This specifies a byte offset into - the target dataset's display. - in: query - name: offset - required: false - schema: - anyOf: - - type: integer - - type: 'null' - description: Set this for datatypes that allow chunked display through the - display_data method to enable chunking. This specifies a byte offset into - the target dataset's display. - title: Offset - - description: 'If offset is set, this recommends ''how large'' the next chunk - should be. This is not respected or interpreted uniformly and should be - interpreted as a very loose recommendation. Different datatypes interpret - ''largeness'' differently - for bam datasets this is a number of lines whereas - for tabular datatypes this is interpreted as a number of bytes. ' - in: query - name: ck_size - required: false - schema: - anyOf: - - type: integer - - type: 'null' - description: 'If offset is set, this recommends ''how large'' the next chunk - should be. This is not respected or interpreted uniformly and should be - interpreted as a very loose recommendation. Different datatypes interpret - ''largeness'' differently - for bam datasets this is a number of lines - whereas for tabular datatypes this is interpreted as a number of bytes. ' - title: Ck Size - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Displays (preview) or downloads dataset content. - tags: - - datasets - - datasets - head: - description: Streams the dataset for download or the contents preview to be - displayed in a browser. - operationId: display_api_datasets__history_content_id__display_head - parameters: - - description: The ID of the History Dataset. - in: path - name: history_content_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: Whether to get preview contents to be directly displayed on the - web. If preview is False (default) the contents will be downloaded instead. - in: query - name: preview - required: false - schema: - default: false - description: Whether to get preview contents to be directly displayed on - the web. If preview is False (default) the contents will be downloaded - instead. - title: Preview - type: boolean - - description: If non-null, get the specified filename from the extra files - for this dataset. - in: query - name: filename - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: If non-null, get the specified filename from the extra files - for this dataset. - title: Filename - - description: The file extension when downloading the display data. Use the - value `data` to let the server infer it from the data type. - in: query - name: to_ext - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: The file extension when downloading the display data. Use the - value `data` to let the server infer it from the data type. - title: To Ext - - description: The query parameter 'raw' should be considered experimental and - may be dropped at some point in the future without warning. Generally, data - should be processed by its datatype prior to display. - in: query - name: raw - required: false - schema: - default: false - description: The query parameter 'raw' should be considered experimental - and may be dropped at some point in the future without warning. Generally, - data should be processed by its datatype prior to display. - title: Raw - type: boolean - - description: Set this for datatypes that allow chunked display through the - display_data method to enable chunking. This specifies a byte offset into - the target dataset's display. - in: query - name: offset - required: false - schema: - anyOf: - - type: integer - - type: 'null' - description: Set this for datatypes that allow chunked display through the - display_data method to enable chunking. This specifies a byte offset into - the target dataset's display. - title: Offset - - description: 'If offset is set, this recommends ''how large'' the next chunk - should be. This is not respected or interpreted uniformly and should be - interpreted as a very loose recommendation. Different datatypes interpret - ''largeness'' differently - for bam datasets this is a number of lines whereas - for tabular datatypes this is interpreted as a number of bytes. ' - in: query - name: ck_size - required: false - schema: - anyOf: - - type: integer - - type: 'null' - description: 'If offset is set, this recommends ''how large'' the next chunk - should be. This is not respected or interpreted uniformly and should be - interpreted as a very loose recommendation. Different datatypes interpret - ''largeness'' differently - for bam datasets this is a number of lines - whereas for tabular datatypes this is interpreted as a number of bytes. ' - title: Ck Size - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Check if dataset content can be previewed or downloaded. - tags: - - datasets - - datasets - /api/datasets/{history_content_id}/metadata_file: - get: - operationId: datasets__get_metadata_file - parameters: - - description: The ID of the History Dataset. - in: path - name: history_content_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The name of the metadata file to retrieve. - in: query - name: metadata_file - required: true - schema: - description: The name of the metadata file to retrieve. - title: Metadata File - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns the metadata file associated with this history item. - tags: - - datasets - - datasets - head: - operationId: get_metadata_file_datasets_api_datasets__history_content_id__metadata_file_head - parameters: - - description: The ID of the History Dataset. - in: path - name: history_content_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The name of the metadata file to retrieve. - in: query - name: metadata_file - required: true - schema: - description: The name of the metadata file to retrieve. - title: Metadata File - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Check if metadata file can be downloaded. - tags: - - datasets - - datasets - /api/datatypes: - get: - description: Gets the list of all available data types. - operationId: index_api_datatypes_get - parameters: - - description: Whether to return only the datatype's extension rather than the - datatype's details - in: query - name: extension_only - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: true - description: Whether to return only the datatype's extension rather than - the datatype's details - title: Extension only - - description: Whether to return only datatypes which can be uploaded - in: query - name: upload_only - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: true - description: Whether to return only datatypes which can be uploaded - title: Upload only - responses: - '200': - content: - application/json: - schema: - anyOf: - - items: - $ref: '#/components/schemas/DatatypeDetails' - type: array - - items: - type: string - type: array - title: Response Index Api Datatypes Get - description: List of data types - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: [] - summary: Lists all available data types - tags: - - datatypes - - datatypes - /api/datatypes/converters: - get: - description: Gets the list of all installed converters. - operationId: converters_api_datatypes_converters_get - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DatatypeConverterList' - description: List of all datatype converters - security: [] - summary: Returns the list of all installed converters - tags: - - datatypes - - datatypes - /api/datatypes/edam_data: - get: - description: Gets a map of datatypes and their corresponding EDAM data. - operationId: edam_data_api_datatypes_edam_data_get - responses: - '200': - content: - application/json: - schema: - additionalProperties: - type: string - title: Response Edam Data Api Datatypes Edam Data Get - type: object - description: Dictionary/map of datatypes and EDAM data - security: [] - summary: Returns a dictionary/map of datatypes and EDAM data - tags: - - datatypes - - datatypes - /api/datatypes/edam_data/detailed: - get: - description: 'Gets a map of datatypes and their corresponding EDAM data. - - EDAM data contains the EDAM iri, label, and definition.' - operationId: edam_data_detailed_api_datatypes_edam_data_detailed_get - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DatatypesEDAMDetailsDict' - description: Dictionary of EDAM data details containing the EDAM iri, label, - and definition - security: [] - summary: Returns a dictionary of datatypes and EDAM data details - tags: - - datatypes - - datatypes - /api/datatypes/edam_formats: - get: - description: Gets a map of datatypes and their corresponding EDAM formats. - operationId: edam_formats_api_datatypes_edam_formats_get - responses: - '200': - content: - application/json: - schema: - additionalProperties: - type: string - title: Response Edam Formats Api Datatypes Edam Formats Get - type: object - description: Dictionary/map of datatypes and EDAM formats - security: [] - summary: Returns a dictionary/map of datatypes and EDAM formats - tags: - - datatypes - - datatypes - /api/datatypes/edam_formats/detailed: - get: - description: 'Gets a map of datatypes and their corresponding EDAM formats. - - EDAM formats contain the EDAM iri, label, and definition.' - operationId: edam_formats_detailed_api_datatypes_edam_formats_detailed_get - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DatatypesEDAMDetailsDict' - description: Dictionary of EDAM format details containing the EDAM iri, - label, and definition - security: [] - summary: Returns a dictionary of datatypes and EDAM format details - tags: - - datatypes - - datatypes - /api/datatypes/mapping: - get: - description: Gets mappings for data types. - operationId: mapping_api_datatypes_mapping_get - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DatatypesMap' - description: Dictionary to map data types with their classes - security: [] - summary: Returns mappings for data types and their implementing classes - tags: - - datatypes - - datatypes - /api/datatypes/sniffers: - get: - description: Gets the list of all installed data type sniffers. - operationId: sniffers_api_datatypes_sniffers_get - responses: - '200': - content: - application/json: - schema: - items: - type: string - title: Response Sniffers Api Datatypes Sniffers Get - type: array - description: List of datatype sniffers - security: [] - summary: Returns the list of all installed sniffers - tags: - - datatypes - - datatypes - /api/datatypes/types_and_mapping: - get: - description: 'Combines the datatype information from (/api/datatypes) and the - - mapping information from (/api/datatypes/mapping) into a single - - response.' - operationId: types_and_mapping_api_datatypes_types_and_mapping_get - parameters: - - description: Whether to return only the datatype's extension rather than the - datatype's details - in: query - name: extension_only - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: true - description: Whether to return only the datatype's extension rather than - the datatype's details - title: Extension only - - description: Whether to return only datatypes which can be uploaded - in: query - name: upload_only - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: true - description: Whether to return only datatypes which can be uploaded - title: Upload only - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DatatypesCombinedMap' - description: Dictionary to map data types with their classes - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: [] - summary: Returns all the data types extensions and their mappings - tags: - - datatypes - - datatypes - /api/display_applications: - get: - description: Returns the list of display applications. - operationId: display_applications_index_api_display_applications_get - responses: - '200': - content: - application/json: - schema: - items: - $ref: '#/components/schemas/DisplayApplication' - title: Response Display Applications Index Api Display Applications - Get - type: array - description: Successful Response - security: [] - summary: Returns the list of display applications. - tags: - - display_applications - - display_applications - /api/display_applications/reload: - post: - description: Reloads the list of display applications. - operationId: display_applications_reload_api_display_applications_reload_post - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - anyOf: - - additionalProperties: - items: - type: string - type: array - type: object - - type: 'null' - title: Payload - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ReloadFeedback' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Reloads the list of display applications. - tags: - - display_applications - - display_applications - /api/drs_download/{object_id}: - get: - operationId: download_api_drs_download__object_id__get - parameters: - - description: The ID of the group - in: path - name: object_id - required: true - schema: - description: The ID of the group - title: Object ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Download - tags: - - drs - - drs - /api/folders/{folder_id}/contents: - get: - description: 'Returns a list of a folder''s contents (files and sub-folders). - - - Additional metadata for the folder is provided in the response as a separate - object containing data - - for breadcrumb path building, permissions and other folder''s details. - - - *Note*: When sorting, folders always have priority (they show-up before any - dataset regardless of the sorting). - - - **Security note**: - - - Accessing a library folder or sub-folder requires only access to the parent - library. - - - Deleted folders can only be accessed by admins or users with `MODIFY` permission. - - - Datasets may be public, private or restricted (to a group of users). Listing - deleted datasets has the same requirements as folders.' - operationId: index_api_folders__folder_id__contents_get - parameters: - - description: The encoded identifier of the library folder. - in: path - name: folder_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Folder ID - type: string - - description: Maximum number of contents to return. - in: query - name: limit - required: false - schema: - default: 10 - description: Maximum number of contents to return. - title: Limit - type: integer - - description: Return contents from this specified position. For example, if - ``limit`` is set to 100 and ``offset`` to 200, contents between position - 200-299 will be returned. - in: query - name: offset - required: false - schema: - default: 0 - description: Return contents from this specified position. For example, - if ``limit`` is set to 100 and ``offset`` to 200, contents between position - 200-299 will be returned. - title: Offset - type: integer - - description: Used to filter the contents. Only the folders and files which - name contains this text will be returned. - in: query - name: search_text - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Used to filter the contents. Only the folders and files which - name contains this text will be returned. - title: Search Text - - description: Returns also deleted contents. Deleted contents can only be retrieved - by Administrators or users with - in: query - name: include_deleted - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: false - description: Returns also deleted contents. Deleted contents can only be - retrieved by Administrators or users with - title: Include Deleted - - description: Sort results by specified field. - in: query - name: order_by - required: false - schema: - default: name - description: Sort results by specified field. - enum: - - name - - description - - type - - size - - update_time - title: Sort By - type: string - - description: Sort results in descending order. - in: query - name: sort_desc - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: false - description: Sort results in descending order. - title: Sort Descending - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/LibraryFolderContentsIndexResult' - description: The contents of the folder that match the query parameters. - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns a list of a folder's contents (files and sub-folders) with - additional metadata about the folder. - tags: - - data libraries folders - - data libraries folders - post: - operationId: add_history_datasets_to_library_api_folders__folder_id__contents_post - parameters: - - description: The encoded identifier of the library folder. - in: path - name: folder_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Folder ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/CreateLibraryFilePayload' - required: true - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Creates a new library file from an existing HDA/HDCA. - tags: - - data libraries folders - - data libraries folders - /api/folders/{id}: - delete: - description: Marks the specified library folder as deleted (or undeleted). - operationId: delete_api_folders__id__delete - parameters: - - description: The encoded identifier of the library folder. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Folder ID - type: string - - description: Whether to restore a deleted library folder. - in: query - name: undelete - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - description: Whether to restore a deleted library folder. - title: Undelete - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/LibraryFolderDetails' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Marks the specified library folder as deleted (or undeleted). - tags: - - data libraries folders - - data libraries folders - get: - description: Returns detailed information about the library folder with the - given ID. - operationId: show_api_folders__id__get - parameters: - - description: The encoded identifier of the library folder. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Folder ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/LibraryFolderDetails' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Displays information about a particular library folder. - tags: - - data libraries folders - - data libraries folders - patch: - description: Updates the information of an existing library folder. - operationId: update_api_folders__id__patch - parameters: - - description: The encoded identifier of the library folder. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Folder ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/UpdateLibraryFolderPayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/LibraryFolderDetails' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Update - tags: - - data libraries folders - - data libraries folders - post: - description: Returns detailed information about the newly created library folder. - operationId: create_api_folders__id__post - parameters: - - description: The encoded identifier of the library folder. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Folder ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/CreateLibraryFolderPayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/LibraryFolderDetails' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Create a new library folder underneath the one specified by the ID. - tags: - - data libraries folders - - data libraries folders - put: - description: Updates the information of an existing library folder. - operationId: update_api_folders__id__put - parameters: - - description: The encoded identifier of the library folder. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Folder ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/UpdateLibraryFolderPayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/LibraryFolderDetails' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Updates the information of an existing library folder. - tags: - - data libraries folders - - data libraries folders - /api/folders/{id}/permissions: - get: - description: 'Gets the current or available permissions of a particular library. - - The results can be paginated and additionally filtered by a query.' - operationId: get_permissions_api_folders__id__permissions_get - parameters: - - description: The encoded identifier of the library folder. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Folder ID - type: string - - description: The scope of the permissions to retrieve. Either the `current` - permissions or the `available`. - in: query - name: scope - required: false - schema: - anyOf: - - $ref: '#/components/schemas/LibraryPermissionScope' - - type: 'null' - description: The scope of the permissions to retrieve. Either the `current` - permissions or the `available`. - title: Scope - - description: The page number to retrieve when paginating the available roles. - in: query - name: page - required: false - schema: - default: 1 - description: The page number to retrieve when paginating the available roles. - title: Page - type: integer - - description: The maximum number of permissions per page when paginating. - in: query - name: page_limit - required: false - schema: - default: 10 - description: The maximum number of permissions per page when paginating. - title: Page Limit - type: integer - - description: Optional search text to retrieve only the roles matching this - query. - in: query - name: q - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Optional search text to retrieve only the roles matching this - query. - title: Query - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/LibraryFolderCurrentPermissions' - - $ref: '#/components/schemas/LibraryAvailablePermissions' - title: Response Get Permissions Api Folders Id Permissions Get - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Gets the current or available permissions of a particular library folder. - tags: - - data libraries folders - - data libraries folders - post: - description: Sets the permissions to manage a library folder. - operationId: set_permissions_api_folders__id__permissions_post - parameters: - - description: The encoded identifier of the library folder. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Folder ID - type: string - - description: Indicates what action should be performed on the Library. Currently - only `set_permissions` is supported. - in: query - name: action - required: false - schema: - anyOf: - - $ref: '#/components/schemas/LibraryFolderPermissionAction' - - type: 'null' - description: Indicates what action should be performed on the Library. Currently - only `set_permissions` is supported. - title: Action - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/LibraryFolderPermissionsPayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/LibraryFolderCurrentPermissions' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Sets the permissions to manage a library folder. - tags: - - data libraries folders - - data libraries folders - /api/forms/{id}: - delete: - operationId: delete_api_forms__id__delete - parameters: - - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Delete - tags: - - forms - - forms - /api/forms/{id}/undelete: - post: - operationId: undelete_api_forms__id__undelete_post - parameters: - - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Undelete - tags: - - forms - - forms - /api/ftp_files: - get: - deprecated: true - description: Lists all remote files available to the user from different sources. - operationId: index_api_ftp_files_get - parameters: - - description: 'The source to load datasets from. Possible values: ftpdir, userdir, - importdir' - in: query - name: target - required: false - schema: - default: ftpdir - description: 'The source to load datasets from. Possible values: ftpdir, - userdir, importdir' - title: Target source - type: string - - description: The requested format of returned data. Either `flat` to simply - list all the files, `jstree` to get a tree representation of the files, - or the default `uri` to list files and directories by their URI. - in: query - name: format - required: false - schema: - anyOf: - - $ref: '#/components/schemas/RemoteFilesFormat' - - type: 'null' - default: uri - description: The requested format of returned data. Either `flat` to simply - list all the files, `jstree` to get a tree representation of the files, - or the default `uri` to list files and directories by their URI. - title: Response format - - description: Whether to recursively lists all sub-directories. This will be - `True` by default depending on the `target`. - in: query - name: recursive - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - description: Whether to recursively lists all sub-directories. This will - be `True` by default depending on the `target`. - title: Recursive - - description: (This only applies when `format` is `jstree`) The value can be - either `folders` or `files` and it will disable the corresponding nodes - of the tree. - in: query - name: disable - required: false - schema: - anyOf: - - $ref: '#/components/schemas/RemoteFilesDisableMode' - - type: 'null' - description: (This only applies when `format` is `jstree`) The value can - be either `folders` or `files` and it will disable the corresponding nodes - of the tree. - title: Disable mode - - description: Whether the query is made with the intention of writing to the - source. If set to True, only entries that can be written to will be returned. - in: query - name: writeable - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - description: Whether the query is made with the intention of writing to - the source. If set to True, only entries that can be written to will be - returned. - title: Writeable - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/ListUriResponse' - - $ref: '#/components/schemas/ListJstreeResponse' - title: Response Index Api Ftp Files Get - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Displays remote files available to the user. Please use /api/remote_files - instead. - tags: - - remote files - - remote files - /api/genomes: - get: - operationId: index_api_genomes_get - parameters: - - description: If true, return genome keys with chromosome lengths - in: query - name: chrom_info - required: false - schema: - description: If true, return genome keys with chromosome lengths - title: ChromInfo - type: boolean - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - items: - type: string - type: array - title: Response Index Api Genomes Get - type: array - description: Installed genomes - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return a list of installed genomes - tags: - - genomes - - genomes - /api/genomes/{id}: - get: - operationId: show_api_genomes__id__get - parameters: - - description: Genome ID - in: path - name: id - required: true - schema: - description: Genome ID - title: Genome ID - type: string - - description: If true, return reference data - in: query - name: reference - required: false - schema: - description: If true, return reference data - title: Reference - type: boolean - - description: Limits size of returned data - in: query - name: num - required: false - schema: - description: Limits size of returned data - title: Number - type: integer - - description: Limits size of returned data - in: query - name: chrom - required: false - schema: - description: Limits size of returned data - title: Chrom - type: string - - description: Limits size of returned data - in: query - name: low - required: false - schema: - description: Limits size of returned data - title: Low - type: integer - - description: Limits size of returned data - in: query - name: high - required: false - schema: - description: Limits size of returned data - title: High - type: integer - - description: Format - in: query - name: format - required: false - schema: - description: Format - title: Format - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - title: Response Show Api Genomes Id Get - description: Information about genome build - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return information about build - tags: - - genomes - - genomes - /api/genomes/{id}/indexes: - get: - operationId: indexes_api_genomes__id__indexes_get - parameters: - - description: Genome ID - in: path - name: id - required: true - schema: - description: Genome ID - title: Genome ID - type: string - - description: Index type - in: query - name: type - required: false - schema: - default: fasta_indexes - description: Index type - title: Index type - type: string - - description: Format - in: query - name: format - required: false - schema: - description: Format - title: Format - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - title: Response Indexes Api Genomes Id Indexes Get - description: Indexes for a genome id for provided type - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return all available indexes for a genome id for provided type - tags: - - genomes - - genomes - /api/genomes/{id}/sequences: - get: - operationId: sequences_api_genomes__id__sequences_get - parameters: - - description: Genome ID - in: path - name: id - required: true - schema: - description: Genome ID - title: Genome ID - type: string - - description: If true, return reference data - in: query - name: reference - required: false - schema: - description: If true, return reference data - title: Reference - type: boolean - - description: Limits size of returned data - in: query - name: chrom - required: false - schema: - description: Limits size of returned data - title: Chrom - type: string - - description: Limits size of returned data - in: query - name: low - required: false - schema: - description: Limits size of returned data - title: Low - type: integer - - description: Limits size of returned data - in: query - name: high - required: false - schema: - description: Limits size of returned data - title: High - type: integer - - description: Format - in: query - name: format - required: false - schema: - description: Format - title: Format - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - title: Response Sequences Api Genomes Id Sequences Get - description: Raw sequence data - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return raw sequence data - tags: - - genomes - - genomes - /api/groups: - get: - operationId: index_api_groups_get - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/GroupListResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Displays a collection (list) of groups. - tags: - - groups - - groups - post: - operationId: create_api_groups_post - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/GroupCreatePayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/GroupListResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Creates a new group. - tags: - - groups - - groups - /api/groups/{group_id}: - delete: - operationId: delete_api_groups__group_id__delete - parameters: - - in: path - name: group_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Delete - tags: - - groups - - groups - get: - operationId: show_group_api_groups__group_id__get - parameters: - - in: path - name: group_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/GroupResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Displays information about a group. - tags: - - groups - - groups - put: - operationId: update_api_groups__group_id__put - parameters: - - in: path - name: group_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/GroupCreatePayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/GroupResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Modifies a group. - tags: - - groups - - groups - /api/groups/{group_id}/purge: - post: - operationId: purge_api_groups__group_id__purge_post - parameters: - - in: path - name: group_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Purge - tags: - - groups - - groups - /api/groups/{group_id}/roles: - get: - operationId: group_roles_api_groups__group_id__roles_get - parameters: - - description: The ID of the group. - in: path - name: group_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/GroupRoleListResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Displays a collection (list) of groups. - tags: - - group_roles - - group_roles - /api/groups/{group_id}/roles/{role_id}: - delete: - operationId: delete_api_groups__group_id__roles__role_id__delete - parameters: - - description: The ID of the group. - in: path - name: group_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The ID of the role. - in: path - name: role_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/GroupRoleResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Removes a role from a group - tags: - - group_roles - - group_roles - get: - operationId: group_role_api_groups__group_id__roles__role_id__get - parameters: - - description: The ID of the group. - in: path - name: group_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The ID of the role. - in: path - name: role_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/GroupRoleResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Displays information about a group role. - tags: - - group_roles - - group_roles - put: - operationId: update_api_groups__group_id__roles__role_id__put - parameters: - - description: The ID of the group. - in: path - name: group_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The ID of the role. - in: path - name: role_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/GroupRoleResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Adds a role to a group - tags: - - group_roles - - group_roles - /api/groups/{group_id}/undelete: - post: - operationId: undelete_api_groups__group_id__undelete_post - parameters: - - in: path - name: group_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Undelete - tags: - - groups - - groups - /api/groups/{group_id}/user/{user_id}: - delete: - description: 'DELETE /api/groups/{encoded_group_id}/users/{encoded_user_id} - - Removes a user from a group' - operationId: delete_api_groups__group_id__user__user_id__delete - parameters: - - description: The ID of the group. - in: path - name: group_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The ID of the user. - in: path - name: user_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/GroupUserResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Removes a user from a group - tags: - - group_users - - group_users - get: - description: Displays information about a group user. - operationId: group_user_api_groups__group_id__user__user_id__get - parameters: - - description: The ID of the group. - in: path - name: group_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The ID of the user. - in: path - name: user_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/GroupUserResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Displays information about a group user. - tags: - - group_users - - group_users - put: - description: 'PUT /api/groups/{encoded_group_id}/users/{encoded_user_id} - - Adds a user to a group' - operationId: update_api_groups__group_id__user__user_id__put - parameters: - - description: The ID of the group. - in: path - name: group_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The ID of the user. - in: path - name: user_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/GroupUserResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Adds a user to a group - tags: - - group_users - - group_users - /api/groups/{group_id}/users: - get: - description: 'GET /api/groups/{encoded_group_id}/users - - Displays a collection (list) of groups.' - operationId: group_users_api_groups__group_id__users_get - parameters: - - description: The ID of the group. - in: path - name: group_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/GroupUserListResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Displays a collection (list) of groups. - tags: - - group_users - - group_users - /api/groups/{group_id}/users/{user_id}: - delete: - description: 'DELETE /api/groups/{encoded_group_id}/users/{encoded_user_id} - - Removes a user from a group' - operationId: delete_api_groups__group_id__users__user_id__delete - parameters: - - description: The ID of the group. - in: path - name: group_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The ID of the user. - in: path - name: user_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/GroupUserResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Removes a user from a group - tags: - - group_users - - group_users - get: - description: Displays information about a group user. - operationId: group_user_api_groups__group_id__users__user_id__get - parameters: - - description: The ID of the group. - in: path - name: group_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The ID of the user. - in: path - name: user_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/GroupUserResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Displays information about a group user. - tags: - - group_users - - group_users - put: - description: 'PUT /api/groups/{encoded_group_id}/users/{encoded_user_id} - - Adds a user to a group' - operationId: update_api_groups__group_id__users__user_id__put - parameters: - - description: The ID of the group. - in: path - name: group_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The ID of the user. - in: path - name: user_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/GroupUserResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Adds a user to a group - tags: - - group_users - - group_users - /api/help/forum/search: - get: - description: 'Search the Galaxy Help forum using the Discourse API. - - - **Note**: This endpoint is for **INTERNAL USE ONLY** and is not part of the - public Galaxy API.' - operationId: search_forum_api_help_forum_search_get - parameters: - - description: Search query to use for searching the Galaxy Help forum. - in: query - name: query - required: true - schema: - description: Search query to use for searching the Galaxy Help forum. - title: Query - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/HelpForumSearchResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Search the Galaxy Help forum. - tags: - - help - - help - /api/histories: - get: - operationId: index_api_histories_get - parameters: - - description: The maximum number of items to return. - in: query - name: limit - required: false - schema: - anyOf: - - minimum: 1 - type: integer - - type: 'null' - description: The maximum number of items to return. - title: Limit - - description: Starts at the beginning skip the first ( offset - 1 ) items and - begin returning at the Nth item - in: query - name: offset - required: false - schema: - anyOf: - - minimum: 0 - type: integer - - type: 'null' - default: 0 - description: Starts at the beginning skip the first ( offset - 1 ) items - and begin returning at the Nth item - title: Offset - - in: query - name: show_own - required: false - schema: - default: true - title: Show histories owned by user. - type: boolean - - in: query - name: show_published - required: false - schema: - default: true - title: Include published histories. - type: boolean - - in: query - name: show_shared - required: false - schema: - default: false - title: Include histories shared with authenticated user. - type: boolean - - description: Sort index by this specified attribute - in: query - name: sort_by - required: false - schema: - default: update_time - description: Sort index by this specified attribute - enum: - - create_time - - name - - update_time - - username - title: Sort attribute - type: string - - description: Sort in descending order? - in: query - name: sort_desc - required: false - schema: - default: true - description: Sort in descending order? - title: Sort Descending - type: boolean - - description: 'A mix of free text and GitHub-style tags used to filter the - index operation. - - - ## Query Structure - - - GitHub-style filter tags (not be confused with Galaxy tags) are tags of - the form - - `:` or `:''''`. - The tag name - - *generally* (but not exclusively) corresponds to the name of an attribute - on the model - - being indexed (i.e. a column in the database). - - - If the tag is quoted, the attribute will be filtered exactly. If the tag - is unquoted, - - generally a partial match will be used to filter the query (i.e. in terms - of the implementation - - this means the database operation `ILIKE` will typically be used). - - - Once the tagged filters are extracted from the search query, the remaining - text is just - - used to search various documented attributes of the object. - - - ## GitHub-style Tags Available - - - `name` - - : The history''s name. - - - `annotation` - - : The history''s annotation. (The tag `a` can be used a short hand alias - for this tag to filter on this attribute.) - - - `tag` - - : The history''s tags. (The tag `t` can be used a short hand alias for this - tag to filter on this attribute.) - - - ## Free Text - - - Free text search terms will be searched against the following attributes - of the - - Historys: `title`, `description`, `slug`, `tag`. - - - ' - in: query - name: search - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: 'A mix of free text and GitHub-style tags used to filter the - index operation. - - - ## Query Structure - - - GitHub-style filter tags (not be confused with Galaxy tags) are tags of - the form - - `:` or `:''''`. - The tag name - - *generally* (but not exclusively) corresponds to the name of an attribute - on the model - - being indexed (i.e. a column in the database). - - - If the tag is quoted, the attribute will be filtered exactly. If the tag - is unquoted, - - generally a partial match will be used to filter the query (i.e. in terms - of the implementation - - this means the database operation `ILIKE` will typically be used). - - - Once the tagged filters are extracted from the search query, the remaining - text is just - - used to search various documented attributes of the object. - - - ## GitHub-style Tags Available - - - `name` - - : The history''s name. - - - `annotation` - - : The history''s annotation. (The tag `a` can be used a short hand alias - for this tag to filter on this attribute.) - - - `tag` - - : The history''s tags. (The tag `t` can be used a short hand alias for - this tag to filter on this attribute.) - - - ## Free Text - - - Free text search terms will be searched against the following attributes - of the - - Historys: `title`, `description`, `slug`, `tag`. - - - ' - title: Search query. - - description: Whether all histories from other users in this Galaxy should - be included. Only admins are allowed to query all histories. - in: query - name: all - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: false - description: Whether all histories from other users in this Galaxy should - be included. Only admins are allowed to query all histories. - title: All Histories - - deprecated: true - description: Whether to return only deleted items. - in: query - name: deleted - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: false - description: Whether to return only deleted items. - title: Deleted Only - - description: Generally a property name to filter by followed by an (often - optional) hyphen and operator string. - in: query - name: q - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: Generally a property name to filter by followed by an (often - optional) hyphen and operator string. - examples: - - create_time-gt - title: Filter Query - - description: The value to filter by. - in: query - name: qv - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: The value to filter by. - examples: - - '2015-01-29' - title: Filter Value - - description: String containing one of the valid ordering attributes followed - (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. - Orders can be stacked as a comma-separated list of values. - in: query - name: order - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: String containing one of the valid ordering attributes followed - (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. - Orders can be stacked as a comma-separated list of values. - title: Order - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - anyOf: - - $ref: '#/components/schemas/HistoryDetailed' - - $ref: '#/components/schemas/HistorySummary' - - $ref: '#/components/schemas/HistoryMinimal' - title: Response Index Api Histories Get - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns histories available to the current user. - tags: - - histories - - histories - post: - description: The new history can also be copied form a existing history or imported - from an archive or URL. - operationId: create_api_histories_post - parameters: - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/x-www-form-urlencoded: - schema: - allOf: - - $ref: '#/components/schemas/Body_create_api_histories_post' - title: Body - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/JobImportHistoryResponse' - - $ref: '#/components/schemas/HistoryDetailed' - - $ref: '#/components/schemas/HistorySummary' - - $ref: '#/components/schemas/HistoryMinimal' - title: Response Create Api Histories Post - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Creates a new history. - tags: - - histories - - histories - /api/histories/archived: - get: - description: 'Get a list of all archived histories for the current user. - - - Archived histories are histories are not part of the active histories of the - user but they can be accessed using this endpoint.' - operationId: get_archived_histories_api_histories_archived_get - parameters: - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: Generally a property name to filter by followed by an (often - optional) hyphen and operator string. - in: query - name: q - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: Generally a property name to filter by followed by an (often - optional) hyphen and operator string. - examples: - - create_time-gt - title: Filter Query - - description: The value to filter by. - in: query - name: qv - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: The value to filter by. - examples: - - '2015-01-29' - title: Filter Value - - description: Starts at the beginning skip the first ( offset - 1 ) items and - begin returning at the Nth item - in: query - name: offset - required: false - schema: - anyOf: - - minimum: 0 - type: integer - - type: 'null' - default: 0 - description: Starts at the beginning skip the first ( offset - 1 ) items - and begin returning at the Nth item - title: Offset - - description: The maximum number of items to return. - in: query - name: limit - required: false - schema: - anyOf: - - minimum: 1 - type: integer - - type: 'null' - description: The maximum number of items to return. - title: Limit - - description: String containing one of the valid ordering attributes followed - (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. - Orders can be stacked as a comma-separated list of values. - in: query - name: order - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: String containing one of the valid ordering attributes followed - (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. - Orders can be stacked as a comma-separated list of values. - title: Order - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - anyOf: - - $ref: '#/components/schemas/ArchivedHistorySummary' - - $ref: '#/components/schemas/ArchivedHistoryDetailed' - - {} - title: Response Get Archived Histories Api Histories Archived Get - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get a list of all archived histories for the current user. - tags: - - histories - - histories - /api/histories/batch/delete: - put: - operationId: batch_delete_api_histories_batch_delete_put - parameters: - - in: query - name: purge - required: false - schema: - default: false - title: Purge - type: boolean - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/DeleteHistoriesPayload' - required: true - responses: - '200': - content: - application/json: - schema: - items: - anyOf: - - $ref: '#/components/schemas/HistoryDetailed' - - $ref: '#/components/schemas/HistorySummary' - - $ref: '#/components/schemas/HistoryMinimal' - title: Response Batch Delete Api Histories Batch Delete Put - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Marks several histories with the given IDs as deleted. - tags: - - histories - - histories - /api/histories/batch/undelete: - put: - operationId: batch_undelete_api_histories_batch_undelete_put - parameters: - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/UndeleteHistoriesPayload' - required: true - responses: - '200': - content: - application/json: - schema: - items: - anyOf: - - $ref: '#/components/schemas/HistoryDetailed' - - $ref: '#/components/schemas/HistorySummary' - - $ref: '#/components/schemas/HistoryMinimal' - title: Response Batch Undelete Api Histories Batch Undelete Put - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Marks several histories with the given IDs as undeleted. - tags: - - histories - - histories - /api/histories/count: - get: - operationId: count_api_histories_count_get - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - title: Response Count Api Histories Count Get - type: integer - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns number of histories for the current user. - tags: - - histories - - histories - /api/histories/deleted: - get: - operationId: index_deleted_api_histories_deleted_get - parameters: - - description: Whether all histories from other users in this Galaxy should - be included. Only admins are allowed to query all histories. - in: query - name: all - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: false - description: Whether all histories from other users in this Galaxy should - be included. Only admins are allowed to query all histories. - title: All Histories - - description: Generally a property name to filter by followed by an (often - optional) hyphen and operator string. - in: query - name: q - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: Generally a property name to filter by followed by an (often - optional) hyphen and operator string. - examples: - - create_time-gt - title: Filter Query - - description: The value to filter by. - in: query - name: qv - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: The value to filter by. - examples: - - '2015-01-29' - title: Filter Value - - description: Starts at the beginning skip the first ( offset - 1 ) items and - begin returning at the Nth item - in: query - name: offset - required: false - schema: - anyOf: - - minimum: 0 - type: integer - - type: 'null' - default: 0 - description: Starts at the beginning skip the first ( offset - 1 ) items - and begin returning at the Nth item - title: Offset - - description: The maximum number of items to return. - in: query - name: limit - required: false - schema: - anyOf: - - minimum: 1 - type: integer - - type: 'null' - description: The maximum number of items to return. - title: Limit - - description: String containing one of the valid ordering attributes followed - (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. - Orders can be stacked as a comma-separated list of values. - in: query - name: order - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: String containing one of the valid ordering attributes followed - (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. - Orders can be stacked as a comma-separated list of values. - title: Order - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - anyOf: - - $ref: '#/components/schemas/HistoryDetailed' - - $ref: '#/components/schemas/HistorySummary' - - $ref: '#/components/schemas/HistoryMinimal' - title: Response Index Deleted Api Histories Deleted Get - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns deleted histories for the current user. - tags: - - histories - - histories - /api/histories/deleted/{history_id}/undelete: - post: - operationId: undelete_api_histories_deleted__history_id__undelete_post - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/HistoryDetailed' - - $ref: '#/components/schemas/HistorySummary' - - $ref: '#/components/schemas/HistoryMinimal' - title: Response Undelete Api Histories Deleted History Id Undelete - Post - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Restores a deleted history with the given ID (that hasn't been purged). - tags: - - histories - - histories - /api/histories/from_store: - post: - operationId: create_from_store_api_histories_from_store_post - parameters: - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/CreateHistoryFromStore' - required: true - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/HistoryDetailed' - - $ref: '#/components/schemas/HistorySummary' - - $ref: '#/components/schemas/HistoryMinimal' - title: Response Create From Store Api Histories From Store Post - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Create histories from a model store. - tags: - - histories - - histories - /api/histories/from_store_async: - post: - operationId: create_from_store_async_api_histories_from_store_async_post - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/CreateHistoryFromStore' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/AsyncTaskResultSummary' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Launch a task to create histories from a model store. - tags: - - histories - - histories - /api/histories/most_recently_used: - get: - operationId: show_recent_api_histories_most_recently_used_get - parameters: - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/HistoryDetailed' - - $ref: '#/components/schemas/HistorySummary' - - $ref: '#/components/schemas/HistoryMinimal' - title: Response Show Recent Api Histories Most Recently Used Get - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns the most recently used history of the user. - tags: - - histories - - histories - /api/histories/published: - get: - operationId: published_api_histories_published_get - parameters: - - description: Generally a property name to filter by followed by an (often - optional) hyphen and operator string. - in: query - name: q - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: Generally a property name to filter by followed by an (often - optional) hyphen and operator string. - examples: - - create_time-gt - title: Filter Query - - description: The value to filter by. - in: query - name: qv - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: The value to filter by. - examples: - - '2015-01-29' - title: Filter Value - - description: Starts at the beginning skip the first ( offset - 1 ) items and - begin returning at the Nth item - in: query - name: offset - required: false - schema: - anyOf: - - minimum: 0 - type: integer - - type: 'null' - default: 0 - description: Starts at the beginning skip the first ( offset - 1 ) items - and begin returning at the Nth item - title: Offset - - description: The maximum number of items to return. - in: query - name: limit - required: false - schema: - anyOf: - - minimum: 1 - type: integer - - type: 'null' - description: The maximum number of items to return. - title: Limit - - description: String containing one of the valid ordering attributes followed - (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. - Orders can be stacked as a comma-separated list of values. - in: query - name: order - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: String containing one of the valid ordering attributes followed - (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. - Orders can be stacked as a comma-separated list of values. - title: Order - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - anyOf: - - $ref: '#/components/schemas/HistoryDetailed' - - $ref: '#/components/schemas/HistorySummary' - - $ref: '#/components/schemas/HistoryMinimal' - title: Response Published Api Histories Published Get - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return all histories that are published. - tags: - - histories - - histories - /api/histories/shared_with_me: - get: - operationId: shared_with_me_api_histories_shared_with_me_get - parameters: - - description: Generally a property name to filter by followed by an (often - optional) hyphen and operator string. - in: query - name: q - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: Generally a property name to filter by followed by an (often - optional) hyphen and operator string. - examples: - - create_time-gt - title: Filter Query - - description: The value to filter by. - in: query - name: qv - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: The value to filter by. - examples: - - '2015-01-29' - title: Filter Value - - description: Starts at the beginning skip the first ( offset - 1 ) items and - begin returning at the Nth item - in: query - name: offset - required: false - schema: - anyOf: - - minimum: 0 - type: integer - - type: 'null' - default: 0 - description: Starts at the beginning skip the first ( offset - 1 ) items - and begin returning at the Nth item - title: Offset - - description: The maximum number of items to return. - in: query - name: limit - required: false - schema: - anyOf: - - minimum: 1 - type: integer - - type: 'null' - description: The maximum number of items to return. - title: Limit - - description: String containing one of the valid ordering attributes followed - (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. - Orders can be stacked as a comma-separated list of values. - in: query - name: order - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: String containing one of the valid ordering attributes followed - (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. - Orders can be stacked as a comma-separated list of values. - title: Order - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - anyOf: - - $ref: '#/components/schemas/HistoryDetailed' - - $ref: '#/components/schemas/HistorySummary' - - $ref: '#/components/schemas/HistoryMinimal' - title: Response Shared With Me Api Histories Shared With Me Get - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return all histories that are shared with the current user. - tags: - - histories - - histories - /api/histories/{history_id}: - delete: - operationId: delete_api_histories__history_id__delete - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - in: query - name: purge - required: false - schema: - default: false - title: Purge - type: boolean - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/DeleteHistoryPayload' - - type: 'null' - title: Payload - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/HistoryDetailed' - - $ref: '#/components/schemas/HistorySummary' - - $ref: '#/components/schemas/HistoryMinimal' - title: Response Delete Api Histories History Id Delete - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Marks the history with the given ID as deleted. - tags: - - histories - - histories - get: - operationId: history_api_histories__history_id__get - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/HistoryDetailed' - - $ref: '#/components/schemas/HistorySummary' - - $ref: '#/components/schemas/HistoryMinimal' - title: Response History Api Histories History Id Get - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns the history with the given ID. - tags: - - histories - - histories - put: - operationId: update_api_histories__history_id__put - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - description: Object containing any of the editable fields of the history. - title: Payload - required: true - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/HistoryDetailed' - - $ref: '#/components/schemas/HistorySummary' - - $ref: '#/components/schemas/HistoryMinimal' - title: Response Update Api Histories History Id Put - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Updates the values for the history with the given ID. - tags: - - histories - - histories - /api/histories/{history_id}/archive: - post: - description: 'Marks the given history as ''archived'' and returns the history. - - - Archiving a history will remove it from the list of active histories of the - user but it will still be - - accessible via the `/api/histories/{id}` or the `/api/histories/archived` - endpoints. - - - Associating an export record: - - - - Optionally, an export record (containing information about a recent snapshot - of the history) can be associated with the - - archived history by providing an `archive_export_id` in the payload. The export - record must belong to the history and - - must be in the ready state. - - - When associating an export record, the history can be purged after it has - been archived using the `purge_history` flag. - - - If the history is already archived, this endpoint will return a 409 Conflict - error, indicating that the history is already archived. - - If the history was not purged after it was archived, you can restore it using - the `/api/histories/{id}/archive/restore` endpoint.' - operationId: archive_history_api_histories__history_id__archive_post - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/ArchiveHistoryRequestPayload' - - type: 'null' - title: Payload - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/ArchivedHistorySummary' - - $ref: '#/components/schemas/ArchivedHistoryDetailed' - - {} - title: Response Archive History Api Histories History Id Archive - Post - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Archive a history. - tags: - - histories - - histories - /api/histories/{history_id}/archive/restore: - put: - description: 'Restores an archived history and returns it. - - - Restoring an archived history will add it back to the list of active histories - of the user (unless it was purged). - - - **Warning**: Please note that histories that are associated with an archive - export might be purged after export, so un-archiving them - - will not restore the datasets that were in the history before it was archived. - You will need to import back the archive export - - record to restore the history and its datasets as a new copy. See `/api/histories/from_store_async` - for more information.' - operationId: restore_archived_history_api_histories__history_id__archive_restore_put - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: If true, the history will be un-archived even if it has an associated - archive export record and was purged. - in: query - name: force - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - description: If true, the history will be un-archived even if it has an - associated archive export record and was purged. - title: Force - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/HistoryDetailed' - - $ref: '#/components/schemas/HistorySummary' - - $ref: '#/components/schemas/HistoryMinimal' - title: Response Restore Archived History Api Histories History Id Archive - Restore Put - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Restore an archived history. - tags: - - histories - - histories - /api/histories/{history_id}/citations: - get: - operationId: citations_api_histories__history_id__citations_get - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: {} - title: Response Citations Api Histories History Id Citations Get - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return all the citations for the tools used to produce the datasets - in the history. - tags: - - histories - - histories - /api/histories/{history_id}/contents: - get: - description: 'Return a list of `HDA`/`HDCA` data for the history with the given - ``ID``. - - - - The contents can be filtered and queried using the appropriate parameters. - - - The amount of information returned for each item can be customized. - - - **Note**: Anonymous users are allowed to get their current history contents.' - operationId: history_contents__index - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: Only `dev` value is allowed. Set it to use the latest version - of this endpoint. **All parameters marked as `deprecated` will be ignored - when this parameter is set.** - in: query - name: v - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Only `dev` value is allowed. Set it to use the latest version - of this endpoint. **All parameters marked as `deprecated` will be ignored - when this parameter is set.** - examples: - - dev - title: Version - - deprecated: true - description: Legacy name for the `dataset_details` parameter. - in: query - name: details - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Legacy name for the `dataset_details` parameter. - title: Details - - deprecated: true - description: A comma-separated list of encoded `HDA/HDCA` IDs. If this list - is provided, only information about the specific datasets will be returned. - Also, setting this value will return `all` details of the content item. - in: query - name: ids - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: A comma-separated list of encoded `HDA/HDCA` IDs. If this list - is provided, only information about the specific datasets will be returned. - Also, setting this value will return `all` details of the content item. - title: IDs - - deprecated: true - description: A list or comma-separated list of kinds of contents to return - (currently just `dataset` and `dataset_collection` are available). If unset, - all types will be returned. - in: query - name: types - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: A list or comma-separated list of kinds of contents to return - (currently just `dataset` and `dataset_collection` are available). If - unset, all types will be returned. - title: Types - - deprecated: true - description: Whether to return deleted or undeleted datasets only. Leave unset - for both. - in: query - name: deleted - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - description: Whether to return deleted or undeleted datasets only. Leave - unset for both. - title: Deleted - - deprecated: true - description: Whether to return visible or hidden datasets only. Leave unset - for both. - in: query - name: visible - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - description: Whether to return visible or hidden datasets only. Leave unset - for both. - title: Visible - - description: Whether to return only shareable or not shareable datasets. Leave - unset for both. - in: query - name: shareable - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - description: Whether to return only shareable or not shareable datasets. - Leave unset for both. - title: Shareable - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: Generally a property name to filter by followed by an (often - optional) hyphen and operator string. - in: query - name: q - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: Generally a property name to filter by followed by an (often - optional) hyphen and operator string. - examples: - - create_time-gt - title: Filter Query - - description: The value to filter by. - in: query - name: qv - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: The value to filter by. - examples: - - '2015-01-29' - title: Filter Value - - description: Starts at the beginning skip the first ( offset - 1 ) items and - begin returning at the Nth item - in: query - name: offset - required: false - schema: - anyOf: - - minimum: 0 - type: integer - - type: 'null' - default: 0 - description: Starts at the beginning skip the first ( offset - 1 ) items - and begin returning at the Nth item - title: Offset - - description: The maximum number of items to return. - in: query - name: limit - required: false - schema: - anyOf: - - minimum: 1 - type: integer - - type: 'null' - description: The maximum number of items to return. - title: Limit - - description: String containing one of the valid ordering attributes followed - (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. - Orders can be stacked as a comma-separated list of values. - in: query - name: order - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: String containing one of the valid ordering attributes followed - (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. - Orders can be stacked as a comma-separated list of values. - title: Order - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/HistoryContentsResult' - anyOf: - - $ref: '#/components/schemas/HistoryContentsResult' - - $ref: '#/components/schemas/HistoryContentsWithStatsResult' - title: Response History Contents Index - application/vnd.galaxy.history.contents.stats+json: - schema: - $ref: '#/components/schemas/HistoryContentsWithStatsResult' - description: The contents of the history that match the query. - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns the contents of the given history. - tags: - - histories - - histories - post: - deprecated: true - description: Create a new `HDA` or `HDCA` in the given History. - operationId: history_contents__create - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The type of the target history element. - in: query - name: type - required: false - schema: - anyOf: - - $ref: '#/components/schemas/HistoryContentType' - - type: 'null' - description: The type of the target history element. - examples: - - dataset - title: Content Type - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/CreateHistoryContentPayload' - required: true - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/HDADetailed' - - $ref: '#/components/schemas/HDASummary' - - $ref: '#/components/schemas/HDCADetailed' - - $ref: '#/components/schemas/HDCASummary' - - $ref: '#/components/schemas/CustomHistoryItem' - - items: - anyOf: - - $ref: '#/components/schemas/HDADetailed' - - $ref: '#/components/schemas/HDASummary' - - $ref: '#/components/schemas/HDCADetailed' - - $ref: '#/components/schemas/HDCASummary' - - $ref: '#/components/schemas/CustomHistoryItem' - type: array - title: Response History Contents Create - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Create a new `HDA` or `HDCA` in the given History. - tags: - - histories - - histories - put: - description: 'Batch update specific properties of a set items contained in the - given History. - - - If you provide an invalid/unknown property key the request will not fail, - but no changes - - will be made to the items.' - operationId: update_batch_api_histories__history_id__contents_put - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/UpdateHistoryContentsBatchPayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/HistoryContentsResult' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Batch update specific properties of a set items contained in the given - History. - tags: - - histories - - histories - /api/histories/{history_id}/contents/archive: - get: - description: 'Build and return a compressed archive of the selected history - contents. - - - **Note**: this is a volatile endpoint and settings and behavior may change.' - operationId: history_contents__archive - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The name that the Archive will have (defaults to history name). - in: query - name: filename - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: The name that the Archive will have (defaults to history name). - title: Filename - - description: Whether to return the archive and file paths only (as JSON) and - not an actual archive file. - in: query - name: dry_run - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: true - description: Whether to return the archive and file paths only (as JSON) - and not an actual archive file. - title: Dry Run - - description: Generally a property name to filter by followed by an (often - optional) hyphen and operator string. - in: query - name: q - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: Generally a property name to filter by followed by an (often - optional) hyphen and operator string. - examples: - - create_time-gt - title: Filter Query - - description: The value to filter by. - in: query - name: qv - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: The value to filter by. - examples: - - '2015-01-29' - title: Filter Value - - description: Starts at the beginning skip the first ( offset - 1 ) items and - begin returning at the Nth item - in: query - name: offset - required: false - schema: - anyOf: - - minimum: 0 - type: integer - - type: 'null' - default: 0 - description: Starts at the beginning skip the first ( offset - 1 ) items - and begin returning at the Nth item - title: Offset - - description: The maximum number of items to return. - in: query - name: limit - required: false - schema: - anyOf: - - minimum: 1 - type: integer - - type: 'null' - description: The maximum number of items to return. - title: Limit - - description: String containing one of the valid ordering attributes followed - (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. - Orders can be stacked as a comma-separated list of values. - in: query - name: order - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: String containing one of the valid ordering attributes followed - (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. - Orders can be stacked as a comma-separated list of values. - title: Order - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Build and return a compressed archive of the selected history contents. - tags: - - histories - - histories - /api/histories/{history_id}/contents/archive/{filename}.{format}: - get: - description: 'Build and return a compressed archive of the selected history - contents. - - - **Note**: this is a volatile endpoint and settings and behavior may change.' - operationId: history_contents__archive_named - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The name that the Archive will have (defaults to history name). - in: path - name: filename - required: true - schema: - description: The name that the Archive will have (defaults to history name). - title: Filename - type: string - - deprecated: true - description: Output format of the archive. - in: path - name: format - required: true - schema: - description: Output format of the archive. - title: Format - type: string - - description: Whether to return the archive and file paths only (as JSON) and - not an actual archive file. - in: query - name: dry_run - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: true - description: Whether to return the archive and file paths only (as JSON) - and not an actual archive file. - title: Dry Run - - description: Generally a property name to filter by followed by an (often - optional) hyphen and operator string. - in: query - name: q - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: Generally a property name to filter by followed by an (often - optional) hyphen and operator string. - examples: - - create_time-gt - title: Filter Query - - description: The value to filter by. - in: query - name: qv - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: The value to filter by. - examples: - - '2015-01-29' - title: Filter Value - - description: Starts at the beginning skip the first ( offset - 1 ) items and - begin returning at the Nth item - in: query - name: offset - required: false - schema: - anyOf: - - minimum: 0 - type: integer - - type: 'null' - default: 0 - description: Starts at the beginning skip the first ( offset - 1 ) items - and begin returning at the Nth item - title: Offset - - description: The maximum number of items to return. - in: query - name: limit - required: false - schema: - anyOf: - - minimum: 1 - type: integer - - type: 'null' - description: The maximum number of items to return. - title: Limit - - description: String containing one of the valid ordering attributes followed - (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. - Orders can be stacked as a comma-separated list of values. - in: query - name: order - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: String containing one of the valid ordering attributes followed - (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. - Orders can be stacked as a comma-separated list of values. - title: Order - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Build and return a compressed archive of the selected history contents. - tags: - - histories - - histories - /api/histories/{history_id}/contents/bulk: - put: - description: 'Executes an operation on a set of items contained in the given - History. - - - The items to be processed can be explicitly set or determined by a dynamic - query.' - operationId: bulk_operation_api_histories__history_id__contents_bulk_put - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: Generally a property name to filter by followed by an (often - optional) hyphen and operator string. - in: query - name: q - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: Generally a property name to filter by followed by an (often - optional) hyphen and operator string. - examples: - - create_time-gt - title: Filter Query - - description: The value to filter by. - in: query - name: qv - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: The value to filter by. - examples: - - '2015-01-29' - title: Filter Value - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/HistoryContentBulkOperationPayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/HistoryContentBulkOperationResult' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Executes an operation on a set of items contained in the given History. - tags: - - histories - - histories - /api/histories/{history_id}/contents/dataset_collections/{id}/download: - get: - description: 'Download the content of a history dataset collection as a `zip` - archive - - while maintaining approximate collection structure.' - operationId: history_contents__download_collection - parameters: - - description: The ID of the `HDCA`. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The encoded database identifier of the History. - title: History Id - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Download the content of a dataset collection as a `zip` archive. - tags: - - histories - - histories - /api/histories/{history_id}/contents/datasets/{id}/materialize: - post: - operationId: materialize_dataset_api_histories__history_id__contents_datasets__id__materialize_post - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The ID of the item (`HDA`/`HDCA`) - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/AsyncTaskResultSummary' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Materialize a deferred dataset into real, usable dataset. - tags: - - histories - - histories - /api/histories/{history_id}/contents/{dataset_id}/permissions: - put: - description: Set permissions of the given history dataset to the given role - ids. - operationId: update_permissions_api_histories__history_id__contents__dataset_id__permissions_put - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The ID of the item (`HDA`/`HDCA`) - in: path - name: dataset_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - examples: - - access_ids: [] - action: set_permissions - manage_ids: [] - modify_ids: [] - title: Payload - type: object - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DatasetAssociationRoles' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Set permissions of the given history dataset to the given role ids. - tags: - - histories - - histories - /api/histories/{history_id}/contents/{history_content_id}/display: - get: - description: Streams the dataset for download or the contents preview to be - displayed in a browser. - operationId: history_contents_display_api_histories__history_id__contents__history_content_id__display_get - parameters: - - description: The ID of the History Dataset. - in: path - name: history_content_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - in: path - name: history_id - required: true - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - title: History Id - - description: Whether to get preview contents to be directly displayed on the - web. If preview is False (default) the contents will be downloaded instead. - in: query - name: preview - required: false - schema: - default: false - description: Whether to get preview contents to be directly displayed on - the web. If preview is False (default) the contents will be downloaded - instead. - title: Preview - type: boolean - - description: If non-null, get the specified filename from the extra files - for this dataset. - in: query - name: filename - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: If non-null, get the specified filename from the extra files - for this dataset. - title: Filename - - description: The file extension when downloading the display data. Use the - value `data` to let the server infer it from the data type. - in: query - name: to_ext - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: The file extension when downloading the display data. Use the - value `data` to let the server infer it from the data type. - title: To Ext - - description: The query parameter 'raw' should be considered experimental and - may be dropped at some point in the future without warning. Generally, data - should be processed by its datatype prior to display. - in: query - name: raw - required: false - schema: - default: false - description: The query parameter 'raw' should be considered experimental - and may be dropped at some point in the future without warning. Generally, - data should be processed by its datatype prior to display. - title: Raw - type: boolean - - description: Set this for datatypes that allow chunked display through the - display_data method to enable chunking. This specifies a byte offset into - the target dataset's display. - in: query - name: offset - required: false - schema: - anyOf: - - type: integer - - type: 'null' - description: Set this for datatypes that allow chunked display through the - display_data method to enable chunking. This specifies a byte offset into - the target dataset's display. - title: Offset - - description: 'If offset is set, this recommends ''how large'' the next chunk - should be. This is not respected or interpreted uniformly and should be - interpreted as a very loose recommendation. Different datatypes interpret - ''largeness'' differently - for bam datasets this is a number of lines whereas - for tabular datatypes this is interpreted as a number of bytes. ' - in: query - name: ck_size - required: false - schema: - anyOf: - - type: integer - - type: 'null' - description: 'If offset is set, this recommends ''how large'' the next chunk - should be. This is not respected or interpreted uniformly and should be - interpreted as a very loose recommendation. Different datatypes interpret - ''largeness'' differently - for bam datasets this is a number of lines - whereas for tabular datatypes this is interpreted as a number of bytes. ' - title: Ck Size - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Displays (preview) or downloads dataset content. - tags: - - datasets - - datasets - - histories - head: - description: Streams the dataset for download or the contents preview to be - displayed in a browser. - operationId: history_contents_display_api_histories__history_id__contents__history_content_id__display_head - parameters: - - description: The ID of the History Dataset. - in: path - name: history_content_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - in: path - name: history_id - required: true - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - title: History Id - - description: Whether to get preview contents to be directly displayed on the - web. If preview is False (default) the contents will be downloaded instead. - in: query - name: preview - required: false - schema: - default: false - description: Whether to get preview contents to be directly displayed on - the web. If preview is False (default) the contents will be downloaded - instead. - title: Preview - type: boolean - - description: If non-null, get the specified filename from the extra files - for this dataset. - in: query - name: filename - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: If non-null, get the specified filename from the extra files - for this dataset. - title: Filename - - description: The file extension when downloading the display data. Use the - value `data` to let the server infer it from the data type. - in: query - name: to_ext - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: The file extension when downloading the display data. Use the - value `data` to let the server infer it from the data type. - title: To Ext - - description: The query parameter 'raw' should be considered experimental and - may be dropped at some point in the future without warning. Generally, data - should be processed by its datatype prior to display. - in: query - name: raw - required: false - schema: - default: false - description: The query parameter 'raw' should be considered experimental - and may be dropped at some point in the future without warning. Generally, - data should be processed by its datatype prior to display. - title: Raw - type: boolean - - description: Set this for datatypes that allow chunked display through the - display_data method to enable chunking. This specifies a byte offset into - the target dataset's display. - in: query - name: offset - required: false - schema: - anyOf: - - type: integer - - type: 'null' - description: Set this for datatypes that allow chunked display through the - display_data method to enable chunking. This specifies a byte offset into - the target dataset's display. - title: Offset - - description: 'If offset is set, this recommends ''how large'' the next chunk - should be. This is not respected or interpreted uniformly and should be - interpreted as a very loose recommendation. Different datatypes interpret - ''largeness'' differently - for bam datasets this is a number of lines whereas - for tabular datatypes this is interpreted as a number of bytes. ' - in: query - name: ck_size - required: false - schema: - anyOf: - - type: integer - - type: 'null' - description: 'If offset is set, this recommends ''how large'' the next chunk - should be. This is not respected or interpreted uniformly and should be - interpreted as a very loose recommendation. Different datatypes interpret - ''largeness'' differently - for bam datasets this is a number of lines - whereas for tabular datatypes this is interpreted as a number of bytes. ' - title: Ck Size - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Check if dataset content can be previewed or downloaded. - tags: - - datasets - - datasets - - histories - /api/histories/{history_id}/contents/{history_content_id}/extra_files: - get: - operationId: extra_files_history_api_histories__history_id__contents__history_content_id__extra_files_get - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The ID of the History Dataset. - in: path - name: history_content_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DatasetExtraFiles' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get the list of extra files/directories associated with a dataset. - tags: - - datasets - - datasets - - histories - /api/histories/{history_id}/contents/{history_content_id}/metadata_file: - get: - operationId: history_contents__get_metadata_file - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The ID of the History Dataset. - in: path - name: history_content_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The name of the metadata file to retrieve. - in: query - name: metadata_file - required: true - schema: - description: The name of the metadata file to retrieve. - title: Metadata File - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns the metadata file associated with this history item. - tags: - - datasets - - datasets - - histories - /api/histories/{history_id}/contents/{history_content_id}/tags: - get: - operationId: index_api_histories__history_id__contents__history_content_id__tags_get - parameters: - - in: path - name: history_content_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - - in: path - name: history_id - required: true - schema: - title: History ID - type: string - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ItemTagsListResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Show tags based on history_content_id - tags: - - histories - /api/histories/{history_id}/contents/{history_content_id}/tags/{tag_name}: - delete: - operationId: delete_api_histories__history_id__contents__history_content_id__tags__tag_name__delete - parameters: - - in: path - name: history_content_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - in: path - name: tag_name - required: true - schema: - title: Tag Name - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - - in: path - name: history_id - required: true - schema: - title: History ID - type: string - responses: - '200': - content: - application/json: - schema: - title: Response Delete Api Histories History Id Contents History - Content Id Tags Tag Name Delete - type: boolean - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Delete tag based on history_content_id - tags: - - histories - get: - operationId: show_api_histories__history_id__contents__history_content_id__tags__tag_name__get - parameters: - - in: path - name: history_content_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - in: path - name: tag_name - required: true - schema: - title: Tag Name - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - - in: path - name: history_id - required: true - schema: - title: History ID - type: string - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ItemTagsResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Show tag based on history_content_id - tags: - - histories - post: - operationId: create_api_histories__history_id__contents__history_content_id__tags__tag_name__post - parameters: - - in: path - name: history_content_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - in: path - name: tag_name - required: true - schema: - title: Tag Name - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - - in: path - name: history_id - required: true - schema: - title: History ID - type: string - requestBody: - content: - application/json: - schema: - allOf: - - $ref: '#/components/schemas/ItemTagsCreatePayload' - title: Payload - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ItemTagsResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Create tag based on history_content_id - tags: - - histories - put: - operationId: update_api_histories__history_id__contents__history_content_id__tags__tag_name__put - parameters: - - in: path - name: history_content_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - in: path - name: tag_name - required: true - schema: - title: Tag Name - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - - in: path - name: history_id - required: true - schema: - title: History ID - type: string - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/ItemTagsCreatePayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ItemTagsResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Update tag based on history_content_id - tags: - - histories - /api/histories/{history_id}/contents/{id}: - delete: - description: 'Delete the history content with the given ``ID`` and query specified - type (defaults to dataset). - - - **Note**: Currently does not stop any active jobs for which this dataset is - an output.' - operationId: history_contents__delete_legacy - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The ID of the item (`HDA`/`HDCA`) - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The type of the target history element. - in: query - name: type - required: false - schema: - allOf: - - $ref: '#/components/schemas/HistoryContentType' - default: dataset - description: The type of the target history element. - examples: - - dataset - title: Content Type - - deprecated: true - description: Whether to remove from disk the target HDA or child HDAs of the - target HDCA. - in: query - name: purge - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: false - description: Whether to remove from disk the target HDA or child HDAs of - the target HDCA. - title: Purge - - deprecated: true - description: When deleting a dataset collection, whether to also delete containing - datasets. - in: query - name: recursive - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: false - description: When deleting a dataset collection, whether to also delete - containing datasets. - title: Recursive - - deprecated: true - description: Whether to stop the creating job if all outputs of the job have - been deleted. - in: query - name: stop_job - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: false - description: Whether to stop the creating job if all outputs of the job - have been deleted. - title: Stop Job - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - allOf: - - $ref: '#/components/schemas/DeleteHistoryContentPayload' - title: Payload - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DeleteHistoryContentResult' - description: Request has been executed. - '202': - content: - application/json: - schema: - $ref: '#/components/schemas/DeleteHistoryContentResult' - description: Request accepted, processing will finish later. - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Delete the history dataset with the given ``ID``. - tags: - - histories - - histories - get: - deprecated: true - description: 'Return detailed information about an `HDA` or `HDCA` within a - history. - - - **Note**: Anonymous users are allowed to get their current history contents.' - operationId: history_contents__show_legacy - parameters: - - description: The ID of the item (`HDA`/`HDCA`) - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The type of the target history element. - in: query - name: type - required: false - schema: - allOf: - - $ref: '#/components/schemas/HistoryContentType' - default: dataset - description: The type of the target history element. - examples: - - dataset - title: Content Type - - description: This value can be used to broadly restrict the magnitude of the - number of elements returned via the API for large collections. The number - of actual elements returned may be "a bit" more than this number or "a lot" - less - varying on the depth of nesting, balance of nesting at each level, - and size of target collection. The consumer of this API should not expect - a stable number or pre-calculable number of elements to be produced given - this parameter - the only promise is that this API will not respond with - an order of magnitude more elements estimated with this value. The UI uses - this parameter to fetch a "balanced" concept of the "start" of large collections - at every depth of the collection. - in: query - name: fuzzy_count - required: false - schema: - anyOf: - - type: integer - - type: 'null' - description: This value can be used to broadly restrict the magnitude of - the number of elements returned via the API for large collections. The - number of actual elements returned may be "a bit" more than this number - or "a lot" less - varying on the depth of nesting, balance of nesting - at each level, and size of target collection. The consumer of this API - should not expect a stable number or pre-calculable number of elements - to be produced given this parameter - the only promise is that this API - will not respond with an order of magnitude more elements estimated with - this value. The UI uses this parameter to fetch a "balanced" concept of - the "start" of large collections at every depth of the collection. - title: Fuzzy Count - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/HDADetailed' - - $ref: '#/components/schemas/HDASummary' - - $ref: '#/components/schemas/HDCADetailed' - - $ref: '#/components/schemas/HDCASummary' - - $ref: '#/components/schemas/CustomHistoryItem' - title: Response History Contents Show Legacy - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return detailed information about an HDA within a history. ``/api/histories/{history_id}/contents/{type}s/{id}`` - should be used instead. - tags: - - histories - - histories - put: - deprecated: true - description: Updates the values for the history content item with the given - ``ID``. - operationId: history_contents__update_legacy - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The ID of the item (`HDA`/`HDCA`) - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The type of the target history element. - in: query - name: type - required: false - schema: - allOf: - - $ref: '#/components/schemas/HistoryContentType' - default: dataset - description: The type of the target history element. - examples: - - dataset - title: Content Type - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/UpdateHistoryContentsPayload' - required: true - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/HDADetailed' - - $ref: '#/components/schemas/HDASummary' - - $ref: '#/components/schemas/HDCADetailed' - - $ref: '#/components/schemas/HDCASummary' - - $ref: '#/components/schemas/CustomHistoryItem' - title: Response History Contents Update Legacy - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Updates the values for the history content item with the given ``ID`` - and query specified type. ``/api/histories/{history_id}/contents/{type}s/{id}`` - should be used instead. - tags: - - histories - - histories - /api/histories/{history_id}/contents/{id}/validate: - put: - description: Validates the metadata associated with a dataset within a History. - operationId: validate_api_histories__history_id__contents__id__validate_put - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The ID of the item (`HDA`/`HDCA`) - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - title: Response Validate Api Histories History Id Contents Id Validate - Put - type: object - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Validates the metadata associated with a dataset within a History. - tags: - - histories - - histories - /api/histories/{history_id}/contents/{type}s: - get: - description: 'Return a list of either `HDA`/`HDCA` data for the history with - the given ``ID``. - - - - The contents can be filtered and queried using the appropriate parameters. - - - The amount of information returned for each item can be customized. - - - **Note**: Anonymous users are allowed to get their current history contents.' - operationId: history_contents__index_typed - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The type of the target history element. - in: path - name: type - required: true - schema: - allOf: - - $ref: '#/components/schemas/HistoryContentType' - description: The type of the target history element. - examples: - - dataset - title: Content Type - - description: Only `dev` value is allowed. Set it to use the latest version - of this endpoint. **All parameters marked as `deprecated` will be ignored - when this parameter is set.** - in: query - name: v - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Only `dev` value is allowed. Set it to use the latest version - of this endpoint. **All parameters marked as `deprecated` will be ignored - when this parameter is set.** - examples: - - dev - title: Version - - deprecated: true - description: Legacy name for the `dataset_details` parameter. - in: query - name: details - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Legacy name for the `dataset_details` parameter. - title: Details - - deprecated: true - description: A comma-separated list of encoded `HDA/HDCA` IDs. If this list - is provided, only information about the specific datasets will be returned. - Also, setting this value will return `all` details of the content item. - in: query - name: ids - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: A comma-separated list of encoded `HDA/HDCA` IDs. If this list - is provided, only information about the specific datasets will be returned. - Also, setting this value will return `all` details of the content item. - title: IDs - - deprecated: true - description: A list or comma-separated list of kinds of contents to return - (currently just `dataset` and `dataset_collection` are available). If unset, - all types will be returned. - in: query - name: types - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: A list or comma-separated list of kinds of contents to return - (currently just `dataset` and `dataset_collection` are available). If - unset, all types will be returned. - title: Types - - deprecated: true - description: Whether to return deleted or undeleted datasets only. Leave unset - for both. - in: query - name: deleted - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - description: Whether to return deleted or undeleted datasets only. Leave - unset for both. - title: Deleted - - deprecated: true - description: Whether to return visible or hidden datasets only. Leave unset - for both. - in: query - name: visible - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - description: Whether to return visible or hidden datasets only. Leave unset - for both. - title: Visible - - description: Whether to return only shareable or not shareable datasets. Leave - unset for both. - in: query - name: shareable - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - description: Whether to return only shareable or not shareable datasets. - Leave unset for both. - title: Shareable - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: Generally a property name to filter by followed by an (often - optional) hyphen and operator string. - in: query - name: q - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: Generally a property name to filter by followed by an (often - optional) hyphen and operator string. - examples: - - create_time-gt - title: Filter Query - - description: The value to filter by. - in: query - name: qv - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: The value to filter by. - examples: - - '2015-01-29' - title: Filter Value - - description: Starts at the beginning skip the first ( offset - 1 ) items and - begin returning at the Nth item - in: query - name: offset - required: false - schema: - anyOf: - - minimum: 0 - type: integer - - type: 'null' - default: 0 - description: Starts at the beginning skip the first ( offset - 1 ) items - and begin returning at the Nth item - title: Offset - - description: The maximum number of items to return. - in: query - name: limit - required: false - schema: - anyOf: - - minimum: 1 - type: integer - - type: 'null' - description: The maximum number of items to return. - title: Limit - - description: String containing one of the valid ordering attributes followed - (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. - Orders can be stacked as a comma-separated list of values. - in: query - name: order - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: String containing one of the valid ordering attributes followed - (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. - Orders can be stacked as a comma-separated list of values. - title: Order - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/HistoryContentsResult' - - $ref: '#/components/schemas/HistoryContentsWithStatsResult' - title: Response History Contents Index Typed - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns the contents of the given history filtered by type. - tags: - - histories - - histories - post: - description: Create a new `HDA` or `HDCA` in the given History. - operationId: history_contents__create_typed - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The type of the target history element. - in: path - name: type - required: true - schema: - allOf: - - $ref: '#/components/schemas/HistoryContentType' - description: The type of the target history element. - examples: - - dataset - title: Content Type - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/CreateHistoryContentPayload' - required: true - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/HDADetailed' - - $ref: '#/components/schemas/HDASummary' - - $ref: '#/components/schemas/HDCADetailed' - - $ref: '#/components/schemas/HDCASummary' - - $ref: '#/components/schemas/CustomHistoryItem' - - items: - anyOf: - - $ref: '#/components/schemas/HDADetailed' - - $ref: '#/components/schemas/HDASummary' - - $ref: '#/components/schemas/HDCADetailed' - - $ref: '#/components/schemas/HDCASummary' - - $ref: '#/components/schemas/CustomHistoryItem' - type: array - title: Response History Contents Create Typed - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Create a new `HDA` or `HDCA` in the given History. - tags: - - histories - - histories - /api/histories/{history_id}/contents/{type}s/{id}: - delete: - description: 'Delete the history content with the given ``ID`` and path specified - type. - - - **Note**: Currently does not stop any active jobs for which this dataset is - an output.' - operationId: history_contents__delete_typed - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The ID of the item (`HDA`/`HDCA`) - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The type of the target history element. - in: path - name: type - required: true - schema: - allOf: - - $ref: '#/components/schemas/HistoryContentType' - description: The type of the target history element. - examples: - - dataset - title: Content Type - - deprecated: true - description: Whether to remove from disk the target HDA or child HDAs of the - target HDCA. - in: query - name: purge - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: false - description: Whether to remove from disk the target HDA or child HDAs of - the target HDCA. - title: Purge - - deprecated: true - description: When deleting a dataset collection, whether to also delete containing - datasets. - in: query - name: recursive - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: false - description: When deleting a dataset collection, whether to also delete - containing datasets. - title: Recursive - - deprecated: true - description: Whether to stop the creating job if all outputs of the job have - been deleted. - in: query - name: stop_job - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: false - description: Whether to stop the creating job if all outputs of the job - have been deleted. - title: Stop Job - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - allOf: - - $ref: '#/components/schemas/DeleteHistoryContentPayload' - title: Payload - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DeleteHistoryContentResult' - description: Request has been executed. - '202': - content: - application/json: - schema: - $ref: '#/components/schemas/DeleteHistoryContentResult' - description: Request accepted, processing will finish later. - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Delete the history content with the given ``ID`` and path specified - type. - tags: - - histories - - histories - get: - description: 'Return detailed information about an `HDA` or `HDCA` within a - history. - - - **Note**: Anonymous users are allowed to get their current history contents.' - operationId: history_contents__show - parameters: - - description: The ID of the item (`HDA`/`HDCA`) - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The type of the target history element. - in: path - name: type - required: true - schema: - allOf: - - $ref: '#/components/schemas/HistoryContentType' - description: The type of the target history element. - examples: - - dataset - title: Content Type - - description: This value can be used to broadly restrict the magnitude of the - number of elements returned via the API for large collections. The number - of actual elements returned may be "a bit" more than this number or "a lot" - less - varying on the depth of nesting, balance of nesting at each level, - and size of target collection. The consumer of this API should not expect - a stable number or pre-calculable number of elements to be produced given - this parameter - the only promise is that this API will not respond with - an order of magnitude more elements estimated with this value. The UI uses - this parameter to fetch a "balanced" concept of the "start" of large collections - at every depth of the collection. - in: query - name: fuzzy_count - required: false - schema: - anyOf: - - type: integer - - type: 'null' - description: This value can be used to broadly restrict the magnitude of - the number of elements returned via the API for large collections. The - number of actual elements returned may be "a bit" more than this number - or "a lot" less - varying on the depth of nesting, balance of nesting - at each level, and size of target collection. The consumer of this API - should not expect a stable number or pre-calculable number of elements - to be produced given this parameter - the only promise is that this API - will not respond with an order of magnitude more elements estimated with - this value. The UI uses this parameter to fetch a "balanced" concept of - the "start" of large collections at every depth of the collection. - title: Fuzzy Count - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/HDADetailed' - - $ref: '#/components/schemas/HDASummary' - - $ref: '#/components/schemas/HDCADetailed' - - $ref: '#/components/schemas/HDCASummary' - - $ref: '#/components/schemas/CustomHistoryItem' - title: Response History Contents Show - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return detailed information about a specific HDA or HDCA with the given - `ID` within a history. - tags: - - histories - - histories - put: - description: Updates the values for the history content item with the given - ``ID``. - operationId: history_contents__update_typed - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The ID of the item (`HDA`/`HDCA`) - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The type of the target history element. - in: path - name: type - required: true - schema: - allOf: - - $ref: '#/components/schemas/HistoryContentType' - description: The type of the target history element. - examples: - - dataset - title: Content Type - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/UpdateHistoryContentsPayload' - required: true - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/HDADetailed' - - $ref: '#/components/schemas/HDASummary' - - $ref: '#/components/schemas/HDCADetailed' - - $ref: '#/components/schemas/HDCASummary' - - $ref: '#/components/schemas/CustomHistoryItem' - title: Response History Contents Update Typed - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Updates the values for the history content item with the given ``ID`` - and path specified type. - tags: - - histories - - histories - /api/histories/{history_id}/contents/{type}s/{id}/jobs_summary: - get: - description: 'Return detailed information about an `HDA` or `HDCAs` jobs. - - - **Warning**: We allow anyone to fetch job state information about any object - they - - can guess an encoded ID for - it isn''t considered protected data. This keeps - - polling IDs as part of state calculation for large histories and collections - as - - efficient as possible.' - operationId: show_jobs_summary_api_histories__history_id__contents__type_s__id__jobs_summary_get - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The ID of the item (`HDA`/`HDCA`) - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The type of the target history element. - in: path - name: type - required: true - schema: - allOf: - - $ref: '#/components/schemas/HistoryContentType' - description: The type of the target history element. - examples: - - dataset - title: Content Type - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - discriminator: - mapping: - ImplicitCollectionJobs: '#/components/schemas/ImplicitCollectionJobsStateSummary' - Job: '#/components/schemas/JobStateSummary' - WorkflowInvocation: '#/components/schemas/WorkflowInvocationStateSummary' - propertyName: model - oneOf: - - $ref: '#/components/schemas/JobStateSummary' - - $ref: '#/components/schemas/ImplicitCollectionJobsStateSummary' - - $ref: '#/components/schemas/WorkflowInvocationStateSummary' - title: Response Show Jobs Summary Api Histories History Id Contents Type - S Id Jobs Summary Get - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return detailed information about an `HDA` or `HDCAs` jobs. - tags: - - histories - - histories - /api/histories/{history_id}/contents/{type}s/{id}/prepare_store_download: - post: - operationId: prepare_store_download_api_histories__history_id__contents__type_s__id__prepare_store_download_post - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The ID of the item (`HDA`/`HDCA`) - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The type of the target history element. - in: path - name: type - required: true - schema: - allOf: - - $ref: '#/components/schemas/HistoryContentType' - description: The type of the target history element. - examples: - - dataset - title: Content Type - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/StoreExportPayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/AsyncFile' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Prepare a dataset or dataset collection for export-style download. - tags: - - histories - - histories - /api/histories/{history_id}/contents/{type}s/{id}/write_store: - post: - operationId: write_store_api_histories__history_id__contents__type_s__id__write_store_post - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The ID of the item (`HDA`/`HDCA`) - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The type of the target history element. - in: path - name: type - required: true - schema: - allOf: - - $ref: '#/components/schemas/HistoryContentType' - description: The type of the target history element. - examples: - - dataset - title: Content Type - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/WriteStoreToPayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/AsyncTaskResultSummary' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Prepare a dataset or dataset collection for export-style download and - write to supplied URI. - tags: - - histories - - histories - /api/histories/{history_id}/contents_from_store: - post: - description: 'Create history contents from model store. - - Input can be a tarfile created with build_objects script distributed - - with galaxy-data, from an exported history with files stripped out, - - or hand-crafted JSON dictionary.' - operationId: create_from_store_api_histories__history_id__contents_from_store_post - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Comma-separated list of keys to be passed to the serializer - in: query - name: keys - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Comma-separated list of keys to be passed to the serializer - title: Keys - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/CreateHistoryContentFromStore' - required: true - responses: - '200': - content: - application/json: - schema: - items: - anyOf: - - $ref: '#/components/schemas/HDADetailed' - - $ref: '#/components/schemas/HDASummary' - - $ref: '#/components/schemas/HDCADetailed' - - $ref: '#/components/schemas/HDCASummary' - - $ref: '#/components/schemas/CustomHistoryItem' - title: Response Create From Store Api Histories History Id Contents - From Store Post - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Create contents from store. - tags: - - histories - - histories - /api/histories/{history_id}/custom_builds_metadata: - get: - operationId: get_custom_builds_metadata_api_histories__history_id__custom_builds_metadata_get - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/CustomBuildsMetadataResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns meta data for custom builds. - tags: - - histories - - histories - /api/histories/{history_id}/disable_link_access: - put: - description: Makes this item inaccessible by a URL link and return the current - sharing status. - operationId: disable_link_access_api_histories__history_id__disable_link_access_put - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/SharingStatus' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Makes this item inaccessible by a URL link. - tags: - - histories - - histories - /api/histories/{history_id}/enable_link_access: - put: - description: Makes this item accessible by a URL link and return the current - sharing status. - operationId: enable_link_access_api_histories__history_id__enable_link_access_put - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/SharingStatus' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Makes this item accessible by a URL link. - tags: - - histories - - histories - /api/histories/{history_id}/exports: - get: - description: 'By default the legacy job-based history exports (jeha) are returned. - - - Change the `accept` content type header to return the new task-based history - exports.' - operationId: get_history_exports_api_histories__history_id__exports_get - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The maximum number of items to return. - in: query - name: limit - required: false - schema: - anyOf: - - minimum: 1 - type: integer - - type: 'null' - description: The maximum number of items to return. - title: Limit - - description: Starts at the beginning skip the first ( offset - 1 ) items and - begin returning at the Nth item - in: query - name: offset - required: false - schema: - anyOf: - - minimum: 0 - type: integer - - type: 'null' - default: 0 - description: Starts at the beginning skip the first ( offset - 1 ) items - and begin returning at the Nth item - title: Offset - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/JobExportHistoryArchiveListResponse' - anyOf: - - $ref: '#/components/schemas/JobExportHistoryArchiveListResponse' - - $ref: '#/components/schemas/ExportTaskListResponse' - title: Response Get History Exports Api Histories History Id Exports - Get - application/vnd.galaxy.task.export+json: - schema: - $ref: '#/components/schemas/ExportTaskListResponse' - description: A list of history exports - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get previous history exports. - tags: - - histories - - histories - put: - deprecated: true - description: 'This will start a job to create a history export archive. - - - Calling this endpoint multiple times will return the 202 status code until - the archive - - has been completely generated and is ready to download. When ready, it will - return - - the 200 status code along with the download link information. - - - If the history will be exported to a `directory_uri`, instead of returning - the download - - link information, the Job ID will be returned so it can be queried to determine - when - - the file has been written. - - - **Deprecation notice**: Please use `/api/histories/{id}/prepare_store_download` - or - - `/api/histories/{id}/write_store` instead.' - operationId: archive_export_api_histories__history_id__exports_put - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/ExportHistoryArchivePayload' - - type: 'null' - title: Payload - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/JobExportHistoryArchiveModel' - - $ref: '#/components/schemas/JobIdResponse' - title: Response Archive Export Api Histories History Id Exports - Put - description: Object containing url to fetch export from. - '202': - description: The exported archive file is not ready yet. - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Start job (if needed) to create history export for corresponding history. - tags: - - histories - - histories - /api/histories/{history_id}/exports/{jeha_id}: - get: - deprecated: true - description: 'See ``PUT /api/histories/{id}/exports`` to initiate the creation - - of the history export - when ready, that route will return 200 status - - code (instead of 202) and this route can be used to download the archive. - - - **Deprecation notice**: Please use `/api/histories/{id}/prepare_store_download` - or - - `/api/histories/{id}/write_store` instead.' - operationId: history_archive_download_api_histories__history_id__exports__jeha_id__get - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The ID of the specific Job Export History Association or `latest` - (default) to download the last generated archive. - in: path - name: jeha_id - required: true - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - const: latest - description: The ID of the specific Job Export History Association or `latest` - (default) to download the last generated archive. - examples: - - latest - title: Job Export History ID - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - description: The archive file containing the History. - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: If ready and available, return raw contents of exported history as - a downloadable archive. - tags: - - histories - - histories - /api/histories/{history_id}/jobs_summary: - get: - description: 'Return job state summary info for jobs, implicit groups jobs for - collections or workflow invocations. - - - **Warning**: We allow anyone to fetch job state information about any object - they - - can guess an encoded ID for - it isn''t considered protected data. This keeps - - polling IDs as part of state calculation for large histories and collections - as - - efficient as possible.' - operationId: index_jobs_summary_api_histories__history_id__jobs_summary_get - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: A comma-separated list of encoded ids of job summary objects - to return - if `ids` is specified types must also be specified and have - same length. - in: query - name: ids - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: A comma-separated list of encoded ids of job summary objects - to return - if `ids` is specified types must also be specified and have - same length. - title: IDs - - description: A comma-separated list of type of object represented by elements - in the `ids` array - any of `Job`, `ImplicitCollectionJob`, or `WorkflowInvocation`. - in: query - name: types - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: A comma-separated list of type of object represented by elements - in the `ids` array - any of `Job`, `ImplicitCollectionJob`, or `WorkflowInvocation`. - title: Types - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - discriminator: - mapping: - ImplicitCollectionJobs: '#/components/schemas/ImplicitCollectionJobsStateSummary' - Job: '#/components/schemas/JobStateSummary' - WorkflowInvocation: '#/components/schemas/WorkflowInvocationStateSummary' - propertyName: model - oneOf: - - $ref: '#/components/schemas/JobStateSummary' - - $ref: '#/components/schemas/ImplicitCollectionJobsStateSummary' - - $ref: '#/components/schemas/WorkflowInvocationStateSummary' - title: Response Index Jobs Summary Api Histories History Id Jobs - Summary Get - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return job state summary info for jobs, implicit groups jobs for collections - or workflow invocations. - tags: - - histories - - histories - /api/histories/{history_id}/materialize: - post: - operationId: materialize_to_history_api_histories__history_id__materialize_post - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/MaterializeDatasetInstanceAPIRequest' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/AsyncTaskResultSummary' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Materialize a deferred library or HDA dataset into real, usable dataset - in specified history. - tags: - - histories - - histories - /api/histories/{history_id}/prepare_store_download: - post: - operationId: prepare_store_download_api_histories__history_id__prepare_store_download_post - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/StoreExportPayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/AsyncFile' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return a short term storage token to monitor download of the history. - tags: - - histories - - histories - /api/histories/{history_id}/publish: - put: - description: Makes this item publicly available by a URL link and return the - current sharing status. - operationId: publish_api_histories__history_id__publish_put - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/SharingStatus' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Makes this item public and accessible by a URL link. - tags: - - histories - - histories - /api/histories/{history_id}/share_with_users: - put: - description: Shares this item with specific users and return the current sharing - status. - operationId: share_with_users_api_histories__history_id__share_with_users_put - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/ShareWithPayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ShareHistoryWithStatus' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Share this item with specific users. - tags: - - histories - - histories - /api/histories/{history_id}/sharing: - get: - description: Return the sharing status of the item. - operationId: sharing_api_histories__history_id__sharing_get - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/SharingStatus' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get the current sharing status of the given item. - tags: - - histories - - histories - /api/histories/{history_id}/slug: - put: - description: Sets a new slug to access this item by URL. The new slug must be - unique. - operationId: set_slug_api_histories__history_id__slug_put - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/SetSlugPayload' - required: true - responses: - '204': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Set a new slug for this shared item. - tags: - - histories - - histories - /api/histories/{history_id}/tags: - get: - operationId: index_api_histories__history_id__tags_get - parameters: - - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ItemTagsListResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Show tags based on history_id - tags: - - histories - /api/histories/{history_id}/tags/{tag_name}: - delete: - operationId: delete_api_histories__history_id__tags__tag_name__delete - parameters: - - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - in: path - name: tag_name - required: true - schema: - title: Tag Name - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - title: Response Delete Api Histories History Id Tags Tag Name Delete - type: boolean - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Delete tag based on history_id - tags: - - histories - get: - operationId: show_api_histories__history_id__tags__tag_name__get - parameters: - - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - in: path - name: tag_name - required: true - schema: - title: Tag Name - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ItemTagsResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Show tag based on history_id - tags: - - histories - post: - operationId: create_api_histories__history_id__tags__tag_name__post - parameters: - - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - in: path - name: tag_name - required: true - schema: - title: Tag Name - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - allOf: - - $ref: '#/components/schemas/ItemTagsCreatePayload' - title: Payload - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ItemTagsResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Create tag based on history_id - tags: - - histories - put: - operationId: update_api_histories__history_id__tags__tag_name__put - parameters: - - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - in: path - name: tag_name - required: true - schema: - title: Tag Name - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/ItemTagsCreatePayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ItemTagsResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Update tag based on history_id - tags: - - histories - /api/histories/{history_id}/unpublish: - put: - description: Removes this item from the published list and return the current - sharing status. - operationId: unpublish_api_histories__history_id__unpublish_put - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/SharingStatus' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Removes this item from the published list. - tags: - - histories - - histories - /api/histories/{history_id}/write_store: - post: - operationId: write_store_api_histories__history_id__write_store_post - parameters: - - description: The encoded database identifier of the History. - in: path - name: history_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/WriteStoreToPayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/AsyncTaskResultSummary' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Prepare history for export-style download and write to supplied URI. - tags: - - histories - - histories - /api/invocations: - get: - operationId: index_invocations_api_invocations_get - parameters: - - description: Return only invocations for this Workflow ID - in: query - name: workflow_id - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: Return only invocations for this Workflow ID - title: Workflow ID - - description: Return only invocations for this History ID - in: query - name: history_id - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: Return only invocations for this History ID - title: History ID - - description: Return only invocations for this Job ID - in: query - name: job_id - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: Return only invocations for this Job ID - title: Job ID - - description: Return invocations for this User ID. - in: query - name: user_id - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: Return invocations for this User ID. - title: User ID - - description: Sort Workflow Invocations by this attribute - in: query - name: sort_by - required: false - schema: - anyOf: - - $ref: '#/components/schemas/InvocationSortByEnum' - - type: 'null' - description: Sort Workflow Invocations by this attribute - title: Sort By - - description: Sort in descending order? - in: query - name: sort_desc - required: false - schema: - default: false - description: Sort in descending order? - title: Sort Descending - type: boolean - - description: Set to false to only include terminal Invocations. - in: query - name: include_terminal - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: true - description: Set to false to only include terminal Invocations. - title: Include Terminal - - description: Limit the number of invocations to return. - in: query - name: limit - required: false - schema: - anyOf: - - type: integer - - type: 'null' - description: Limit the number of invocations to return. - title: Limit - - description: Number of invocations to skip. - in: query - name: offset - required: false - schema: - anyOf: - - type: integer - - type: 'null' - description: Number of invocations to skip. - title: Offset - - description: Is provided workflow id for Workflow instead of StoredWorkflow? - in: query - name: instance - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: false - description: Is provided workflow id for Workflow instead of StoredWorkflow? - title: Instance - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Include details for individual invocation steps and populate - a steps attribute in the resulting dictionary. - in: query - name: step_details - required: false - schema: - default: false - description: Include details for individual invocation steps and populate - a steps attribute in the resulting dictionary. - title: Include step details - type: boolean - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - $ref: '#/components/schemas/WorkflowInvocationResponse' - title: Response Index Invocations Api Invocations Get - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get the list of a user's workflow invocations. - tags: - - workflows - - workflows - /api/invocations/from_store: - post: - description: Create invocation(s) from a supplied model store. - operationId: create_invocations_from_store_api_invocations_from_store_post - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - allOf: - - $ref: '#/components/schemas/CreateInvocationsFromStorePayload' - description: The values and serialization parameters for creating invocations - from a supplied model store. - title: Create invocations from store - required: true - responses: - '200': - content: - application/json: - schema: - items: - $ref: '#/components/schemas/WorkflowInvocationResponse' - title: Response Create Invocations From Store Api Invocations From - Store Post - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Create Invocations From Store - tags: - - workflows - - workflows - /api/invocations/steps/{step_id}: - get: - operationId: step_api_invocations_steps__step_id__get - parameters: - - description: The encoded database identifier of the WorkflowInvocationStep. - in: path - name: step_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/InvocationStep' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Show details of workflow invocation step. - tags: - - workflows - - workflows - /api/invocations/{invocation_id}: - delete: - operationId: cancel_invocation_api_invocations__invocation_id__delete - parameters: - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: Include details for individual invocation steps and populate - a steps attribute in the resulting dictionary. - in: query - name: step_details - required: false - schema: - default: false - description: Include details for individual invocation steps and populate - a steps attribute in the resulting dictionary. - title: Include step details - type: boolean - - description: "Populate the invocation step state with the job state instead\ - \ of the invocation step state.\n This will also produce one step\ - \ per job in mapping jobs to mimic the older behavior with respect to collections.\n\ - \ Partially scheduled steps may provide incomplete information and\ - \ the listed steps outputs\n are not the mapped over step outputs\ - \ but the individual job outputs." - in: query - name: legacy_job_state - required: false - schema: - default: false - description: "Populate the invocation step state with the job state instead\ - \ of the invocation step state.\n This will also produce one step\ - \ per job in mapping jobs to mimic the older behavior with respect to\ - \ collections.\n Partially scheduled steps may provide incomplete\ - \ information and the listed steps outputs\n are not the mapped\ - \ over step outputs but the individual job outputs." - title: Replace with job state - type: boolean - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/WorkflowInvocationResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Cancel the specified workflow invocation. - tags: - - workflows - - workflows - get: - operationId: show_invocation_api_invocations__invocation_id__get - parameters: - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: Include details for individual invocation steps and populate - a steps attribute in the resulting dictionary. - in: query - name: step_details - required: false - schema: - default: false - description: Include details for individual invocation steps and populate - a steps attribute in the resulting dictionary. - title: Include step details - type: boolean - - description: "Populate the invocation step state with the job state instead\ - \ of the invocation step state.\n This will also produce one step\ - \ per job in mapping jobs to mimic the older behavior with respect to collections.\n\ - \ Partially scheduled steps may provide incomplete information and\ - \ the listed steps outputs\n are not the mapped over step outputs\ - \ but the individual job outputs." - in: query - name: legacy_job_state - required: false - schema: - default: false - description: "Populate the invocation step state with the job state instead\ - \ of the invocation step state.\n This will also produce one step\ - \ per job in mapping jobs to mimic the older behavior with respect to\ - \ collections.\n Partially scheduled steps may provide incomplete\ - \ information and the listed steps outputs\n are not the mapped\ - \ over step outputs but the individual job outputs." - title: Replace with job state - type: boolean - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/WorkflowInvocationResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get detailed description of a workflow invocation. - tags: - - workflows - - workflows - /api/invocations/{invocation_id}/biocompute: - get: - deprecated: true - description: "The BioCompute Object endpoints are in beta - important details\ - \ such\nas how inputs and outputs are represented, how the workflow is encoded,\n\ - and how author and version information is encoded, and how URLs are\ngenerated\ - \ will very likely change in important ways over time.\n\n**Deprecation Notice**:\ - \ please use the asynchronous short_term_storage export system instead.\n\n\ - 1. call POST `api/invocations/{id}/prepare_store_download` with payload:\n\ - \ ```\n {\n model_store_format: bco.json\n }\n ```\n2.\ - \ Get `storageRequestId` from response and poll GET `api/short_term_storage/${storageRequestId}/ready`\ - \ until `SUCCESS`\n\n3. Get the resulting file with `api/short_term_storage/${storageRequestId}`" - operationId: export_invocation_bco_api_invocations__invocation_id__biocompute_get - parameters: - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - in: query - name: merge_history_metadata - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: false - title: Merge History Metadata - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return a BioCompute Object for the workflow invocation. - tags: - - workflows - - workflows - /api/invocations/{invocation_id}/biocompute/download: - get: - deprecated: true - description: "The BioCompute Object endpoints are in beta - important details\ - \ such\nas how inputs and outputs are represented, how the workflow is encoded,\n\ - and how author and version information is encoded, and how URLs are\ngenerated\ - \ will very likely change in important ways over time.\n\n**Deprecation Notice**:\ - \ please use the asynchronous short_term_storage export system instead.\n\n\ - 1. call POST `api/invocations/{id}/prepare_store_download` with payload:\n\ - \ ```\n {\n model_store_format: bco.json\n }\n ```\n2.\ - \ Get `storageRequestId` from response and poll GET `api/short_term_storage/${storageRequestId}/ready`\ - \ until `SUCCESS`\n\n3. Get the resulting file with `api/short_term_storage/${storageRequestId}`" - operationId: download_invocation_bco_api_invocations__invocation_id__biocompute_download_get - parameters: - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - in: query - name: merge_history_metadata - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: false - title: Merge History Metadata - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return a BioCompute Object for the workflow invocation as a file for - download. - tags: - - workflows - - workflows - /api/invocations/{invocation_id}/jobs_summary: - get: - description: 'Warning: We allow anyone to fetch job state information about - any object they - - can guess an encoded ID for - it isn''t considered protected data. This keeps - - polling IDs as part of state calculation for large histories and collections - as - - efficient as possible.' - operationId: invocation_jobs_summary_api_invocations__invocation_id__jobs_summary_get - parameters: - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/InvocationJobsResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get job state summary info aggregated across all current jobs of the - workflow invocation. - tags: - - workflows - - workflows - /api/invocations/{invocation_id}/prepare_store_download: - post: - operationId: prepare_store_download_api_invocations__invocation_id__prepare_store_download_post - parameters: - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/PrepareStoreDownloadPayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/AsyncFile' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Prepare a workflow invocation export-style download. - tags: - - workflows - - workflows - /api/invocations/{invocation_id}/report: - get: - operationId: show_invocation_report_api_invocations__invocation_id__report_get - parameters: - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/InvocationReport' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get JSON summarizing invocation for reporting. - tags: - - workflows - - workflows - /api/invocations/{invocation_id}/report.pdf: - get: - operationId: show_invocation_report_pdf_api_invocations__invocation_id__report_pdf_get - parameters: - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get PDF summarizing invocation for reporting. - tags: - - workflows - - workflows - /api/invocations/{invocation_id}/step_jobs_summary: - get: - description: 'Warning: We allow anyone to fetch job state information about - any object they - - can guess an encoded ID for - it isn''t considered protected data. This keeps - - polling IDs as part of state calculation for large histories and collections - as - - efficient as possible.' - operationId: invocation_step_jobs_summary_api_invocations__invocation_id__step_jobs_summary_get - parameters: - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - anyOf: - - $ref: '#/components/schemas/InvocationStepJobsResponseStepModel' - - $ref: '#/components/schemas/InvocationStepJobsResponseJobModel' - - $ref: '#/components/schemas/InvocationStepJobsResponseCollectionJobsModel' - title: Response Invocation Step Jobs Summary Api Invocations Invocation - Id Step Jobs Summary Get - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get job state summary info aggregated per step of the workflow invocation. - tags: - - workflows - - workflows - /api/invocations/{invocation_id}/steps/{step_id}: - get: - description: An alias for `GET /api/invocations/steps/{step_id}`. `invocation_id` - is ignored. - operationId: invocation_step_api_invocations__invocation_id__steps__step_id__get - parameters: - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The encoded database identifier of the WorkflowInvocationStep. - in: path - name: step_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/InvocationStep' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Show details of workflow invocation step. - tags: - - workflows - - workflows - put: - operationId: update_invocation_step_api_invocations__invocation_id__steps__step_id__put - parameters: - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The encoded database identifier of the WorkflowInvocationStep. - in: path - name: step_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/InvocationUpdatePayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/InvocationStep' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Update state of running workflow step invocation - still very nebulous - but this would be for stuff like confirming paused steps can proceed etc. - tags: - - workflows - - workflows - /api/invocations/{invocation_id}/write_store: - post: - operationId: write_store_api_invocations__invocation_id__write_store_post - parameters: - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/WriteInvocationStoreToPayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/AsyncTaskResultSummary' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Prepare a workflow invocation export-style download and write to supplied - URI. - tags: - - workflows - - workflows - /api/job_lock: - get: - description: Get job lock status. - operationId: job_lock_status_api_job_lock_get - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/JobLock' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Job Lock Status - tags: - - job_lock - put: - description: Set job lock status. - operationId: update_job_lock_api_job_lock_put - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/JobLock' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/JobLock' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Update Job Lock - tags: - - job_lock - /api/jobs: - get: - operationId: index_api_jobs_get - parameters: - - description: If true, and requester is an admin, will return external job - id and user email. This is only available to admins. - in: query - name: user_details - required: false - schema: - default: false - description: If true, and requester is an admin, will return external job - id and user email. This is only available to admins. - title: Include user details - type: boolean - - description: an encoded user id to restrict query to, must be own id if not - admin user - in: query - name: user_id - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: an encoded user id to restrict query to, must be own id if - not admin user - title: User ID - - description: Determines columns to return. Defaults to 'collection'. - in: query - name: view - required: false - schema: - allOf: - - $ref: '#/components/schemas/JobIndexViewEnum' - default: collection - description: Determines columns to return. Defaults to 'collection'. - title: View - - description: Limit listing of jobs to those that are updated after specified - date (e.g. '2014-01-01') - in: query - name: date_range_min - required: false - schema: - anyOf: - - format: date-time - type: string - - format: date - type: string - - type: 'null' - description: Limit listing of jobs to those that are updated after specified - date (e.g. '2014-01-01') - title: Date Range Minimum - - description: Limit listing of jobs to those that are updated before specified - date (e.g. '2014-01-01') - in: query - name: date_range_max - required: false - schema: - anyOf: - - format: date-time - type: string - - format: date - type: string - - type: 'null' - description: Limit listing of jobs to those that are updated before specified - date (e.g. '2014-01-01') - title: Date Range Maximum - - description: Limit listing of jobs to those that match the history_id. If - none, jobs from any history may be returned. - in: query - name: history_id - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: Limit listing of jobs to those that match the history_id. If - none, jobs from any history may be returned. - title: History ID - - description: Limit listing of jobs to those that match the specified workflow - ID. If none, jobs from any workflow (or from no workflows) may be returned. - in: query - name: workflow_id - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: Limit listing of jobs to those that match the specified workflow - ID. If none, jobs from any workflow (or from no workflows) may be returned. - title: Workflow ID - - description: Limit listing of jobs to those that match the specified workflow - invocation ID. If none, jobs from any workflow invocation (or from no workflows) - may be returned. - in: query - name: invocation_id - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: Limit listing of jobs to those that match the specified workflow - invocation ID. If none, jobs from any workflow invocation (or from no - workflows) may be returned. - title: Invocation ID - - description: Limit listing of jobs to those that match the specified implicit - collection job ID. If none, jobs from any implicit collection execution - (or from no implicit collection execution) may be returned. - in: query - name: implicit_collection_jobs_id - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: Limit listing of jobs to those that match the specified implicit - collection job ID. If none, jobs from any implicit collection execution - (or from no implicit collection execution) may be returned. - title: Implicit Collection Jobs ID - - description: Sort results by specified field. - in: query - name: order_by - required: false - schema: - allOf: - - $ref: '#/components/schemas/JobIndexSortByEnum' - default: update_time - description: Sort results by specified field. - title: Sort By - - description: 'A mix of free text and GitHub-style tags used to filter the - index operation. - - - ## Query Structure - - - GitHub-style filter tags (not be confused with Galaxy tags) are tags of - the form - - `:` or `:''''`. - The tag name - - *generally* (but not exclusively) corresponds to the name of an attribute - on the model - - being indexed (i.e. a column in the database). - - - If the tag is quoted, the attribute will be filtered exactly. If the tag - is unquoted, - - generally a partial match will be used to filter the query (i.e. in terms - of the implementation - - this means the database operation `ILIKE` will typically be used). - - - Once the tagged filters are extracted from the search query, the remaining - text is just - - used to search various documented attributes of the object. - - - ## GitHub-style Tags Available - - - `user` - - : The user email of the user that executed the Job. (The tag `u` can be - used a short hand alias for this tag to filter on this attribute.) - - - `tool_id` - - : The tool ID corresponding to the job. (The tag `t` can be used a short - hand alias for this tag to filter on this attribute.) - - - `runner` - - : The job runner name used to execute the job. (The tag `r` can be used - a short hand alias for this tag to filter on this attribute.) This tag is - only available for requests using admin keys and/or sessions. - - - `handler` - - : The job handler name used to execute the job. (The tag `h` can be used - a short hand alias for this tag to filter on this attribute.) This tag is - only available for requests using admin keys and/or sessions. - - - ## Free Text - - - Free text search terms will be searched against the following attributes - of the - - Jobs: `user`, `tool`, `handler`, `runner`. - - - ' - in: query - name: search - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: 'A mix of free text and GitHub-style tags used to filter the - index operation. - - - ## Query Structure - - - GitHub-style filter tags (not be confused with Galaxy tags) are tags of - the form - - `:` or `:''''`. - The tag name - - *generally* (but not exclusively) corresponds to the name of an attribute - on the model - - being indexed (i.e. a column in the database). - - - If the tag is quoted, the attribute will be filtered exactly. If the tag - is unquoted, - - generally a partial match will be used to filter the query (i.e. in terms - of the implementation - - this means the database operation `ILIKE` will typically be used). - - - Once the tagged filters are extracted from the search query, the remaining - text is just - - used to search various documented attributes of the object. - - - ## GitHub-style Tags Available - - - `user` - - : The user email of the user that executed the Job. (The tag `u` can be - used a short hand alias for this tag to filter on this attribute.) - - - `tool_id` - - : The tool ID corresponding to the job. (The tag `t` can be used a short - hand alias for this tag to filter on this attribute.) - - - `runner` - - : The job runner name used to execute the job. (The tag `r` can be used - a short hand alias for this tag to filter on this attribute.) This tag - is only available for requests using admin keys and/or sessions. - - - `handler` - - : The job handler name used to execute the job. (The tag `h` can be used - a short hand alias for this tag to filter on this attribute.) This tag - is only available for requests using admin keys and/or sessions. - - - ## Free Text - - - Free text search terms will be searched against the following attributes - of the - - Jobs: `user`, `tool`, `handler`, `runner`. - - - ' - title: Search query. - - description: Maximum number of jobs to return. - in: query - name: limit - required: false - schema: - default: 500 - description: Maximum number of jobs to return. - title: Limit - type: integer - - description: Return jobs starting from this specified position. For example, - if ``limit`` is set to 100 and ``offset`` to 200, jobs 200-299 will be returned. - in: query - name: offset - required: false - schema: - default: 0 - description: Return jobs starting from this specified position. For example, - if ``limit`` is set to 100 and ``offset`` to 200, jobs 200-299 will be - returned. - title: Offset - type: integer - - description: A list or comma-separated list of states to filter job query - on. If unspecified, jobs of any state may be returned. - in: query - name: state - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: A list or comma-separated list of states to filter job query - on. If unspecified, jobs of any state may be returned. - title: States - - description: Limit listing of jobs to those that match one of the included - tool_ids. If none, all are returned - in: query - name: tool_id - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: Limit listing of jobs to those that match one of the included - tool_ids. If none, all are returned - title: Tool ID(s) - - description: Limit listing of jobs to those that match one of the included - tool ID sql-like patterns. If none, all are returned - in: query - name: tool_id_like - required: false - schema: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: Limit listing of jobs to those that match one of the included - tool ID sql-like patterns. If none, all are returned - title: Tool ID Pattern(s) - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - anyOf: - - $ref: '#/components/schemas/ShowFullJobResponse' - - $ref: '#/components/schemas/EncodedJobDetails' - - $ref: '#/components/schemas/JobSummary' - title: Response Index Api Jobs Get - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Index - tags: - - jobs - - jobs - /api/jobs/search: - post: - description: 'This method is designed to scan the list of previously run jobs - and find records of jobs that had - - the exact some input parameters and datasets. This can be used to minimize - the amount of repeated work, and simply - - recycle the old results.' - operationId: search_jobs_api_jobs_search_post - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - allOf: - - $ref: '#/components/schemas/SearchJobsPayload' - description: The values to search an Job - title: Search job - required: true - responses: - '200': - content: - application/json: - schema: - items: - $ref: '#/components/schemas/EncodedJobDetails' - title: Response Search Jobs Api Jobs Search Post - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return jobs for current user - tags: - - jobs - - jobs - /api/jobs/{job_id}: - delete: - operationId: cancel_job_api_jobs__job_id__delete - parameters: - - description: The ID of the job - in: path - name: job_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/DeleteJobPayload' - - type: 'null' - description: The values to delete/cancel a job - title: Delete/cancel job - responses: - '200': - content: - application/json: - schema: - title: Response Cancel Job Api Jobs Job Id Delete - type: boolean - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Cancels specified job - tags: - - jobs - - jobs - get: - operationId: show_job_api_jobs__job_id__get - parameters: - - description: The ID of the job - in: path - name: job_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: Show extra information. - in: query - name: full - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: false - description: Show extra information. - title: Full show - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/ShowFullJobResponse' - - $ref: '#/components/schemas/EncodedJobDetails' - title: Response Show Job Api Jobs Job Id Get - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return dictionary containing description of job data. - tags: - - jobs - - jobs - /api/jobs/{job_id}/common_problems: - get: - operationId: check_common_problems_api_jobs__job_id__common_problems_get - parameters: - - description: The ID of the job - in: path - name: job_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/JobInputSummary' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Check inputs and job for common potential problems to aid in error - reporting - tags: - - jobs - - jobs - /api/jobs/{job_id}/destination_params: - get: - operationId: destination_params_job_api_jobs__job_id__destination_params_get - parameters: - - description: The ID of the job - in: path - name: job_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/JobDestinationParams' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return destination parameters for specified job. - tags: - - jobs - - jobs - /api/jobs/{job_id}/error: - post: - operationId: report_error_api_jobs__job_id__error_post - parameters: - - description: The ID of the job - in: path - name: job_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - allOf: - - $ref: '#/components/schemas/ReportJobErrorPayload' - description: The values to report an Error - title: Report error - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/JobErrorSummary' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Submits a bug report via the API. - tags: - - jobs - - jobs - /api/jobs/{job_id}/inputs: - get: - operationId: get_inputs_api_jobs__job_id__inputs_get - parameters: - - description: The ID of the job - in: path - name: job_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - $ref: '#/components/schemas/JobInputAssociation' - title: Response Get Inputs Api Jobs Job Id Inputs Get - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns input datasets created by a job. - tags: - - jobs - - jobs - /api/jobs/{job_id}/metrics: - get: - operationId: get_metrics_api_jobs__job_id__metrics_get - parameters: - - description: The ID of the job - in: path - name: job_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - deprecated: true - description: Whether this dataset belongs to a history (HDA) or a library - (LDDA). - in: query - name: hda_ldda - required: false - schema: - anyOf: - - $ref: '#/components/schemas/DatasetSourceType' - - type: 'null' - default: hda - description: Whether this dataset belongs to a history (HDA) or a library - (LDDA). - title: HDA or LDDA - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - anyOf: - - $ref: '#/components/schemas/JobMetric' - - type: 'null' - title: Response Get Metrics Api Jobs Job Id Metrics Get - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return job metrics for specified job. - tags: - - jobs - - jobs - /api/jobs/{job_id}/oidc-tokens: - get: - description: Allows remote job running mechanisms to get a fresh OIDC token - that can be used on remote side to authorize user. It is not meant to represent - part of Galaxy's stable, user facing API - operationId: get_token_api_jobs__job_id__oidc_tokens_get - parameters: - - in: path - name: job_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Job Id - type: string - - description: A key used to authenticate this request as acting onbehalf or - a job runner for the specified job - in: query - name: job_key - required: true - schema: - description: A key used to authenticate this request as acting onbehalf - or a job runner for the specified job - title: Job Key - type: string - - description: OIDC provider name - in: query - name: provider - required: true - schema: - description: OIDC provider name - title: Provider - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - text/plain: - schema: - type: string - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get a fresh OIDC token - tags: - - remote files - - remote files - - oidc_tokens - /api/jobs/{job_id}/outputs: - get: - operationId: get_outputs_api_jobs__job_id__outputs_get - parameters: - - description: The ID of the job - in: path - name: job_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - $ref: '#/components/schemas/JobOutputAssociation' - title: Response Get Outputs Api Jobs Job Id Outputs Get - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns output datasets created by a job. - tags: - - jobs - - jobs - /api/jobs/{job_id}/parameters_display: - get: - description: 'Resolve parameters as a list for nested display. - - This API endpoint is unstable and tied heavily to Galaxy''s JS client code, - - this endpoint will change frequently.' - operationId: resolve_parameters_display_api_jobs__job_id__parameters_display_get - parameters: - - description: The ID of the job - in: path - name: job_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - deprecated: true - description: Whether this dataset belongs to a history (HDA) or a library - (LDDA). - in: query - name: hda_ldda - required: false - schema: - anyOf: - - $ref: '#/components/schemas/DatasetSourceType' - - type: 'null' - default: hda - description: Whether this dataset belongs to a history (HDA) or a library - (LDDA). - title: HDA or LDDA - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/JobDisplayParametersSummary' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Resolve parameters as a list for nested display. - tags: - - jobs - - jobs - /api/jobs/{job_id}/resume: - put: - operationId: resume_paused_job_api_jobs__job_id__resume_put - parameters: - - description: The ID of the job - in: path - name: job_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - $ref: '#/components/schemas/JobOutputAssociation' - title: Response Resume Paused Job Api Jobs Job Id Resume Put - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Resumes a paused job. - tags: - - jobs - - jobs - /api/libraries: - get: - description: Returns a list of summary data for all libraries. - operationId: index_api_libraries_get - parameters: - - description: Whether to include deleted libraries in the result. - in: query - name: deleted - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - description: Whether to include deleted libraries in the result. - title: Display deleted - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/LibrarySummaryList' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns a list of summary data for all libraries. - tags: - - libraries - - libraries - post: - description: Creates a new library and returns its summary information. Currently, - only admin users can create libraries. - operationId: create_api_libraries_post - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/CreateLibraryPayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/LibrarySummary' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Creates a new library and returns its summary information. - tags: - - libraries - - libraries - /api/libraries/deleted: - get: - description: Returns a list of summary data for all libraries marked as deleted. - operationId: index_deleted_api_libraries_deleted_get - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/LibrarySummaryList' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns a list of summary data for all libraries marked as deleted. - tags: - - libraries - - libraries - /api/libraries/from_store: - post: - operationId: create_from_store_api_libraries_from_store_post - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/CreateLibrariesFromStore' - required: true - responses: - '200': - content: - application/json: - schema: - items: - $ref: '#/components/schemas/LibrarySummary' - title: Response Create From Store Api Libraries From Store Post - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Create libraries from a model store. - tags: - - libraries - - libraries - /api/libraries/{id}: - delete: - description: 'Marks the specified library as deleted (or undeleted). - - Currently, only admin users can delete or restore libraries.' - operationId: delete_api_libraries__id__delete - parameters: - - description: The ID of the Library. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: Whether to restore a deleted library. - in: query - name: undelete - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - description: Whether to restore a deleted library. - title: Undelete - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/DeleteLibraryPayload' - - type: 'null' - title: Payload - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/LibrarySummary' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Marks the specified library as deleted (or undeleted). - tags: - - libraries - - libraries - get: - description: Returns summary information about a particular library. - operationId: show_api_libraries__id__get - parameters: - - description: The ID of the Library. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/LibrarySummary' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns summary information about a particular library. - tags: - - libraries - - libraries - patch: - description: Updates the information of an existing library. - operationId: update_api_libraries__id__patch - parameters: - - description: The ID of the Library. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/UpdateLibraryPayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/LibrarySummary' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Updates the information of an existing library. - tags: - - libraries - - libraries - /api/libraries/{id}/permissions: - get: - description: 'Gets the current or available permissions of a particular library. - - The results can be paginated and additionally filtered by a query.' - operationId: get_permissions_api_libraries__id__permissions_get - parameters: - - description: The ID of the Library. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The scope of the permissions to retrieve. Either the `current` - permissions or the `available`. - in: query - name: scope - required: false - schema: - anyOf: - - $ref: '#/components/schemas/LibraryPermissionScope' - - type: 'null' - description: The scope of the permissions to retrieve. Either the `current` - permissions or the `available`. - title: Scope - - description: Indicates whether the roles available for the library access - are requested. - in: query - name: is_library_access - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - description: Indicates whether the roles available for the library access - are requested. - title: Is Library Access - - description: The page number to retrieve when paginating the available roles. - in: query - name: page - required: false - schema: - default: 1 - description: The page number to retrieve when paginating the available roles. - title: Page - type: integer - - description: The maximum number of permissions per page when paginating. - in: query - name: page_limit - required: false - schema: - default: 10 - description: The maximum number of permissions per page when paginating. - title: Page Limit - type: integer - - description: Optional search text to retrieve only the roles matching this - query. - in: query - name: q - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Optional search text to retrieve only the roles matching this - query. - title: Query - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/LibraryCurrentPermissions' - - $ref: '#/components/schemas/LibraryAvailablePermissions' - title: Response Get Permissions Api Libraries Id Permissions Get - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Gets the current or available permissions of a particular library. - tags: - - libraries - - libraries - post: - description: Sets the permissions to access and manipulate a library. - operationId: set_permissions_api_libraries__id__permissions_post - parameters: - - description: The ID of the Library. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: Indicates what action should be performed on the Library. - in: query - name: action - required: false - schema: - anyOf: - - $ref: '#/components/schemas/LibraryPermissionAction' - - type: 'null' - description: Indicates what action should be performed on the Library. - title: Action - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/LibraryPermissionsPayload' - - $ref: '#/components/schemas/LegacyLibraryPermissionsPayload' - title: Payload - required: true - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/LibraryLegacySummary' - - $ref: '#/components/schemas/LibraryCurrentPermissions' - title: Response Set Permissions Api Libraries Id Permissions Post - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Sets the permissions to access and manipulate a library. - tags: - - libraries - - libraries - /api/licenses: - get: - description: Returns an index with all the available [SPDX licenses](https://spdx.org/licenses/). - operationId: index_api_licenses_get - responses: - '200': - content: - application/json: - schema: - items: - $ref: '#/components/schemas/LicenseMetadataModel' - title: Response Index Api Licenses Get - type: array - description: List of SPDX licenses - security: [] - summary: Lists all available SPDX licenses - tags: - - licenses - - licenses - /api/licenses/{id}: - get: - description: 'Returns the license metadata associated with the given - - [SPDX license short ID](https://spdx.github.io/spdx-spec/appendix-I-SPDX-license-list/).' - operationId: get_api_licenses__id__get - parameters: - - description: The [SPDX license short identifier](https://spdx.github.io/spdx-spec/appendix-I-SPDX-license-list/) - in: path - name: id - required: true - schema: - description: The [SPDX license short identifier](https://spdx.github.io/spdx-spec/appendix-I-SPDX-license-list/) - examples: - - Apache-2.0 - title: SPDX license short ID - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/LicenseMetadataModel' - description: SPDX license metadata - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: [] - summary: Gets the SPDX license metadata associated with the short identifier - tags: - - licenses - - licenses - /api/metrics: - post: - description: Record any metrics sent and return some status object. - operationId: create_api_metrics_post - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/CreateMetricsPayload' - required: true - responses: - '200': - content: - application/json: - schema: - title: Response Create Api Metrics Post - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Records a collection of metrics. - tags: - - metrics - - metrics - /api/notifications: - delete: - operationId: delete_user_notifications_api_notifications_delete - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/NotificationsBatchRequest' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/NotificationsBatchUpdateResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Deletes a list of notifications received by the user in a single request. - tags: - - notifications - - notifications - get: - description: 'Anonymous users cannot receive personal notifications, only broadcasted - notifications. - - - You can use the `limit` and `offset` parameters to paginate through the notifications.' - operationId: get_user_notifications_api_notifications_get - parameters: - - in: query - name: limit - required: false - schema: - anyOf: - - type: integer - - type: 'null' - default: 20 - title: Limit - - in: query - name: offset - required: false - schema: - anyOf: - - type: integer - - type: 'null' - title: Offset - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/UserNotificationListResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns the list of notifications associated with the user. - tags: - - notifications - - notifications - post: - description: Sends a notification to a list of recipients (users, groups or - roles). - operationId: send_notification_api_notifications_post - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/NotificationCreateRequest' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/NotificationCreatedResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Sends a notification to a list of recipients (users, groups or roles). - tags: - - notifications - - notifications - put: - operationId: update_user_notifications_api_notifications_put - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/UserNotificationsBatchUpdateRequest' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/NotificationsBatchUpdateResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Updates a list of notifications with the requested values in a single - request. - tags: - - notifications - - notifications - /api/notifications/broadcast: - get: - description: Only Admin users can access inactive notifications (scheduled or - recently expired). - operationId: get_all_broadcasted_api_notifications_broadcast_get - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/BroadcastNotificationListResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns all currently active broadcasted notifications. - tags: - - notifications - - notifications - post: - description: 'Broadcasted notifications are a special kind of notification that - are always accessible to all users, including anonymous users. - - They are typically used to display important information such as maintenance - windows or new features. - - These notifications are displayed differently from regular notifications, - usually in a banner at the top or bottom of the page. - - - Broadcasted notifications can include action links that are displayed as buttons. - - This allows users to easily perform tasks such as filling out surveys, accepting - legal agreements, or accessing new tutorials. - - - Some key features of broadcasted notifications include: - - - They are not associated with a specific user, so they cannot be deleted - or marked as read. - - - They can be scheduled to be displayed in the future or to expire after a - certain time. - - - By default, broadcasted notifications are published immediately and expire - six months after publication. - - - Only admins can create, edit, reschedule, or expire broadcasted notifications - as needed.' - operationId: broadcast_notification_api_notifications_broadcast_post - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/BroadcastNotificationCreateRequest' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/NotificationCreatedResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Broadcasts a notification to every user in the system. - tags: - - notifications - - notifications - /api/notifications/broadcast/{notification_id}: - get: - description: Only Admin users can access inactive notifications (scheduled or - recently expired). - operationId: get_broadcasted_api_notifications_broadcast__notification_id__get - parameters: - - description: The ID of the Notification. - in: path - name: notification_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/BroadcastNotificationResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns the information of a specific broadcasted notification. - tags: - - notifications - - notifications - put: - description: Only Admins can update broadcasted notifications. This is useful - to reschedule, edit or expire broadcasted notifications. - operationId: update_broadcasted_notification_api_notifications_broadcast__notification_id__put - parameters: - - description: The ID of the Notification. - in: path - name: notification_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/NotificationBroadcastUpdateRequest' - required: true - responses: - '204': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Updates the state of a broadcasted notification. - tags: - - notifications - - notifications - /api/notifications/preferences: - get: - description: Anonymous users cannot have notification preferences. They will - receive only broadcasted notifications. - operationId: get_notification_preferences_api_notifications_preferences_get - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/UserNotificationPreferences' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns the current user's preferences for notifications. - tags: - - notifications - - notifications - put: - description: 'Anonymous users cannot have notification preferences. They will - receive only broadcasted notifications. - - - - Can be used to completely enable/disable notifications for a particular - type (category) - - or to enable/disable a particular channel on each category.' - operationId: update_notification_preferences_api_notifications_preferences_put - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/UpdateUserNotificationPreferencesRequest' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/UserNotificationPreferences' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Updates the user's preferences for notifications. - tags: - - notifications - - notifications - /api/notifications/status: - get: - description: Anonymous users cannot receive personal notifications, only broadcasted - notifications. - operationId: get_notifications_status_api_notifications_status_get - parameters: - - in: query - name: since - required: true - schema: - format: date-time - title: Since - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/NotificationStatusSummary' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns the current status summary of the user's notifications since - a particular date. - tags: - - notifications - - notifications - /api/notifications/{notification_id}: - delete: - description: 'When a notification is deleted, it is not immediately removed - from the database, but marked as deleted. - - - - It will not be returned in the list of notifications, but admins can still - access it as long as it is not expired. - - - It will be eventually removed from the database by a background task after - the expiration time. - - - Deleted notifications will be permanently deleted when the expiration time - is reached.' - operationId: delete_user_notification_api_notifications__notification_id__delete - parameters: - - description: The ID of the Notification. - in: path - name: notification_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '204': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Deletes a notification received by the user. - tags: - - notifications - - notifications - get: - operationId: show_notification_api_notifications__notification_id__get - parameters: - - description: The ID of the Notification. - in: path - name: notification_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/UserNotificationResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Displays information about a notification received by the user. - tags: - - notifications - - notifications - put: - operationId: update_user_notification_api_notifications__notification_id__put - parameters: - - description: The ID of the Notification. - in: path - name: notification_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/UserNotificationUpdateRequest' - required: true - responses: - '204': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Updates the state of a notification received by the user. - tags: - - notifications - - notifications - /api/object_stores: - get: - operationId: index_api_object_stores_get - parameters: - - description: Restrict index query to user selectable object stores, the current - implementation requires this to be true. - in: query - name: selectable - required: false - schema: - default: false - description: Restrict index query to user selectable object stores, the - current implementation requires this to be true. - title: Selectable - type: boolean - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - $ref: '#/components/schemas/ConcreteObjectStoreModel' - title: Response Index Api Object Stores Get - type: array - description: A list of the configured object stores. - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get a list of (currently only concrete) object stores configured with - this Galaxy instance. - tags: - - object sstore - - object sstore - /api/object_stores/{object_store_id}: - get: - operationId: show_info_api_object_stores__object_store_id__get - parameters: - - description: The concrete object store ID. - in: path - name: object_store_id - required: true - schema: - description: The concrete object store ID. - title: Concrete Object Store ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ConcreteObjectStoreModel' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get information about a concrete object store configured with Galaxy. - tags: - - object sstore - - object sstore - /api/pages: - get: - description: Get a list with summary information of all Pages available to the - user. - operationId: index_api_pages_get - parameters: - - description: Whether to include deleted pages in the result. - in: query - name: deleted - required: false - schema: - default: false - description: Whether to include deleted pages in the result. - title: Display deleted - type: boolean - - in: query - name: user_id - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - title: Encoded user ID to restrict query to, must be own id if not an admin - user - - in: query - name: show_published - required: false - schema: - default: true - title: Include published pages. - type: boolean - - in: query - name: show_shared - required: false - schema: - default: false - title: Include pages shared with authenticated user. - type: boolean - - description: Sort page index by this specified attribute on the page model - in: query - name: sort_by - required: false - schema: - default: update_time - description: Sort page index by this specified attribute on the page model - enum: - - update_time - - title - - username - title: Sort attribute - type: string - - description: Sort in descending order? - in: query - name: sort_desc - required: false - schema: - default: false - description: Sort in descending order? - title: Sort Descending - type: boolean - - in: query - name: limit - required: false - schema: - default: 100 - exclusiveMaximum: 1000 - title: Limit number of queries. - type: integer - - in: query - name: offset - required: false - schema: - default: 0 - title: Number of pages to skip in sorted query (to enable pagination). - type: integer - - description: 'A mix of free text and GitHub-style tags used to filter the - index operation. - - - ## Query Structure - - - GitHub-style filter tags (not be confused with Galaxy tags) are tags of - the form - - `:` or `:''''`. - The tag name - - *generally* (but not exclusively) corresponds to the name of an attribute - on the model - - being indexed (i.e. a column in the database). - - - If the tag is quoted, the attribute will be filtered exactly. If the tag - is unquoted, - - generally a partial match will be used to filter the query (i.e. in terms - of the implementation - - this means the database operation `ILIKE` will typically be used). - - - Once the tagged filters are extracted from the search query, the remaining - text is just - - used to search various documented attributes of the object. - - - ## GitHub-style Tags Available - - - `title` - - : The page''s title. - - - `slug` - - : The page''s slug. (The tag `s` can be used a short hand alias for this - tag to filter on this attribute.) - - - `tag` - - : The page''s tags. (The tag `t` can be used a short hand alias for this - tag to filter on this attribute.) - - - `user` - - : The page''s owner''s username. (The tag `u` can be used a short hand alias - for this tag to filter on this attribute.) - - - ## Free Text - - - Free text search terms will be searched against the following attributes - of the - - Pages: `title`, `slug`, `tag`, `user`. - - - ' - in: query - name: search - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: 'A mix of free text and GitHub-style tags used to filter the - index operation. - - - ## Query Structure - - - GitHub-style filter tags (not be confused with Galaxy tags) are tags of - the form - - `:` or `:''''`. - The tag name - - *generally* (but not exclusively) corresponds to the name of an attribute - on the model - - being indexed (i.e. a column in the database). - - - If the tag is quoted, the attribute will be filtered exactly. If the tag - is unquoted, - - generally a partial match will be used to filter the query (i.e. in terms - of the implementation - - this means the database operation `ILIKE` will typically be used). - - - Once the tagged filters are extracted from the search query, the remaining - text is just - - used to search various documented attributes of the object. - - - ## GitHub-style Tags Available - - - `title` - - : The page''s title. - - - `slug` - - : The page''s slug. (The tag `s` can be used a short hand alias for this - tag to filter on this attribute.) - - - `tag` - - : The page''s tags. (The tag `t` can be used a short hand alias for this - tag to filter on this attribute.) - - - `user` - - : The page''s owner''s username. (The tag `u` can be used a short hand - alias for this tag to filter on this attribute.) - - - ## Free Text - - - Free text search terms will be searched against the following attributes - of the - - Pages: `title`, `slug`, `tag`, `user`. - - - ' - title: Search query. - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/PageSummaryList' - description: A list with summary page information. - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Lists all Pages viewable by the user. - tags: - - pages - - pages - post: - description: Get a list with details of all Pages available to the user. - operationId: create_api_pages_post - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/CreatePagePayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/PageSummary' - description: The page summary information. - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Create a page and return summary information. - tags: - - pages - - pages - /api/pages/{id}: - delete: - description: Marks the Page with the given ID as deleted. - operationId: delete_api_pages__id__delete - parameters: - - description: The ID of the Page. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '204': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Marks the specific Page as deleted. - tags: - - pages - - pages - get: - description: Return summary information about a specific Page and the content - of the last revision. - operationId: show_api_pages__id__get - parameters: - - description: The ID of the Page. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/PageDetails' - description: The page summary information. - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return a page summary and the content of the last revision. - tags: - - pages - - pages - /api/pages/{id}.pdf: - get: - description: 'Return a PDF document of the last revision of the Page. - - - This feature may not be available in this Galaxy.' - operationId: show_pdf_api_pages__id__pdf_get - parameters: - - description: The ID of the Page. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/pdf: {} - description: PDF document with the last revision of the page. - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - '501': - description: PDF conversion service not available. - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return a PDF document of the last revision of the Page. - tags: - - pages - - pages - /api/pages/{id}/disable_link_access: - put: - description: Makes this item inaccessible by a URL link and return the current - sharing status. - operationId: disable_link_access_api_pages__id__disable_link_access_put - parameters: - - description: The ID of the Page. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/SharingStatus' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Makes this item inaccessible by a URL link. - tags: - - pages - - pages - /api/pages/{id}/enable_link_access: - put: - description: Makes this item accessible by a URL link and return the current - sharing status. - operationId: enable_link_access_api_pages__id__enable_link_access_put - parameters: - - description: The ID of the Page. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/SharingStatus' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Makes this item accessible by a URL link. - tags: - - pages - - pages - /api/pages/{id}/prepare_download: - post: - description: 'Return a STS download link for this page to be downloaded as a - PDF. - - - This feature may not be available in this Galaxy.' - operationId: prepare_pdf_api_pages__id__prepare_download_post - parameters: - - description: The ID of the Page. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/AsyncFile' - description: Short term storage reference for async monitoring of this download. - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - '501': - description: PDF conversion service not available. - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return a PDF document of the last revision of the Page. - tags: - - pages - - pages - /api/pages/{id}/publish: - put: - description: Makes this item publicly available by a URL link and return the - current sharing status. - operationId: publish_api_pages__id__publish_put - parameters: - - description: The ID of the Page. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/SharingStatus' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Makes this item public and accessible by a URL link. - tags: - - pages - - pages - /api/pages/{id}/share_with_users: - put: - description: Shares this item with specific users and return the current sharing - status. - operationId: share_with_users_api_pages__id__share_with_users_put - parameters: - - description: The ID of the Page. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/ShareWithPayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ShareWithStatus' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Share this item with specific users. - tags: - - pages - - pages - /api/pages/{id}/sharing: - get: - description: Return the sharing status of the item. - operationId: sharing_api_pages__id__sharing_get - parameters: - - description: The ID of the Page. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/SharingStatus' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get the current sharing status of the given Page. - tags: - - pages - - pages - /api/pages/{id}/slug: - put: - description: Sets a new slug to access this item by URL. The new slug must be - unique. - operationId: set_slug_api_pages__id__slug_put - parameters: - - description: The ID of the Page. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/SetSlugPayload' - required: true - responses: - '204': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Set a new slug for this shared item. - tags: - - pages - - pages - /api/pages/{id}/unpublish: - put: - description: Removes this item from the published list and return the current - sharing status. - operationId: unpublish_api_pages__id__unpublish_put - parameters: - - description: The ID of the Page. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/SharingStatus' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Removes this item from the published list. - tags: - - pages - - pages - /api/quotas: - get: - description: Displays a list with information of quotas that are currently active. - operationId: index_api_quotas_get - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/QuotaSummaryList' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Displays a list with information of quotas that are currently active. - tags: - - quotas - - quotas - post: - description: Creates a new quota. - operationId: create_api_quotas_post - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/CreateQuotaParams' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/CreateQuotaResult' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Creates a new quota. - tags: - - quotas - - quotas - /api/quotas/deleted: - get: - description: Displays a list with information of quotas that have been deleted. - operationId: index_deleted_api_quotas_deleted_get - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/QuotaSummaryList' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Displays a list with information of quotas that have been deleted. - tags: - - quotas - - quotas - /api/quotas/deleted/{id}: - get: - description: Displays details on a particular quota that has been deleted. - operationId: deleted_quota_api_quotas_deleted__id__get - parameters: - - description: The ID of the Quota. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/QuotaDetails' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Displays details on a particular quota that has been deleted. - tags: - - quotas - - quotas - /api/quotas/deleted/{id}/undelete: - post: - description: Restores a previously deleted quota. - operationId: undelete_api_quotas_deleted__id__undelete_post - parameters: - - description: The ID of the Quota. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - title: Response Undelete Api Quotas Deleted Id Undelete Post - type: string - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Restores a previously deleted quota. - tags: - - quotas - - quotas - /api/quotas/{id}: - delete: - description: Deletes an existing quota. - operationId: delete_api_quotas__id__delete - parameters: - - description: The ID of the Quota. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - allOf: - - $ref: '#/components/schemas/DeleteQuotaPayload' - title: Payload - responses: - '200': - content: - application/json: - schema: - title: Response Delete Api Quotas Id Delete - type: string - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Deletes an existing quota. - tags: - - quotas - - quotas - get: - description: Displays details on a particular active quota. - operationId: quota_api_quotas__id__get - parameters: - - description: The ID of the Quota. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/QuotaDetails' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Displays details on a particular active quota. - tags: - - quotas - - quotas - put: - description: Updates an existing quota. - operationId: update_api_quotas__id__put - parameters: - - description: The ID of the Quota. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/UpdateQuotaParams' - required: true - responses: - '200': - content: - application/json: - schema: - title: Response Update Api Quotas Id Put - type: string - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Updates an existing quota. - tags: - - quotas - - quotas - /api/quotas/{id}/purge: - post: - operationId: purge_api_quotas__id__purge_post - parameters: - - description: The ID of the Quota. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - title: Response Purge Api Quotas Id Purge Post - type: string - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Purges a previously deleted quota. - tags: - - quotas - - quotas - /api/remote_files: - get: - description: Lists all remote files available to the user from different sources. - operationId: index_api_remote_files_get - parameters: - - description: 'The source to load datasets from. Possible values: ftpdir, userdir, - importdir' - in: query - name: target - required: false - schema: - default: ftpdir - description: 'The source to load datasets from. Possible values: ftpdir, - userdir, importdir' - title: Target source - type: string - - description: The requested format of returned data. Either `flat` to simply - list all the files, `jstree` to get a tree representation of the files, - or the default `uri` to list files and directories by their URI. - in: query - name: format - required: false - schema: - anyOf: - - $ref: '#/components/schemas/RemoteFilesFormat' - - type: 'null' - default: uri - description: The requested format of returned data. Either `flat` to simply - list all the files, `jstree` to get a tree representation of the files, - or the default `uri` to list files and directories by their URI. - title: Response format - - description: Whether to recursively lists all sub-directories. This will be - `True` by default depending on the `target`. - in: query - name: recursive - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - description: Whether to recursively lists all sub-directories. This will - be `True` by default depending on the `target`. - title: Recursive - - description: (This only applies when `format` is `jstree`) The value can be - either `folders` or `files` and it will disable the corresponding nodes - of the tree. - in: query - name: disable - required: false - schema: - anyOf: - - $ref: '#/components/schemas/RemoteFilesDisableMode' - - type: 'null' - description: (This only applies when `format` is `jstree`) The value can - be either `folders` or `files` and it will disable the corresponding nodes - of the tree. - title: Disable mode - - description: Whether the query is made with the intention of writing to the - source. If set to True, only entries that can be written to will be returned. - in: query - name: writeable - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - description: Whether the query is made with the intention of writing to - the source. If set to True, only entries that can be written to will be - returned. - title: Writeable - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/ListUriResponse' - - $ref: '#/components/schemas/ListJstreeResponse' - title: Response Index Api Remote Files Get - description: A list with details about the remote files available to the - user. - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Displays remote files available to the user. - tags: - - remote files - - remote files - post: - description: Creates a new entry on the remote files source. - operationId: create_entry_api_remote_files_post - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - allOf: - - $ref: '#/components/schemas/CreateEntryPayload' - description: Information about the entry to create. Depends on the target - file source. - title: Entry Data - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/CreatedEntryResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Creates a new entry (directory/record) on the remote files source. - tags: - - remote files - - remote files - /api/remote_files/plugins: - get: - description: Display plugin information for each of the gxfiles:// URI targets - available. - operationId: plugins_api_remote_files_plugins_get - parameters: - - description: Whether to return browsable filesources only. The default is - `True`, which will omit filesourceslike `http` and `base64` that do not - implement a list method. - in: query - name: browsable_only - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: true - description: Whether to return browsable filesources only. The default is - `True`, which will omit filesourceslike `http` and `base64` that do not - implement a list method. - title: Browsable filesources only - - description: Whether to return **only** filesources of the specified kind. - The default is `None`, which will return all filesources. Multiple values - can be specified by repeating the parameter. - in: query - name: include_kind - required: false - schema: - anyOf: - - items: - $ref: '#/components/schemas/PluginKind' - type: array - - type: 'null' - description: Whether to return **only** filesources of the specified kind. - The default is `None`, which will return all filesources. Multiple values - can be specified by repeating the parameter. - title: Include kind - - description: Whether to exclude filesources of the specified kind from the - list. The default is `None`, which will return all filesources. Multiple - values can be specified by repeating the parameter. - in: query - name: exclude_kind - required: false - schema: - anyOf: - - items: - $ref: '#/components/schemas/PluginKind' - type: array - - type: 'null' - description: Whether to exclude filesources of the specified kind from the - list. The default is `None`, which will return all filesources. Multiple - values can be specified by repeating the parameter. - title: Exclude kind - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/FilesSourcePluginList' - description: A list with details about each plugin. - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Display plugin information for each of the gxfiles:// URI targets available. - tags: - - remote files - - remote files - /api/roles: - get: - operationId: index_api_roles_get - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/RoleListResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Index - tags: - - roles - - roles - post: - operationId: create_api_roles_post - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/RoleDefinitionModel' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/RoleModelResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Create - tags: - - roles - - roles - /api/roles/{id}: - delete: - operationId: delete_api_roles__id__delete - parameters: - - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/RoleModelResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Delete - tags: - - roles - - roles - get: - operationId: show_api_roles__id__get - parameters: - - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/RoleModelResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Show - tags: - - roles - - roles - /api/roles/{id}/purge: - post: - operationId: purge_api_roles__id__purge_post - parameters: - - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/RoleModelResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Purge - tags: - - roles - - roles - /api/roles/{id}/undelete: - post: - operationId: undelete_api_roles__id__undelete_post - parameters: - - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/RoleModelResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Undelete - tags: - - roles - - roles - /api/short_term_storage/{storage_request_id}: - get: - operationId: serve_api_short_term_storage__storage_request_id__get - parameters: - - in: path - name: storage_request_id - required: true - schema: - format: uuid - title: Storage Request Id - type: string - responses: - '200': - description: The archive file containing the History. - '204': - description: Request was cancelled without an exception condition recorded. - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: [] - summary: Serve the staged download specified by request ID. - tags: - - short_term_storage - - short_term_storage - /api/short_term_storage/{storage_request_id}/ready: - get: - operationId: is_ready_api_short_term_storage__storage_request_id__ready_get - parameters: - - in: path - name: storage_request_id - required: true - schema: - format: uuid - title: Storage Request Id - type: string - responses: - '200': - content: - application/json: - schema: - title: Response Is Ready Api Short Term Storage Storage Request Id Ready - Get - type: boolean - description: Boolean indicating if the storage is ready. - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: [] - summary: Determine if specified storage request ID is ready for download. - tags: - - short_term_storage - - short_term_storage - /api/storage/datasets: - delete: - description: '**Warning**: This operation cannot be undone. All objects will - be deleted permanently from the disk.' - operationId: cleanup_datasets_api_storage_datasets_delete - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/CleanupStorageItemsRequest' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/StorageItemsCleanupResult' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Purges a set of datasets by ID from disk. The datasets must be owned - by the user. - tags: - - storage management - - storage management - /api/storage/datasets/discarded: - get: - operationId: discarded_datasets_api_storage_datasets_discarded_get - parameters: - - description: Starts at the beginning skip the first ( offset - 1 ) items and - begin returning at the Nth item - in: query - name: offset - required: false - schema: - anyOf: - - minimum: 0 - type: integer - - type: 'null' - default: 0 - description: Starts at the beginning skip the first ( offset - 1 ) items - and begin returning at the Nth item - title: Offset - - description: The maximum number of items to return. - in: query - name: limit - required: false - schema: - anyOf: - - minimum: 1 - type: integer - - type: 'null' - description: The maximum number of items to return. - title: Limit - - description: String containing one of the valid ordering attributes followed - by '-asc' or '-dsc' for ascending and descending order respectively. - in: query - name: order - required: false - schema: - anyOf: - - $ref: '#/components/schemas/StoredItemOrderBy' - - type: 'null' - description: String containing one of the valid ordering attributes followed - by '-asc' or '-dsc' for ascending and descending order respectively. - title: Order - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - $ref: '#/components/schemas/StoredItem' - title: Response Discarded Datasets Api Storage Datasets Discarded - Get - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns discarded datasets owned by the given user. The results can - be paginated. - tags: - - storage management - - storage management - /api/storage/datasets/discarded/summary: - get: - operationId: discarded_datasets_summary_api_storage_datasets_discarded_summary_get - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/CleanableItemsSummary' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns information with the total storage space taken by discarded - datasets owned by the given user. - tags: - - storage management - - storage management - /api/storage/histories: - delete: - description: '**Warning**: This operation cannot be undone. All objects will - be deleted permanently from the disk.' - operationId: cleanup_histories_api_storage_histories_delete - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/CleanupStorageItemsRequest' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/StorageItemsCleanupResult' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Purges a set of histories by ID. The histories must be owned by the - user. - tags: - - storage management - - storage management - /api/storage/histories/archived: - get: - operationId: archived_histories_api_storage_histories_archived_get - parameters: - - description: Starts at the beginning skip the first ( offset - 1 ) items and - begin returning at the Nth item - in: query - name: offset - required: false - schema: - anyOf: - - minimum: 0 - type: integer - - type: 'null' - default: 0 - description: Starts at the beginning skip the first ( offset - 1 ) items - and begin returning at the Nth item - title: Offset - - description: The maximum number of items to return. - in: query - name: limit - required: false - schema: - anyOf: - - minimum: 1 - type: integer - - type: 'null' - description: The maximum number of items to return. - title: Limit - - description: String containing one of the valid ordering attributes followed - by '-asc' or '-dsc' for ascending and descending order respectively. - in: query - name: order - required: false - schema: - anyOf: - - $ref: '#/components/schemas/StoredItemOrderBy' - - type: 'null' - description: String containing one of the valid ordering attributes followed - by '-asc' or '-dsc' for ascending and descending order respectively. - title: Order - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - $ref: '#/components/schemas/StoredItem' - title: Response Archived Histories Api Storage Histories Archived - Get - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns archived histories owned by the given user that are not purged. - The results can be paginated. - tags: - - storage management - - storage management - /api/storage/histories/archived/summary: - get: - operationId: archived_histories_summary_api_storage_histories_archived_summary_get - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/CleanableItemsSummary' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns information with the total storage space taken by non-purged - archived histories associated with the given user. - tags: - - storage management - - storage management - /api/storage/histories/discarded: - get: - operationId: discarded_histories_api_storage_histories_discarded_get - parameters: - - description: Starts at the beginning skip the first ( offset - 1 ) items and - begin returning at the Nth item - in: query - name: offset - required: false - schema: - anyOf: - - minimum: 0 - type: integer - - type: 'null' - default: 0 - description: Starts at the beginning skip the first ( offset - 1 ) items - and begin returning at the Nth item - title: Offset - - description: The maximum number of items to return. - in: query - name: limit - required: false - schema: - anyOf: - - minimum: 1 - type: integer - - type: 'null' - description: The maximum number of items to return. - title: Limit - - description: String containing one of the valid ordering attributes followed - by '-asc' or '-dsc' for ascending and descending order respectively. - in: query - name: order - required: false - schema: - anyOf: - - $ref: '#/components/schemas/StoredItemOrderBy' - - type: 'null' - description: String containing one of the valid ordering attributes followed - by '-asc' or '-dsc' for ascending and descending order respectively. - title: Order - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - $ref: '#/components/schemas/StoredItem' - title: Response Discarded Histories Api Storage Histories Discarded - Get - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns all discarded histories associated with the given user. - tags: - - storage management - - storage management - /api/storage/histories/discarded/summary: - get: - operationId: discarded_histories_summary_api_storage_histories_discarded_summary_get - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/CleanableItemsSummary' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns information with the total storage space taken by discarded - histories associated with the given user. - tags: - - storage management - - storage management - /api/tags: - put: - description: 'Replaces the tags associated with an item with the new ones specified - in the payload. - - - - The previous tags will be __deleted__. - - - If no tags are provided in the request body, the currently associated tags - will also be __deleted__.' - operationId: update_api_tags_put - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - allOf: - - $ref: '#/components/schemas/ItemTagsPayload' - description: Request body containing the item and the tags to be assigned. - title: Payload - required: true - responses: - '204': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Apply a new set of tags to an item. - tags: - - tags - - tags - /api/tasks/{task_id}/state: - get: - operationId: state_api_tasks__task_id__state_get - parameters: - - in: path - name: task_id - required: true - schema: - format: uuid - title: Task Id - type: string - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/TaskState' - description: String indicating task state. - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: [] - summary: Determine state of task ID - tags: - - tasks - - tasks - /api/tool_data: - get: - description: Get the list of all available data tables. - operationId: index_api_tool_data_get - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ToolDataEntryList' - description: A list with details on individual data tables. - security: [] - summary: Lists all available data tables - tags: - - tool data tables - - tool data tables - post: - operationId: create_api_tool_data_post - parameters: - - in: query - name: tool_data_file_path - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Tool Data File Path - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/ImportToolDataBundle' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/AsyncTaskResultSummary' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Import a data manager bundle - tags: - - tool data tables - - tool data tables - /api/tool_data/{table_name}: - delete: - description: Removes an item from a data table and reloads it to return its - updated details. - operationId: delete_api_tool_data__table_name__delete - parameters: - - description: The name of the tool data table - in: path - name: table_name - required: true - schema: - description: The name of the tool data table - examples: - - all_fasta - title: Data table name - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/ToolDataItem' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ToolDataDetails' - description: A description of the affected data table and its content - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Removes an item from a data table - tags: - - tool data tables - - tool data tables - get: - description: Get details of a given tool data table. - operationId: show_api_tool_data__table_name__get - parameters: - - description: The name of the tool data table - in: path - name: table_name - required: true - schema: - description: The name of the tool data table - examples: - - all_fasta - title: Data table name - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ToolDataDetails' - description: A description of the given data table and its content - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get details of a given data table - tags: - - tool data tables - - tool data tables - /api/tool_data/{table_name}/fields/{field_name}: - get: - description: Reloads a data table and return its details. - operationId: show_field_api_tool_data__table_name__fields__field_name__get - parameters: - - description: The name of the tool data table - in: path - name: table_name - required: true - schema: - description: The name of the tool data table - examples: - - all_fasta - title: Data table name - type: string - - description: The name of the tool data table field - in: path - name: field_name - required: true - schema: - description: The name of the tool data table field - title: Field name - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ToolDataField' - description: Information about a data table field - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get information about a particular field in a tool data table - tags: - - tool data tables - - tool data tables - /api/tool_data/{table_name}/fields/{field_name}/files/{file_name}: - get: - description: Download a file associated with the data table field. - operationId: download_field_file_api_tool_data__table_name__fields__field_name__files__file_name__get - parameters: - - description: The name of the tool data table - in: path - name: table_name - required: true - schema: - description: The name of the tool data table - examples: - - all_fasta - title: Data table name - type: string - - description: The name of the tool data table field - in: path - name: field_name - required: true - schema: - description: The name of the tool data table field - title: Field name - type: string - - description: The name of a file associated with this data table field - in: path - name: file_name - required: true - schema: - description: The name of a file associated with this data table field - title: File name - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - description: Information about a data table field - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get information about a particular field in a tool data table - tags: - - tool data tables - - tool data tables - /api/tool_data/{table_name}/reload: - get: - description: Reloads a data table and return its details. - operationId: reload_api_tool_data__table_name__reload_get - parameters: - - description: The name of the tool data table - in: path - name: table_name - required: true - schema: - description: The name of the tool data table - examples: - - all_fasta - title: Data table name - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ToolDataDetails' - description: A description of the reloaded data table and its content - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Reloads a tool data table - tags: - - tool data tables - - tool data tables - /api/tool_shed_repositories: - get: - operationId: index_api_tool_shed_repositories_get - parameters: - - description: Filter by repository name. - in: query - name: name - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Filter by repository name. - title: Name - - description: Filter by repository owner. - in: query - name: owner - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Filter by repository owner. - title: Owner - - description: Filter by changeset revision. - in: query - name: changeset - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Filter by changeset revision. - title: Changeset - - description: Filter by whether the repository has been deleted. - in: query - name: deleted - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - description: Filter by whether the repository has been deleted. - title: Deleted? - - description: Filter by whether the repository has been uninstalled. - in: query - name: uninstalled - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - description: Filter by whether the repository has been uninstalled. - title: Uninstalled? - responses: - '200': - content: - application/json: - schema: - items: - $ref: '#/components/schemas/InstalledToolShedRepository' - title: Response Index Api Tool Shed Repositories Get - type: array - description: A list of installed tool shed repository objects. - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: [] - summary: Lists installed tool shed repositories. - tags: - - tool_shed_repositories - - tool_shed_repositories - /api/tool_shed_repositories/check_for_updates: - get: - operationId: check_for_updates_api_tool_shed_repositories_check_for_updates_get - parameters: - - in: query - name: id - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - title: Id - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/CheckForUpdatesResponse' - description: A description of the state and updates message. - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Check for updates to the specified repository, or all installed repositories. - tags: - - tool_shed_repositories - - tool_shed_repositories - /api/tool_shed_repositories/{id}: - get: - operationId: show_api_tool_shed_repositories__id__get - parameters: - - description: The encoded database identifier of the installed Tool Shed Repository. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/InstalledToolShedRepository' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: [] - summary: Show installed tool shed repository. - tags: - - tool_shed_repositories - - tool_shed_repositories - /api/tools/fetch: - post: - operationId: fetch_form_api_tools_fetch_post - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - multipart/form-data: - schema: - $ref: '#/components/schemas/Body_fetch_form_api_tools_fetch_post' - required: true - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Upload files to Galaxy - tags: - - tools - - tools - /api/tours: - get: - description: Return list of available tours. - operationId: index_api_tours_get - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/TourList' - description: Successful Response - security: [] - summary: Index - tags: - - tours - - tours - /api/tours/{tour_id}: - get: - description: Return a tour definition. - operationId: show_api_tours__tour_id__get - parameters: - - in: path - name: tour_id - required: true - schema: - title: Tour Id - type: string - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/TourDetails' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: [] - summary: Show - tags: - - tours - - tours - post: - description: Return a tour definition. - operationId: update_tour_api_tours__tour_id__post - parameters: - - in: path - name: tour_id - required: true - schema: - title: Tour Id - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/TourDetails' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Update Tour - tags: - - tours - - tours - /api/users: - get: - description: Return a collection of users. Filters will only work if enabled - in config or user is admin. - operationId: get_users_api_users_get - parameters: - - description: Indicates if the collection will be about deleted users - in: query - name: deleted - required: false - schema: - default: false - description: Indicates if the collection will be about deleted users - title: Deleted users - type: boolean - - description: An email address to filter on - in: query - name: f_email - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: An email address to filter on - title: Email filter - - description: An username address to filter on - in: query - name: f_name - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: An username address to filter on - title: Name filter - - description: Filter on username OR email - in: query - name: f_any - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Filter on username OR email - title: Any filter - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - anyOf: - - $ref: '#/components/schemas/UserModel' - - $ref: '#/components/schemas/LimitedUserModel' - title: Response Get Users Api Users Get - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get Users - tags: - - users - - users - post: - operationId: create_user_api_users_post - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/UserCreationPayload' - - $ref: '#/components/schemas/RemoteUserCreationPayload' - description: The values to add create a user. - title: Create User - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/CreatedUserModel' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Create a new Galaxy user. Only admins can create users for now. - tags: - - users - - users - /api/users/current/recalculate_disk_usage: - put: - description: 'This route will be removed in a future version. - - - Please use `/api/users/current/recalculate_disk_usage` instead.' - operationId: recalculate_disk_usage_api_users_current_recalculate_disk_usage_put - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/AsyncTaskResultSummary' - description: The asynchronous task summary to track the task state. - '204': - description: The background task was submitted but there is no status tracking - ID available. - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Triggers a recalculation of the current user disk usage. - tags: - - users - - users - /api/users/deleted: - get: - description: Return a collection of deleted users. Only admins can see deleted - users. - operationId: get_deleted_users_api_users_deleted_get - parameters: - - description: An email address to filter on - in: query - name: f_email - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: An email address to filter on - title: Email filter - - description: An username address to filter on - in: query - name: f_name - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: An username address to filter on - title: Name filter - - description: Filter on username OR email - in: query - name: f_any - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Filter on username OR email - title: Any filter - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - anyOf: - - $ref: '#/components/schemas/UserModel' - - $ref: '#/components/schemas/LimitedUserModel' - title: Response Get Deleted Users Api Users Deleted Get - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get Deleted Users - tags: - - users - - users - /api/users/deleted/{user_id}: - get: - operationId: get_deleted_user_api_users_deleted__user_id__get - parameters: - - description: The ID of the user. - in: path - name: user_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/DetailedUserModel' - - $ref: '#/components/schemas/AnonUserModel' - title: Response Get Deleted User Api Users Deleted User Id Get - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return information about a deleted user. Only admins can see deleted - users. - tags: - - users - - users - /api/users/deleted/{user_id}/undelete: - post: - operationId: undelete_user_api_users_deleted__user_id__undelete_post - parameters: - - description: The ID of the user. - in: path - name: user_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DetailedUserModel' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Restore a deleted user. Only admins can restore users. - tags: - - users - - users - /api/users/recalculate_disk_usage: - put: - deprecated: true - description: 'This route will be removed in a future version. - - - Please use `/api/users/current/recalculate_disk_usage` instead.' - operationId: recalculate_disk_usage_api_users_recalculate_disk_usage_put - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/AsyncTaskResultSummary' - description: The asynchronous task summary to track the task state. - '204': - description: The background task was submitted but there is no status tracking - ID available. - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Triggers a recalculation of the current user disk usage. - tags: - - users - - users - /api/users/{user_id}: - delete: - operationId: delete_user_api_users__user_id__delete - parameters: - - description: The ID of the user. - in: path - name: user_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/UserDeletionPayload' - - type: 'null' - description: Purge the user. - title: Purge user - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DetailedUserModel' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Delete a user. Only admins can delete others or purge users. - tags: - - users - - users - get: - operationId: get_user_api_users__user_id__get - parameters: - - description: The ID of the user to get or 'current'. - in: path - name: user_id - required: true - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - const: current - description: The ID of the user to get or 'current'. - title: User ID - - description: Indicates if the user is deleted - in: query - name: deleted - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - description: Indicates if the user is deleted - title: Deleted user - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/DetailedUserModel' - - $ref: '#/components/schemas/AnonUserModel' - title: Response Get User Api Users User Id Get - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return information about a specified or the current user. Only admin - can see deleted or other users - tags: - - users - - users - put: - operationId: update_user_api_users__user_id__put - parameters: - - description: The ID of the user to get or 'current'. - in: path - name: user_id - required: true - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - const: current - description: The ID of the user to get or 'current'. - title: User ID - - description: Indicates if the user is deleted - in: query - name: deleted - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - description: Indicates if the user is deleted - title: Deleted user - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - description: The user values to update. - title: Update user - type: object - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DetailedUserModel' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Update the values of a user. Only admin can update others. - tags: - - users - - users - /api/users/{user_id}/api_key: - delete: - operationId: delete_api_key_api_users__user_id__api_key_delete - parameters: - - description: The ID of the user. - in: path - name: user_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '204': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Delete the current API key of the user - tags: - - users - - users - get: - operationId: get_or_create_api_key_api_users__user_id__api_key_get - parameters: - - description: The ID of the user. - in: path - name: user_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - title: Response Get Or Create Api Key Api Users User Id Api Key - Get - type: string - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return the user's API key - tags: - - users - - users - post: - operationId: create_api_key_api_users__user_id__api_key_post - parameters: - - description: The ID of the user. - in: path - name: user_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - title: Response Create Api Key Api Users User Id Api Key Post - type: string - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Create a new API key for the user - tags: - - users - - users - /api/users/{user_id}/api_key/detailed: - get: - operationId: get_api_key_detailed_api_users__user_id__api_key_detailed_get - parameters: - - description: The ID of the user. - in: path - name: user_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/APIKeyModel' - description: The API key of the user. - '204': - description: The user doesn't have an API key. - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return the user's API key with extra information. - tags: - - users - - users - /api/users/{user_id}/beacon: - get: - description: '**Warning**: This endpoint is experimental and might change or - disappear in future versions.' - operationId: get_beacon_settings_api_users__user_id__beacon_get - parameters: - - description: The ID of the user. - in: path - name: user_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/UserBeaconSetting' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return information about beacon share settings - tags: - - users - - users - post: - description: '**Warning**: This endpoint is experimental and might change or - disappear in future versions.' - operationId: set_beacon_settings_api_users__user_id__beacon_post - parameters: - - description: The ID of the user. - in: path - name: user_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/UserBeaconSetting' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/UserBeaconSetting' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Change beacon setting - tags: - - users - - users - /api/users/{user_id}/custom_builds: - get: - operationId: get_custom_builds_api_users__user_id__custom_builds_get - parameters: - - description: The ID of the user. - in: path - name: user_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/CustomBuildsCollection' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: ' Returns collection of custom builds.' - tags: - - users - - users - /api/users/{user_id}/custom_builds/{key}: - delete: - operationId: delete_custom_build_api_users__user_id__custom_builds__key__delete - parameters: - - description: The ID of the user. - in: path - name: user_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The key of the custom build to be deleted. - in: path - name: key - required: true - schema: - description: The key of the custom build to be deleted. - title: Custom build key - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DeletedCustomBuild' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Delete a custom build - tags: - - users - - users - put: - operationId: add_custom_builds_api_users__user_id__custom_builds__key__put - parameters: - - description: The ID of the user. - in: path - name: user_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The key of the custom build to be deleted. - in: path - name: key - required: true - schema: - description: The key of the custom build to be deleted. - title: Custom build key - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - allOf: - - $ref: '#/components/schemas/CustomBuildCreationPayload' - description: The values to add a new custom build. - title: Add custom build - required: true - responses: - '200': - content: - application/json: - schema: - title: Response Add Custom Builds Api Users User Id Custom Builds Key Put - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Add new custom build. - tags: - - users - - users - /api/users/{user_id}/favorites/{object_type}: - put: - operationId: set_favorite_api_users__user_id__favorites__object_type__put - parameters: - - description: The ID of the user. - in: path - name: user_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The object type the user wants to favorite - in: path - name: object_type - required: true - schema: - allOf: - - $ref: '#/components/schemas/FavoriteObjectType' - description: The object type the user wants to favorite - title: Object type - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - allOf: - - $ref: '#/components/schemas/FavoriteObject' - description: The id of an object the user wants to favorite. - title: Set favorite - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/FavoriteObjectsSummary' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Add the object to user's favorites - tags: - - users - - users - /api/users/{user_id}/favorites/{object_type}/{object_id}: - delete: - operationId: remove_favorite_api_users__user_id__favorites__object_type___object_id__delete - parameters: - - description: The ID of the user. - in: path - name: user_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The object type the user wants to favorite - in: path - name: object_type - required: true - schema: - allOf: - - $ref: '#/components/schemas/FavoriteObjectType' - description: The object type the user wants to favorite - title: Object type - - description: The ID of an object the user wants to remove from favorites - in: path - name: object_id - required: true - schema: - description: The ID of an object the user wants to remove from favorites - title: Object ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/FavoriteObjectsSummary' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Remove the object from user's favorites - tags: - - users - - users - /api/users/{user_id}/recalculate_disk_usage: - put: - operationId: recalculate_disk_usage_by_user_id_api_users__user_id__recalculate_disk_usage_put - parameters: - - description: The ID of the user. - in: path - name: user_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/AsyncTaskResultSummary' - description: The asynchronous task summary to track the task state. - '204': - description: The background task was submitted but there is no status tracking - ID available. - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Triggers a recalculation of the current user disk usage. - tags: - - users - - users - /api/users/{user_id}/send_activation_email: - post: - operationId: send_activation_email_api_users__user_id__send_activation_email_post - parameters: - - description: The ID of the user. - in: path - name: user_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Sends activation email to user. - tags: - - users - - users - /api/users/{user_id}/theme/{theme}: - put: - operationId: set_theme_api_users__user_id__theme__theme__put - parameters: - - description: The ID of the user. - in: path - name: user_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The theme of the GUI - in: path - name: theme - required: true - schema: - description: The theme of the GUI - title: Theme - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - title: Response Set Theme Api Users User Id Theme Theme Put - type: string - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Set the user's theme choice - tags: - - users - - users - /api/users/{user_id}/usage: - get: - operationId: get_user_usage_api_users__user_id__usage_get - parameters: - - description: The ID of the user to get or 'current'. - in: path - name: user_id - required: true - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - const: current - description: The ID of the user to get or 'current'. - title: User ID - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - $ref: '#/components/schemas/UserQuotaUsage' - title: Response Get User Usage Api Users User Id Usage Get - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return the user's quota usage summary broken down by quota source - tags: - - users - - users - /api/users/{user_id}/usage/{label}: - get: - operationId: get_user_usage_for_label_api_users__user_id__usage__label__get - parameters: - - description: The ID of the user to get or 'current'. - in: path - name: user_id - required: true - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - const: current - description: The ID of the user to get or 'current'. - title: User ID - - description: The label corresponding to the quota source to fetch usage information - about. - in: path - name: label - required: true - schema: - description: The label corresponding to the quota source to fetch usage - information about. - title: Quota Source Label - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/UserQuotaUsage' - - type: 'null' - title: Response Get User Usage For Label Api Users User Id Usage Label Get - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return the user's quota usage summary for a given quota source label - tags: - - users - - users - /api/version: - get: - description: 'Return Galaxy version information: major/minor version, optional - extra info.' - operationId: version_api_version_get - responses: - '200': - content: - application/json: - schema: - title: Response Version Api Version Get - type: object - description: 'Galaxy version information: major/minor version, optional - extra info' - security: [] - summary: 'Return Galaxy version information: major/minor version, optional extra - info' - tags: - - configuration - - configuration - /api/visualizations: - get: - operationId: index_api_visualizations_get - parameters: - - description: Whether to include deleted visualizations in the result. - in: query - name: deleted - required: false - schema: - default: false - description: Whether to include deleted visualizations in the result. - title: Display deleted - type: boolean - - description: The maximum number of items to return. - in: query - name: limit - required: false - schema: - anyOf: - - minimum: 1 - type: integer - - type: 'null' - description: The maximum number of items to return. - title: Limit - - description: Starts at the beginning skip the first ( offset - 1 ) items and - begin returning at the Nth item - in: query - name: offset - required: false - schema: - anyOf: - - minimum: 0 - type: integer - - type: 'null' - default: 0 - description: Starts at the beginning skip the first ( offset - 1 ) items - and begin returning at the Nth item - title: Offset - - in: query - name: user_id - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - title: Encoded user ID to restrict query to, must be own id if not an admin - user - - in: query - name: show_own - required: false - schema: - default: true - title: Show visualizations owned by user. - type: boolean - - in: query - name: show_published - required: false - schema: - default: true - title: Include published visualizations. - type: boolean - - in: query - name: show_shared - required: false - schema: - default: false - title: Include visualizations shared with authenticated user. - type: boolean - - description: Sort visualization index by this specified attribute on the visualization - model - in: query - name: sort_by - required: false - schema: - default: update_time - description: Sort visualization index by this specified attribute on the - visualization model - enum: - - create_time - - title - - update_time - - username - title: Sort attribute - type: string - - description: Sort in descending order? - in: query - name: sort_desc - required: false - schema: - default: true - description: Sort in descending order? - title: Sort Descending - type: boolean - - description: 'A mix of free text and GitHub-style tags used to filter the - index operation. - - - ## Query Structure - - - GitHub-style filter tags (not be confused with Galaxy tags) are tags of - the form - - `:` or `:''''`. - The tag name - - *generally* (but not exclusively) corresponds to the name of an attribute - on the model - - being indexed (i.e. a column in the database). - - - If the tag is quoted, the attribute will be filtered exactly. If the tag - is unquoted, - - generally a partial match will be used to filter the query (i.e. in terms - of the implementation - - this means the database operation `ILIKE` will typically be used). - - - Once the tagged filters are extracted from the search query, the remaining - text is just - - used to search various documented attributes of the object. - - - ## GitHub-style Tags Available - - - `title` - - : The visualization''s title. - - - `slug` - - : The visualization''s slug. (The tag `s` can be used a short hand alias - for this tag to filter on this attribute.) - - - `tag` - - : The visualization''s tags. (The tag `t` can be used a short hand alias - for this tag to filter on this attribute.) - - - `user` - - : The visualization''s owner''s username. (The tag `u` can be used a short - hand alias for this tag to filter on this attribute.) - - - ## Free Text - - - Free text search terms will be searched against the following attributes - of the - - Visualizations: `title`, `slug`, `tag`, `type`. - - - ' - in: query - name: search - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: 'A mix of free text and GitHub-style tags used to filter the - index operation. - - - ## Query Structure - - - GitHub-style filter tags (not be confused with Galaxy tags) are tags of - the form - - `:` or `:''''`. - The tag name - - *generally* (but not exclusively) corresponds to the name of an attribute - on the model - - being indexed (i.e. a column in the database). - - - If the tag is quoted, the attribute will be filtered exactly. If the tag - is unquoted, - - generally a partial match will be used to filter the query (i.e. in terms - of the implementation - - this means the database operation `ILIKE` will typically be used). - - - Once the tagged filters are extracted from the search query, the remaining - text is just - - used to search various documented attributes of the object. - - - ## GitHub-style Tags Available - - - `title` - - : The visualization''s title. - - - `slug` - - : The visualization''s slug. (The tag `s` can be used a short hand alias - for this tag to filter on this attribute.) - - - `tag` - - : The visualization''s tags. (The tag `t` can be used a short hand alias - for this tag to filter on this attribute.) - - - `user` - - : The visualization''s owner''s username. (The tag `u` can be used a short - hand alias for this tag to filter on this attribute.) - - - ## Free Text - - - Free text search terms will be searched against the following attributes - of the - - Visualizations: `title`, `slug`, `tag`, `type`. - - - ' - title: Search query. - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/VisualizationSummaryList' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Returns visualizations for the current user. - tags: - - visualizations - - visualizations - /api/visualizations/{id}/disable_link_access: - put: - description: Makes this item inaccessible by a URL link and return the current - sharing status. - operationId: disable_link_access_api_visualizations__id__disable_link_access_put - parameters: - - description: The encoded database identifier of the Visualization. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/SharingStatus' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Makes this item inaccessible by a URL link. - tags: - - visualizations - - visualizations - /api/visualizations/{id}/enable_link_access: - put: - description: Makes this item accessible by a URL link and return the current - sharing status. - operationId: enable_link_access_api_visualizations__id__enable_link_access_put - parameters: - - description: The encoded database identifier of the Visualization. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/SharingStatus' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Makes this item accessible by a URL link. - tags: - - visualizations - - visualizations - /api/visualizations/{id}/publish: - put: - description: Makes this item publicly available by a URL link and return the - current sharing status. - operationId: publish_api_visualizations__id__publish_put - parameters: - - description: The encoded database identifier of the Visualization. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/SharingStatus' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Makes this item public and accessible by a URL link. - tags: - - visualizations - - visualizations - /api/visualizations/{id}/share_with_users: - put: - description: Shares this item with specific users and return the current sharing - status. - operationId: share_with_users_api_visualizations__id__share_with_users_put - parameters: - - description: The encoded database identifier of the Visualization. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/ShareWithPayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ShareWithStatus' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Share this item with specific users. - tags: - - visualizations - - visualizations - /api/visualizations/{id}/sharing: - get: - description: Return the sharing status of the item. - operationId: sharing_api_visualizations__id__sharing_get - parameters: - - description: The encoded database identifier of the Visualization. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/SharingStatus' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get the current sharing status of the given Visualization. - tags: - - visualizations - - visualizations - /api/visualizations/{id}/slug: - put: - description: Sets a new slug to access this item by URL. The new slug must be - unique. - operationId: set_slug_api_visualizations__id__slug_put - parameters: - - description: The encoded database identifier of the Visualization. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/SetSlugPayload' - required: true - responses: - '204': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Set a new slug for this shared item. - tags: - - visualizations - - visualizations - /api/visualizations/{id}/unpublish: - put: - description: Removes this item from the published list and return the current - sharing status. - operationId: unpublish_api_visualizations__id__unpublish_put - parameters: - - description: The encoded database identifier of the Visualization. - in: path - name: id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/SharingStatus' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Removes this item from the published list. - tags: - - visualizations - - visualizations - /api/whoami: - get: - description: Return information about the current authenticated user. - operationId: whoami_api_whoami_get - parameters: - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/UserModel' - - type: 'null' - title: Response Whoami Api Whoami Get - description: Information about the current authenticated user - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Return information about the current authenticated user - tags: - - configuration - - configuration - /api/workflows: - get: - description: Lists stored workflows viewable by the user. - operationId: index_api_workflows_get - parameters: - - description: Whether to restrict result to deleted workflows. - in: query - name: show_deleted - required: false - schema: - default: false - description: Whether to restrict result to deleted workflows. - title: Display deleted - type: boolean - - description: Whether to restrict result to hidden workflows. - in: query - name: show_hidden - required: false - schema: - default: false - description: Whether to restrict result to hidden workflows. - title: Display hidden - type: boolean - - description: Whether to include a list of missing tools per workflow entry - in: query - name: missing_tools - required: false - schema: - default: false - description: Whether to include a list of missing tools per workflow entry - title: Display missing tools - type: boolean - - in: query - name: show_published - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - title: Include published workflows. - - in: query - name: show_shared - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - title: Include workflows shared with authenticated user. - - description: In unspecified, default ordering depends on other parameters - but generally the user's own workflows appear first based on update time - in: query - name: sort_by - required: false - schema: - anyOf: - - enum: - - create_time - - update_time - - name - type: string - - type: 'null' - description: In unspecified, default ordering depends on other parameters - but generally the user's own workflows appear first based on update time - title: Sort workflow index by this attribute - - description: Sort in descending order? - in: query - name: sort_desc - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - description: Sort in descending order? - title: Sort Descending - - in: query - name: limit - required: false - schema: - anyOf: - - type: integer - - type: 'null' - title: Limit number of queries. - - in: query - name: offset - required: false - schema: - anyOf: - - type: integer - - type: 'null' - default: 0 - title: Number of workflows to skip in sorted query (to enable pagination). - - description: 'A mix of free text and GitHub-style tags used to filter the - index operation. - - - ## Query Structure - - - GitHub-style filter tags (not be confused with Galaxy tags) are tags of - the form - - `:` or `:''''`. - The tag name - - *generally* (but not exclusively) corresponds to the name of an attribute - on the model - - being indexed (i.e. a column in the database). - - - If the tag is quoted, the attribute will be filtered exactly. If the tag - is unquoted, - - generally a partial match will be used to filter the query (i.e. in terms - of the implementation - - this means the database operation `ILIKE` will typically be used). - - - Once the tagged filters are extracted from the search query, the remaining - text is just - - used to search various documented attributes of the object. - - - ## GitHub-style Tags Available - - - `name` - - : The stored workflow''s name. (The tag `n` can be used a short hand alias - for this tag to filter on this attribute.) - - - `tag` - - : The workflow''s tag, if the tag contains a colon an approach will be made - to match the key and value of the tag separately. (The tag `t` can be used - a short hand alias for this tag to filter on this attribute.) - - - `user` - - : The stored workflow''s owner''s username. (The tag `u` can be used a short - hand alias for this tag to filter on this attribute.) - - - `is:published` - - : Include only published workflows in the final result. Be sure the query - parameter `show_published` is set to `true` if to include all published - workflows and not just the requesting user''s. - - - `is:share_with_me` - - : Include only workflows shared with the requesting user. Be sure the query - parameter `show_shared` is set to `true` if to include shared workflows. - - - ## Free Text - - - Free text search terms will be searched against the following attributes - of the - - Stored Workflows: `name`, `tag`, `user`. - - - ' - in: query - name: search - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: 'A mix of free text and GitHub-style tags used to filter the - index operation. - - - ## Query Structure - - - GitHub-style filter tags (not be confused with Galaxy tags) are tags of - the form - - `:` or `:''''`. - The tag name - - *generally* (but not exclusively) corresponds to the name of an attribute - on the model - - being indexed (i.e. a column in the database). - - - If the tag is quoted, the attribute will be filtered exactly. If the tag - is unquoted, - - generally a partial match will be used to filter the query (i.e. in terms - of the implementation - - this means the database operation `ILIKE` will typically be used). - - - Once the tagged filters are extracted from the search query, the remaining - text is just - - used to search various documented attributes of the object. - - - ## GitHub-style Tags Available - - - `name` - - : The stored workflow''s name. (The tag `n` can be used a short hand alias - for this tag to filter on this attribute.) - - - `tag` - - : The workflow''s tag, if the tag contains a colon an approach will be - made to match the key and value of the tag separately. (The tag `t` can - be used a short hand alias for this tag to filter on this attribute.) - - - `user` - - : The stored workflow''s owner''s username. (The tag `u` can be used a - short hand alias for this tag to filter on this attribute.) - - - `is:published` - - : Include only published workflows in the final result. Be sure the query - parameter `show_published` is set to `true` if to include all published - workflows and not just the requesting user''s. - - - `is:share_with_me` - - : Include only workflows shared with the requesting user. Be sure the - query parameter `show_shared` is set to `true` if to include shared workflows. - - - ## Free Text - - - Free text search terms will be searched against the following attributes - of the - - Stored Workflows: `name`, `tag`, `user`. - - - ' - title: Search query. - - description: Set this to true to skip joining workflow step counts and optimize - the resulting index query. Response objects will not contain step counts. - in: query - name: skip_step_counts - required: false - schema: - default: false - description: Set this to true to skip joining workflow step counts and optimize - the resulting index query. Response objects will not contain step counts. - title: Skip step counts. - type: boolean - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - type: object - title: Response Index Api Workflows Get - type: array - description: A list with summary stored workflow information per viewable - entry. - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Lists stored workflows viewable by the user. - tags: - - workflows - - workflows - /api/workflows/menu: - get: - operationId: get_workflow_menu_api_workflows_menu_get - parameters: - - description: Whether to restrict result to deleted workflows. - in: query - name: show_deleted - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: false - description: Whether to restrict result to deleted workflows. - title: Display deleted - - description: Whether to restrict result to hidden workflows. - in: query - name: show_hidden - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: false - description: Whether to restrict result to hidden workflows. - title: Display hidden - - description: Whether to include a list of missing tools per workflow entry - in: query - name: missing_tools - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: false - description: Whether to include a list of missing tools per workflow entry - title: Display missing tools - - in: query - name: show_published - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - title: Include published workflows. - - in: query - name: show_shared - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - title: Include workflows shared with authenticated user. - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get workflows present in the tools panel. - tags: - - workflows - - workflows - /api/workflows/{workflow_id}: - delete: - operationId: delete_workflow_api_workflows__workflow_id__delete - parameters: - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Add the deleted flag to a workflow. - tags: - - workflows - - workflows - /api/workflows/{workflow_id}/counts: - get: - operationId: workflows__invocation_counts - parameters: - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: Is provided workflow id for Workflow instead of StoredWorkflow? - in: query - name: instance - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: false - description: Is provided workflow id for Workflow instead of StoredWorkflow? - title: Instance - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/RootModel_Dict_str__int__' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get state counts for accessible workflow. - tags: - - workflows - - workflows - /api/workflows/{workflow_id}/disable_link_access: - put: - description: Makes this item inaccessible by a URL link and return the current - sharing status. - operationId: disable_link_access_api_workflows__workflow_id__disable_link_access_put - parameters: - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/SharingStatus' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Makes this item inaccessible by a URL link. - tags: - - workflows - - workflows - /api/workflows/{workflow_id}/enable_link_access: - put: - description: Makes this item accessible by a URL link and return the current - sharing status. - operationId: enable_link_access_api_workflows__workflow_id__enable_link_access_put - parameters: - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/SharingStatus' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Makes this item accessible by a URL link. - tags: - - workflows - - workflows - /api/workflows/{workflow_id}/invocations: - get: - operationId: index_invocations_api_workflows__workflow_id__invocations_get - parameters: - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: Return only invocations for this History ID - in: query - name: history_id - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: Return only invocations for this History ID - title: History ID - - description: Return only invocations for this Job ID - in: query - name: job_id - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: Return only invocations for this Job ID - title: Job ID - - description: Return invocations for this User ID. - in: query - name: user_id - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: Return invocations for this User ID. - title: User ID - - description: Sort Workflow Invocations by this attribute - in: query - name: sort_by - required: false - schema: - anyOf: - - $ref: '#/components/schemas/InvocationSortByEnum' - - type: 'null' - description: Sort Workflow Invocations by this attribute - title: Sort By - - description: Sort in descending order? - in: query - name: sort_desc - required: false - schema: - default: false - description: Sort in descending order? - title: Sort Descending - type: boolean - - description: Set to false to only include terminal Invocations. - in: query - name: include_terminal - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: true - description: Set to false to only include terminal Invocations. - title: Include Terminal - - description: Limit the number of invocations to return. - in: query - name: limit - required: false - schema: - anyOf: - - type: integer - - type: 'null' - description: Limit the number of invocations to return. - title: Limit - - description: Number of invocations to skip. - in: query - name: offset - required: false - schema: - anyOf: - - type: integer - - type: 'null' - description: Number of invocations to skip. - title: Offset - - description: Is provided workflow id for Workflow instead of StoredWorkflow? - in: query - name: instance - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: false - description: Is provided workflow id for Workflow instead of StoredWorkflow? - title: Instance - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Include details for individual invocation steps and populate - a steps attribute in the resulting dictionary. - in: query - name: step_details - required: false - schema: - default: false - description: Include details for individual invocation steps and populate - a steps attribute in the resulting dictionary. - title: Include step details - type: boolean - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - $ref: '#/components/schemas/WorkflowInvocationResponse' - title: Response Index Invocations Api Workflows Workflow Id Invocations - Get - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get the list of a user's workflow invocations. - tags: - - workflows - - workflows - /api/workflows/{workflow_id}/invocations/{invocation_id}: - delete: - description: An alias for `DELETE /api/invocations/{invocation_id}`. `workflow_id` - is ignored. - operationId: cancel_workflow_invocation_api_workflows__workflow_id__invocations__invocation_id__delete - parameters: - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: Include details for individual invocation steps and populate - a steps attribute in the resulting dictionary. - in: query - name: step_details - required: false - schema: - default: false - description: Include details for individual invocation steps and populate - a steps attribute in the resulting dictionary. - title: Include step details - type: boolean - - description: "Populate the invocation step state with the job state instead\ - \ of the invocation step state.\n This will also produce one step\ - \ per job in mapping jobs to mimic the older behavior with respect to collections.\n\ - \ Partially scheduled steps may provide incomplete information and\ - \ the listed steps outputs\n are not the mapped over step outputs\ - \ but the individual job outputs." - in: query - name: legacy_job_state - required: false - schema: - default: false - description: "Populate the invocation step state with the job state instead\ - \ of the invocation step state.\n This will also produce one step\ - \ per job in mapping jobs to mimic the older behavior with respect to\ - \ collections.\n Partially scheduled steps may provide incomplete\ - \ information and the listed steps outputs\n are not the mapped\ - \ over step outputs but the individual job outputs." - title: Replace with job state - type: boolean - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/WorkflowInvocationResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Cancel the specified workflow invocation. - tags: - - workflows - - workflows - get: - description: An alias for `GET /api/invocations/{invocation_id}`. `workflow_id` - is ignored. - operationId: show_workflow_invocation_api_workflows__workflow_id__invocations__invocation_id__get - parameters: - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: Include details for individual invocation steps and populate - a steps attribute in the resulting dictionary. - in: query - name: step_details - required: false - schema: - default: false - description: Include details for individual invocation steps and populate - a steps attribute in the resulting dictionary. - title: Include step details - type: boolean - - description: "Populate the invocation step state with the job state instead\ - \ of the invocation step state.\n This will also produce one step\ - \ per job in mapping jobs to mimic the older behavior with respect to collections.\n\ - \ Partially scheduled steps may provide incomplete information and\ - \ the listed steps outputs\n are not the mapped over step outputs\ - \ but the individual job outputs." - in: query - name: legacy_job_state - required: false - schema: - default: false - description: "Populate the invocation step state with the job state instead\ - \ of the invocation step state.\n This will also produce one step\ - \ per job in mapping jobs to mimic the older behavior with respect to\ - \ collections.\n Partially scheduled steps may provide incomplete\ - \ information and the listed steps outputs\n are not the mapped\ - \ over step outputs but the individual job outputs." - title: Replace with job state - type: boolean - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/WorkflowInvocationResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get detailed description of a workflow invocation. - tags: - - workflows - - workflows - /api/workflows/{workflow_id}/invocations/{invocation_id}/jobs_summary: - get: - description: An alias for `GET /api/invocations/{invocation_id}/jobs_summary`. - `workflow_id` is ignored. - operationId: workflow_invocation_jobs_summary_api_workflows__workflow_id__invocations__invocation_id__jobs_summary_get - parameters: - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/InvocationJobsResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get job state summary info aggregated across all current jobs of the - workflow invocation. - tags: - - workflows - - workflows - /api/workflows/{workflow_id}/invocations/{invocation_id}/report: - get: - description: An alias for `GET /api/invocations/{invocation_id}/report`. `workflow_id` - is ignored. - operationId: show_workflow_invocation_report_api_workflows__workflow_id__invocations__invocation_id__report_get - parameters: - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/InvocationReport' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get JSON summarizing invocation for reporting. - tags: - - workflows - - workflows - /api/workflows/{workflow_id}/invocations/{invocation_id}/report.pdf: - get: - description: An alias for `GET /api/invocations/{invocation_id}/report.pdf`. - `workflow_id` is ignored. - operationId: show_workflow_invocation_report_pdf_api_workflows__workflow_id__invocations__invocation_id__report_pdf_get - parameters: - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get PDF summarizing invocation for reporting. - tags: - - workflows - - workflows - /api/workflows/{workflow_id}/invocations/{invocation_id}/step_jobs_summary: - get: - description: An alias for `GET /api/invocations/{invocation_id}/step_jobs_summary`. - `workflow_id` is ignored. - operationId: workflow_invocation_step_jobs_summary_api_workflows__workflow_id__invocations__invocation_id__step_jobs_summary_get - parameters: - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - anyOf: - - $ref: '#/components/schemas/InvocationStepJobsResponseStepModel' - - $ref: '#/components/schemas/InvocationStepJobsResponseJobModel' - - $ref: '#/components/schemas/InvocationStepJobsResponseCollectionJobsModel' - title: Response Workflow Invocation Step Jobs Summary Api Workflows Workflow - Id Invocations Invocation Id Step Jobs Summary Get - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get job state summary info aggregated per step of the workflow invocation. - tags: - - workflows - - workflows - /api/workflows/{workflow_id}/invocations/{invocation_id}/steps/{step_id}: - get: - description: An alias for `GET /api/invocations/{invocation_id}/steps/{step_id}`. - `workflow_id` and `invocation_id` are ignored. - operationId: workflow_invocation_step_api_workflows__workflow_id__invocations__invocation_id__steps__step_id__get - parameters: - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The encoded database identifier of the WorkflowInvocationStep. - in: path - name: step_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/InvocationStep' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Show details of workflow invocation step. - tags: - - workflows - - workflows - put: - description: An alias for `PUT /api/invocations/{invocation_id}/steps/{step_id}`. - `workflow_id` is ignored. - operationId: update_workflow_invocation_step_api_workflows__workflow_id__invocations__invocation_id__steps__step_id__put - parameters: - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The encoded database identifier of the WorkflowInvocationStep. - in: path - name: step_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/InvocationUpdatePayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/InvocationStep' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Update state of running workflow step invocation. - tags: - - workflows - - workflows - /api/workflows/{workflow_id}/publish: - put: - description: Makes this item publicly available by a URL link and return the - current sharing status. - operationId: publish_api_workflows__workflow_id__publish_put - parameters: - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/SharingStatus' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Makes this item public and accessible by a URL link. - tags: - - workflows - - workflows - /api/workflows/{workflow_id}/share_with_users: - put: - description: Shares this item with specific users and return the current sharing - status. - operationId: share_with_users_api_workflows__workflow_id__share_with_users_put - parameters: - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/ShareWithPayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ShareWithStatus' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Share this item with specific users. - tags: - - workflows - - workflows - /api/workflows/{workflow_id}/sharing: - get: - description: Return the sharing status of the item. - operationId: sharing_api_workflows__workflow_id__sharing_get - parameters: - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/SharingStatus' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get the current sharing status of the given item. - tags: - - workflows - - workflows - /api/workflows/{workflow_id}/slug: - put: - description: Sets a new slug to access this item by URL. The new slug must be - unique. - operationId: set_slug_api_workflows__workflow_id__slug_put - parameters: - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/SetSlugPayload' - required: true - responses: - '204': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Set a new slug for this shared item. - tags: - - workflows - - workflows - /api/workflows/{workflow_id}/tags: - get: - operationId: index_api_workflows__workflow_id__tags_get - parameters: - - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ItemTagsListResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Show tags based on workflow_id - tags: - - workflows - /api/workflows/{workflow_id}/tags/{tag_name}: - delete: - operationId: delete_api_workflows__workflow_id__tags__tag_name__delete - parameters: - - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - in: path - name: tag_name - required: true - schema: - title: Tag Name - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - title: Response Delete Api Workflows Workflow Id Tags Tag Name Delete - type: boolean - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Delete tag based on workflow_id - tags: - - workflows - get: - operationId: show_api_workflows__workflow_id__tags__tag_name__get - parameters: - - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - in: path - name: tag_name - required: true - schema: - title: Tag Name - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ItemTagsResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Show tag based on workflow_id - tags: - - workflows - post: - operationId: create_api_workflows__workflow_id__tags__tag_name__post - parameters: - - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - in: path - name: tag_name - required: true - schema: - title: Tag Name - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - allOf: - - $ref: '#/components/schemas/ItemTagsCreatePayload' - title: Payload - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ItemTagsResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Create tag based on workflow_id - tags: - - workflows - put: - operationId: update_api_workflows__workflow_id__tags__tag_name__put - parameters: - - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - in: path - name: tag_name - required: true - schema: - title: Tag Name - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/ItemTagsCreatePayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ItemTagsResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Update tag based on workflow_id - tags: - - workflows - /api/workflows/{workflow_id}/undelete: - post: - operationId: undelete_workflow_api_workflows__workflow_id__undelete_post - parameters: - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Remove the deleted flag from a workflow. - tags: - - workflows - - workflows - /api/workflows/{workflow_id}/unpublish: - put: - description: Removes this item from the published list and return the current - sharing status. - operationId: unpublish_api_workflows__workflow_id__unpublish_put - parameters: - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/SharingStatus' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Removes this item from the published list. - tags: - - workflows - - workflows - /api/workflows/{workflow_id}/usage: - get: - deprecated: true - operationId: index_invocations_api_workflows__workflow_id__usage_get - parameters: - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: Return only invocations for this History ID - in: query - name: history_id - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: Return only invocations for this History ID - title: History ID - - description: Return only invocations for this Job ID - in: query - name: job_id - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: Return only invocations for this Job ID - title: Job ID - - description: Return invocations for this User ID. - in: query - name: user_id - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: Return invocations for this User ID. - title: User ID - - description: Sort Workflow Invocations by this attribute - in: query - name: sort_by - required: false - schema: - anyOf: - - $ref: '#/components/schemas/InvocationSortByEnum' - - type: 'null' - description: Sort Workflow Invocations by this attribute - title: Sort By - - description: Sort in descending order? - in: query - name: sort_desc - required: false - schema: - default: false - description: Sort in descending order? - title: Sort Descending - type: boolean - - description: Set to false to only include terminal Invocations. - in: query - name: include_terminal - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: true - description: Set to false to only include terminal Invocations. - title: Include Terminal - - description: Limit the number of invocations to return. - in: query - name: limit - required: false - schema: - anyOf: - - type: integer - - type: 'null' - description: Limit the number of invocations to return. - title: Limit - - description: Number of invocations to skip. - in: query - name: offset - required: false - schema: - anyOf: - - type: integer - - type: 'null' - description: Number of invocations to skip. - title: Offset - - description: Is provided workflow id for Workflow instead of StoredWorkflow? - in: query - name: instance - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: false - description: Is provided workflow id for Workflow instead of StoredWorkflow? - title: Instance - - description: View to be passed to the serializer - in: query - name: view - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: View to be passed to the serializer - title: View - - description: Include details for individual invocation steps and populate - a steps attribute in the resulting dictionary. - in: query - name: step_details - required: false - schema: - default: false - description: Include details for individual invocation steps and populate - a steps attribute in the resulting dictionary. - title: Include step details - type: boolean - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - $ref: '#/components/schemas/WorkflowInvocationResponse' - title: Response Index Invocations Api Workflows Workflow Id Usage - Get - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get the list of a user's workflow invocations. - tags: - - workflows - - workflows - /api/workflows/{workflow_id}/usage/{invocation_id}: - delete: - deprecated: true - description: An alias for `DELETE /api/invocations/{invocation_id}`. `workflow_id` - is ignored. - operationId: cancel_workflow_invocation_api_workflows__workflow_id__usage__invocation_id__delete - parameters: - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: Include details for individual invocation steps and populate - a steps attribute in the resulting dictionary. - in: query - name: step_details - required: false - schema: - default: false - description: Include details for individual invocation steps and populate - a steps attribute in the resulting dictionary. - title: Include step details - type: boolean - - description: "Populate the invocation step state with the job state instead\ - \ of the invocation step state.\n This will also produce one step\ - \ per job in mapping jobs to mimic the older behavior with respect to collections.\n\ - \ Partially scheduled steps may provide incomplete information and\ - \ the listed steps outputs\n are not the mapped over step outputs\ - \ but the individual job outputs." - in: query - name: legacy_job_state - required: false - schema: - default: false - description: "Populate the invocation step state with the job state instead\ - \ of the invocation step state.\n This will also produce one step\ - \ per job in mapping jobs to mimic the older behavior with respect to\ - \ collections.\n Partially scheduled steps may provide incomplete\ - \ information and the listed steps outputs\n are not the mapped\ - \ over step outputs but the individual job outputs." - title: Replace with job state - type: boolean - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/WorkflowInvocationResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Cancel the specified workflow invocation. - tags: - - workflows - - workflows - get: - deprecated: true - description: An alias for `GET /api/invocations/{invocation_id}`. `workflow_id` - is ignored. - operationId: show_workflow_invocation_api_workflows__workflow_id__usage__invocation_id__get - parameters: - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: Include details for individual invocation steps and populate - a steps attribute in the resulting dictionary. - in: query - name: step_details - required: false - schema: - default: false - description: Include details for individual invocation steps and populate - a steps attribute in the resulting dictionary. - title: Include step details - type: boolean - - description: "Populate the invocation step state with the job state instead\ - \ of the invocation step state.\n This will also produce one step\ - \ per job in mapping jobs to mimic the older behavior with respect to collections.\n\ - \ Partially scheduled steps may provide incomplete information and\ - \ the listed steps outputs\n are not the mapped over step outputs\ - \ but the individual job outputs." - in: query - name: legacy_job_state - required: false - schema: - default: false - description: "Populate the invocation step state with the job state instead\ - \ of the invocation step state.\n This will also produce one step\ - \ per job in mapping jobs to mimic the older behavior with respect to\ - \ collections.\n Partially scheduled steps may provide incomplete\ - \ information and the listed steps outputs\n are not the mapped\ - \ over step outputs but the individual job outputs." - title: Replace with job state - type: boolean - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/WorkflowInvocationResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get detailed description of a workflow invocation. - tags: - - workflows - - workflows - /api/workflows/{workflow_id}/usage/{invocation_id}/jobs_summary: - get: - deprecated: true - description: An alias for `GET /api/invocations/{invocation_id}/jobs_summary`. - `workflow_id` is ignored. - operationId: workflow_invocation_jobs_summary_api_workflows__workflow_id__usage__invocation_id__jobs_summary_get - parameters: - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/InvocationJobsResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get job state summary info aggregated across all current jobs of the - workflow invocation. - tags: - - workflows - - workflows - /api/workflows/{workflow_id}/usage/{invocation_id}/report: - get: - deprecated: true - description: An alias for `GET /api/invocations/{invocation_id}/report`. `workflow_id` - is ignored. - operationId: show_workflow_invocation_report_api_workflows__workflow_id__usage__invocation_id__report_get - parameters: - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/InvocationReport' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get JSON summarizing invocation for reporting. - tags: - - workflows - - workflows - /api/workflows/{workflow_id}/usage/{invocation_id}/report.pdf: - get: - deprecated: true - description: An alias for `GET /api/invocations/{invocation_id}/report.pdf`. - `workflow_id` is ignored. - operationId: show_workflow_invocation_report_pdf_api_workflows__workflow_id__usage__invocation_id__report_pdf_get - parameters: - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get PDF summarizing invocation for reporting. - tags: - - workflows - - workflows - /api/workflows/{workflow_id}/usage/{invocation_id}/step_jobs_summary: - get: - deprecated: true - description: An alias for `GET /api/invocations/{invocation_id}/step_jobs_summary`. - `workflow_id` is ignored. - operationId: workflow_invocation_step_jobs_summary_api_workflows__workflow_id__usage__invocation_id__step_jobs_summary_get - parameters: - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - items: - anyOf: - - $ref: '#/components/schemas/InvocationStepJobsResponseStepModel' - - $ref: '#/components/schemas/InvocationStepJobsResponseJobModel' - - $ref: '#/components/schemas/InvocationStepJobsResponseCollectionJobsModel' - title: Response Workflow Invocation Step Jobs Summary Api Workflows Workflow - Id Usage Invocation Id Step Jobs Summary Get - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get job state summary info aggregated per step of the workflow invocation. - tags: - - workflows - - workflows - /api/workflows/{workflow_id}/usage/{invocation_id}/steps/{step_id}: - get: - deprecated: true - description: An alias for `GET /api/invocations/{invocation_id}/steps/{step_id}`. - `workflow_id` and `invocation_id` are ignored. - operationId: workflow_invocation_step_api_workflows__workflow_id__usage__invocation_id__steps__step_id__get - parameters: - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The encoded database identifier of the WorkflowInvocationStep. - in: path - name: step_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/InvocationStep' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Show details of workflow invocation step. - tags: - - workflows - - workflows - put: - deprecated: true - description: An alias for `PUT /api/invocations/{invocation_id}/steps/{step_id}`. - `workflow_id` is ignored. - operationId: update_workflow_invocation_step_api_workflows__workflow_id__usage__invocation_id__steps__step_id__put - parameters: - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The encoded database identifier of the Invocation. - in: path - name: invocation_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The encoded database identifier of the WorkflowInvocationStep. - in: path - name: step_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/InvocationUpdatePayload' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/InvocationStep' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Update state of running workflow step invocation. - tags: - - workflows - - workflows - /api/workflows/{workflow_id}/versions: - get: - operationId: show_versions_api_workflows__workflow_id__versions_get - parameters: - - description: The encoded database identifier of the Stored Workflow. - in: path - name: workflow_id - required: true - schema: - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - in: query - name: instance - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: false - title: True when fetching by Workflow ID, False when fetching by StoredWorkflow - ID. - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: List all versions of a workflow. - tags: - - workflows - - workflows - /ga4gh/drs/v1/objects/{object_id}: - get: - operationId: get_object_ga4gh_drs_v1_objects__object_id__get - parameters: - - description: The ID of the group - in: path - name: object_id - required: true - schema: - description: The ID of the group - title: Object ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DrsObject' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get Object - tags: - - drs - - drs - post: - operationId: get_object_ga4gh_drs_v1_objects__object_id__post - parameters: - - description: The ID of the group - in: path - name: object_id - required: true - schema: - description: The ID of the group - title: Object ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DrsObject' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get Object - tags: - - drs - - drs - /ga4gh/drs/v1/objects/{object_id}/access/{access_id}: - get: - operationId: get_access_url_ga4gh_drs_v1_objects__object_id__access__access_id__get - parameters: - - description: The ID of the group - in: path - name: object_id - required: true - schema: - description: The ID of the group - title: Object ID - type: string - - description: The access ID of the access method for objects, unused in Galaxy. - in: path - name: access_id - required: true - schema: - description: The access ID of the access method for objects, unused in Galaxy. - title: Access ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get Access Url - tags: - - drs - - drs - post: - operationId: get_access_url_ga4gh_drs_v1_objects__object_id__access__access_id__post - parameters: - - description: The ID of the group - in: path - name: object_id - required: true - schema: - description: The ID of the group - title: Object ID - type: string - - description: The access ID of the access method for objects, unused in Galaxy. - in: path - name: access_id - required: true - schema: - description: The access ID of the access method for objects, unused in Galaxy. - title: Access ID - type: string - - description: The user ID that will be used to effectively make this API call. - Only admins and designated users can make API calls on behalf of other users. - in: header - name: run-as - required: false - schema: - anyOf: - - example: 0123456789ABCDEF - minLength: 16 - pattern: '[0-9a-fA-F]+' - title: Invocation ID - type: string - - type: 'null' - description: The user ID that will be used to effectively make this API - call. Only admins and designated users can make API calls on behalf of - other users. - title: Run as User - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - - HTTPBearer: [] - summary: Get Access Url - tags: - - drs - - drs - /ga4gh/drs/v1/service-info: - get: - operationId: service_info_ga4gh_drs_v1_service_info_get - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/Service' - description: Successful Response - security: [] - summary: Service Info - tags: - - drs - - drs diff --git a/_shed_schema.yaml b/_shed_schema.yaml deleted file mode 100644 index ae80d3c2b4e1..000000000000 --- a/_shed_schema.yaml +++ /dev/null @@ -1,3010 +0,0 @@ -components: - schemas: - APIKeyResponse: - properties: - api_key: - title: Api Key - type: string - required: - - api_key - title: APIKeyResponse - type: object - Body_repositories__create_revision: - properties: - commit_message: - title: Commit Message - files: - anyOf: - - items: - format: binary - type: string - type: array - - type: 'null' - title: Files - title: Body_repositories__create_revision - type: object - BuildSearchIndexResponse: - properties: - repositories_indexed: - title: Repositories Indexed - type: integer - tools_indexed: - title: Tools Indexed - type: integer - required: - - repositories_indexed - - tools_indexed - title: BuildSearchIndexResponse - type: object - Category: - properties: - deleted: - title: Deleted - type: boolean - description: - title: Description - type: string - id: - title: Id - type: string - name: - title: Name - type: string - repositories: - title: Repositories - type: integer - required: - - id - - name - - description - - deleted - - repositories - title: Category - type: object - Checksum: - properties: - checksum: - description: 'The hex-string encoded checksum for the data. ' - title: Checksum - type: string - type: - description: 'The digest method used to create the checksum. - - The value (e.g. `sha-256`) SHOULD be listed as `Hash Name String` in the - https://github.com/ga4gh-discovery/ga4gh-checksum/blob/master/hash-alg.csv[GA4GH - Checksum Hash Algorithm Registry]. - - Other values MAY be used, as long as implementers are aware of the issues - discussed in https://tools.ietf.org/html/rfc6920#section-9.4[RFC6920]. - - GA4GH may provide more explicit guidance for use of non-IANA-registered - algorithms in the future.' - title: Type - type: string - required: - - checksum - - type - title: Checksum - type: object - CreateCategoryRequest: - properties: - description: - anyOf: - - type: string - - type: 'null' - title: Description - name: - title: Name - type: string - required: - - name - title: CreateCategoryRequest - type: object - CreateRepositoryRequest: - properties: - category_ids[]: - anyOf: - - items: - type: string - type: array - - type: string - - type: 'null' - title: Category IDs - description: - anyOf: - - type: string - - type: 'null' - title: Description - homepage_url: - anyOf: - - type: string - - type: 'null' - title: Homepage Url - name: - title: Name - type: string - remote_repository_url: - anyOf: - - type: string - - type: 'null' - title: Remote Repository Url - synopsis: - title: Synopsis - type: string - type: - default: unrestricted - enum: - - repository_suite_definition - - tool_dependency_definition - - unrestricted - title: Type - type: string - required: - - name - - synopsis - - category_ids[] - title: CreateRepositoryRequest - type: object - CreateUserRequest: - properties: - email: - title: Email - type: string - password: - title: Password - type: string - username: - title: Username - type: string - required: - - username - - email - - password - title: CreateUserRequest - type: object - DescriptorType: - enum: - - CWL - - WDL - - NFL - - GALAXY - - SMK - title: DescriptorType - type: string - DescriptorTypeVersion: - title: DescriptorTypeVersion - type: string - DetailedRepository: - properties: - create_time: - title: Create Time - type: string - deleted: - title: Deleted - type: boolean - deprecated: - title: Deprecated - type: boolean - description: - title: Description - type: string - homepage_url: - anyOf: - - type: string - - type: 'null' - title: Homepage Url - id: - title: Id - type: string - long_description: - anyOf: - - type: string - - type: 'null' - title: Long Description - name: - title: Name - type: string - owner: - title: Owner - type: string - private: - title: Private - type: boolean - remote_repository_url: - anyOf: - - type: string - - type: 'null' - title: Remote Repository Url - times_downloaded: - title: Times Downloaded - type: integer - type: - title: Type - type: string - update_time: - title: Update Time - type: string - user_id: - title: User Id - type: string - required: - - id - - name - - owner - - type - - description - - user_id - - private - - deleted - - times_downloaded - - deprecated - - create_time - - update_time - - long_description - title: DetailedRepository - type: object - FailedRepositoryUpdateMessage: - properties: - err_msg: - title: Err Msg - type: string - required: - - err_msg - title: FailedRepositoryUpdateMessage - type: object - HTTPValidationError: - properties: - detail: - items: - $ref: '#/components/schemas/ValidationError' - title: Detail - type: array - title: HTTPValidationError - type: object - ImageData: - properties: - checksum: - anyOf: - - items: - $ref: '#/components/schemas/Checksum' - type: array - - type: 'null' - description: A production (immutable) tool version is required to have a - hashcode. Not required otherwise, but might be useful to detect changes. This - exposes the hashcode for specific image versions to verify that the container - version pulled is actually the version that was indexed by the registry. - examples: - - checksum: 77af4d6b9913e693e8d0b4b294fa62ade6054e6b2f1ffb617ac955dd63fb0182 - type: sha256 - title: Checksum - image_name: - anyOf: - - type: string - - type: 'null' - description: Used in conjunction with a registry_url if provided to locate - images. - examples: - - quay.io/seqware/seqware_full/1.1 - - ubuntu:latest - title: Image Name - image_type: - anyOf: - - $ref: '#/components/schemas/ImageType' - - type: 'null' - registry_host: - anyOf: - - type: string - - type: 'null' - description: A docker registry or a URL to a Singularity registry. Used - along with image_name to locate a specific image. - examples: - - registry.hub.docker.com - title: Registry Host - size: - anyOf: - - type: integer - - type: 'null' - description: Size of the container in bytes. - title: Size - updated: - anyOf: - - type: string - - type: 'null' - description: Last time the container was updated. - title: Updated - title: ImageData - type: object - ImageType: - enum: - - Docker - - Singularity - - Conda - title: ImageType - type: string - InstallInfo: - properties: - metadata_info: - anyOf: - - $ref: '#/components/schemas/RepositoryMetadataInstallInfo' - - type: 'null' - repo_info: - anyOf: - - $ref: '#/components/schemas/RepositoryExtraInstallInfo' - - type: 'null' - title: InstallInfo - type: object - Organization: - properties: - name: - description: Name of the organization responsible for the service - examples: - - My organization - title: Name - type: string - url: - description: URL of the website of the organization (RFC 3986 format) - examples: - - https://example.com - format: uri - minLength: 1 - title: Url - type: string - required: - - name - - url - title: Organization - type: object - RepositoriesByCategory: - properties: - description: - title: Description - type: string - id: - title: Id - type: string - name: - title: Name - type: string - repositories: - items: - $ref: '#/components/schemas/Repository' - title: Repositories - type: array - repository_count: - title: Repository Count - type: integer - required: - - id - - name - - description - - repository_count - - repositories - title: RepositoriesByCategory - type: object - Repository: - properties: - create_time: - title: Create Time - type: string - deleted: - title: Deleted - type: boolean - deprecated: - title: Deprecated - type: boolean - description: - title: Description - type: string - homepage_url: - anyOf: - - type: string - - type: 'null' - title: Homepage Url - id: - title: Id - type: string - name: - title: Name - type: string - owner: - title: Owner - type: string - private: - title: Private - type: boolean - remote_repository_url: - anyOf: - - type: string - - type: 'null' - title: Remote Repository Url - times_downloaded: - title: Times Downloaded - type: integer - type: - title: Type - type: string - update_time: - title: Update Time - type: string - user_id: - title: User Id - type: string - required: - - id - - name - - owner - - type - - description - - user_id - - private - - deleted - - times_downloaded - - deprecated - - create_time - - update_time - title: Repository - type: object - RepositoryDependency: - properties: - changeset_revision: - title: Changeset Revision - type: string - downloadable: - title: Downloadable - type: boolean - has_repository_dependencies: - title: Has Repository Dependencies - type: boolean - id: - title: Id - type: string - includes_datatypes: - anyOf: - - type: boolean - - type: 'null' - title: Includes Datatypes - includes_tool_dependencies: - anyOf: - - type: boolean - - type: 'null' - title: Includes Tool Dependencies - includes_tools: - title: Includes Tools - type: boolean - includes_tools_for_display_in_tool_panel: - title: Includes Tools For Display In Tool Panel - type: boolean - includes_workflows: - anyOf: - - type: boolean - - type: 'null' - title: Includes Workflows - invalid_tools: - items: - type: string - title: Invalid Tools - type: array - malicious: - title: Malicious - type: boolean - missing_test_components: - title: Missing Test Components - type: boolean - numeric_revision: - title: Numeric Revision - type: integer - repository: - $ref: '#/components/schemas/Repository' - repository_dependencies: - items: - $ref: '#/components/schemas/RepositoryDependency' - title: Repository Dependencies - type: array - repository_id: - title: Repository Id - type: string - tools: - anyOf: - - items: - $ref: '#/components/schemas/RepositoryTool' - type: array - - type: 'null' - title: Tools - required: - - id - - repository - - repository_dependencies - - invalid_tools - - repository_id - - numeric_revision - - changeset_revision - - malicious - - downloadable - - missing_test_components - - has_repository_dependencies - - includes_tools - - includes_tools_for_display_in_tool_panel - title: RepositoryDependency - type: object - RepositoryExtraInstallInfo: - properties: - changeset_revision: - title: Changeset Revision - type: string - ctx_rev: - title: Ctx Rev - type: string - description: - title: Description - type: string - name: - title: Name - type: string - repository_clone_url: - title: Repository Clone Url - type: string - repository_dependencies: - anyOf: - - type: object - - type: 'null' - title: Repository Dependencies - repository_owner: - title: Repository Owner - type: string - required: - - name - - description - - repository_clone_url - - changeset_revision - - ctx_rev - - repository_owner - title: RepositoryExtraInstallInfo - type: object - RepositoryMetadata: - additionalProperties: - $ref: '#/components/schemas/RepositoryRevisionMetadata' - title: RepositoryMetadata - type: object - RepositoryMetadataInstallInfo: - properties: - changeset_revision: - title: Changeset Revision - type: string - downloadable: - title: Downloadable - type: boolean - has_repository_dependencies: - title: Has Repository Dependencies - type: boolean - id: - title: Id - type: string - includes_tools: - title: Includes Tools - type: boolean - includes_tools_for_display_in_tool_panel: - title: Includes Tools For Display In Tool Panel - type: boolean - malicious: - title: Malicious - type: boolean - repository_id: - title: Repository Id - type: string - url: - title: Url - type: string - valid_tools: - items: - $ref: '#/components/schemas/ValidTool' - title: Valid Tools - type: array - required: - - id - - changeset_revision - - downloadable - - has_repository_dependencies - - includes_tools - - includes_tools_for_display_in_tool_panel - - malicious - - repository_id - - url - - valid_tools - title: RepositoryMetadataInstallInfo - type: object - RepositoryPermissions: - properties: - allow_push: - items: - type: string - title: Allow Push - type: array - can_manage: - title: Can Manage - type: boolean - can_push: - title: Can Push - type: boolean - required: - - allow_push - - can_manage - - can_push - title: RepositoryPermissions - type: object - RepositoryRevisionMetadata: - properties: - changeset_revision: - title: Changeset Revision - type: string - downloadable: - title: Downloadable - type: boolean - has_repository_dependencies: - title: Has Repository Dependencies - type: boolean - id: - title: Id - type: string - includes_datatypes: - anyOf: - - type: boolean - - type: 'null' - title: Includes Datatypes - includes_tool_dependencies: - anyOf: - - type: boolean - - type: 'null' - title: Includes Tool Dependencies - includes_tools: - title: Includes Tools - type: boolean - includes_tools_for_display_in_tool_panel: - title: Includes Tools For Display In Tool Panel - type: boolean - includes_workflows: - anyOf: - - type: boolean - - type: 'null' - title: Includes Workflows - invalid_tools: - items: - type: string - title: Invalid Tools - type: array - malicious: - title: Malicious - type: boolean - missing_test_components: - title: Missing Test Components - type: boolean - numeric_revision: - title: Numeric Revision - type: integer - repository: - $ref: '#/components/schemas/Repository' - repository_dependencies: - items: - $ref: '#/components/schemas/RepositoryDependency' - title: Repository Dependencies - type: array - repository_id: - title: Repository Id - type: string - tools: - anyOf: - - items: - $ref: '#/components/schemas/RepositoryTool' - type: array - - type: 'null' - title: Tools - required: - - id - - repository - - repository_dependencies - - invalid_tools - - repository_id - - numeric_revision - - changeset_revision - - malicious - - downloadable - - missing_test_components - - has_repository_dependencies - - includes_tools - - includes_tools_for_display_in_tool_panel - title: RepositoryRevisionMetadata - type: object - RepositoryRevisionReadmes: - additionalProperties: - type: string - title: RepositoryRevisionReadmes - type: object - RepositorySearchHit: - properties: - repository: - $ref: '#/components/schemas/RepositorySearchResult' - score: - title: Score - type: number - required: - - score - - repository - title: RepositorySearchHit - type: object - RepositorySearchResult: - properties: - approved: - title: Approved - type: boolean - categories: - title: Categories - type: string - description: - title: Description - type: string - full_last_updated: - title: Full Last Updated - type: string - homepage_url: - anyOf: - - type: string - - type: 'null' - title: Homepage Url - id: - title: Id - type: string - last_update: - anyOf: - - type: string - - type: 'null' - title: Last Update - long_description: - anyOf: - - type: string - - type: 'null' - title: Long Description - name: - title: Name - type: string - remote_repository_url: - anyOf: - - type: string - - type: 'null' - title: Remote Repository Url - repo_lineage: - title: Repo Lineage - type: string - repo_owner_username: - title: Repo Owner Username - type: string - times_downloaded: - title: Times Downloaded - type: integer - required: - - id - - name - - repo_owner_username - - description - - full_last_updated - - repo_lineage - - approved - - times_downloaded - - categories - title: RepositorySearchResult - type: object - RepositorySearchResults: - properties: - hits: - items: - $ref: '#/components/schemas/RepositorySearchHit' - title: Hits - type: array - hostname: - title: Hostname - type: string - page: - title: Page - type: string - page_size: - title: Page Size - type: string - total_results: - title: Total Results - type: string - required: - - total_results - - page - - page_size - - hostname - - hits - title: RepositorySearchResults - type: object - RepositoryTool: - properties: - description: - title: Description - type: string - guid: - title: Guid - type: string - id: - title: Id - type: string - name: - title: Name - type: string - requirements: - items: {} - title: Requirements - type: array - tool_config: - title: Tool Config - type: string - tool_type: - title: Tool Type - type: string - version: - title: Version - type: string - required: - - description - - guid - - id - - name - - requirements - - tool_config - - tool_type - - version - title: RepositoryTool - type: object - RepositoryUpdate: - anyOf: - - $ref: '#/components/schemas/ValidRepostiroyUpdateMessage' - - $ref: '#/components/schemas/FailedRepositoryUpdateMessage' - title: RepositoryUpdate - ResetMetadataOnRepositoryResponse: - properties: - repository_status: - items: - type: string - title: Repository Status - type: array - start_time: - title: Start Time - type: string - status: - title: Status - type: string - stop_time: - title: Stop Time - type: string - required: - - status - - repository_status - - start_time - - stop_time - title: ResetMetadataOnRepositoryResponse - type: object - Service: - properties: - contactUrl: - anyOf: - - format: uri - minLength: 1 - type: string - - type: 'null' - description: URL of the contact for the provider of this service, e.g. a - link to a contact form (RFC 3986 format), or an email (RFC 2368 format). - examples: - - mailto:support@example.com - title: Contacturl - createdAt: - anyOf: - - format: date-time - type: string - - type: 'null' - description: Timestamp describing when the service was first deployed and - available (RFC 3339 format) - examples: - - '2019-06-04T12:58:19Z' - title: Createdat - description: - anyOf: - - type: string - - type: 'null' - description: Description of the service. Should be human readable and provide - information about the service. - examples: - - This service provides... - title: Description - documentationUrl: - anyOf: - - format: uri - minLength: 1 - type: string - - type: 'null' - description: URL of the documentation of this service (RFC 3986 format). - This should help someone learn how to use your service, including any - specifics required to access data, e.g. authentication. - examples: - - https://docs.myservice.example.com - title: Documentationurl - environment: - anyOf: - - type: string - - type: 'null' - description: Environment the service is running in. Use this to distinguish - between production, development and testing/staging deployments. Suggested - values are prod, test, dev, staging. However this is advised and not enforced. - examples: - - test - title: Environment - id: - description: Unique ID of this service. Reverse domain name notation is - recommended, though not required. The identifier should attempt to be - globally unique so it can be used in downstream aggregator services e.g. - Service Registry. - examples: - - org.ga4gh.myservice - title: Id - type: string - name: - description: Name of this service. Should be human readable. - examples: - - My project - title: Name - type: string - organization: - allOf: - - $ref: '#/components/schemas/Organization' - description: Organization providing the service - type: - $ref: '#/components/schemas/ServiceType' - updatedAt: - anyOf: - - format: date-time - type: string - - type: 'null' - description: Timestamp describing when the service was last updated (RFC - 3339 format) - examples: - - '2019-06-04T12:58:19Z' - title: Updatedat - version: - description: Version of the service being described. Semantic versioning - is recommended, but other identifiers, such as dates or commit hashes, - are also allowed. The version should be changed whenever the service is - updated. - examples: - - 1.0.0 - title: Version - type: string - required: - - id - - name - - type - - organization - - version - title: Service - type: object - ServiceType: - properties: - artifact: - description: Name of the API or GA4GH specification implemented. Official - GA4GH types should be assigned as part of standards approval process. - Custom artifacts are supported. - examples: - - beacon - title: Artifact - type: string - group: - description: Namespace in reverse domain name format. Use `org.ga4gh` for - implementations compliant with official GA4GH specifications. For services - with custom APIs not standardized by GA4GH, or implementations diverging - from official GA4GH specifications, use a different namespace (e.g. your - organization's reverse domain name). - examples: - - org.ga4gh - title: Group - type: string - version: - description: Version of the API or specification. GA4GH specifications use - semantic versioning. - examples: - - 1.0.0 - title: Version - type: string - required: - - group - - artifact - - version - title: ServiceType - type: object - Tool: - properties: - aliases: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: "Support for this parameter is optional for tool registries\ - \ that support aliases.\nA list of strings that can be used to identify\ - \ this tool which could be straight up URLs. \nThis can be used to expose\ - \ alternative ids (such as GUIDs) for a tool\nfor registries. Can be used\ - \ to match tools across registries." - title: Aliases - checker_url: - anyOf: - - type: string - - type: 'null' - description: Optional url to the checker tool that will exit successfully - if this tool produced the expected result given test data. - title: Checker Url - description: - anyOf: - - type: string - - type: 'null' - description: The description of the tool. - title: Description - has_checker: - anyOf: - - type: boolean - - type: 'null' - description: Whether this tool has a checker tool associated with it. - title: Has Checker - id: - description: A unique identifier of the tool, scoped to this registry. - examples: - - 123456 - title: Id - type: string - meta_version: - anyOf: - - type: string - - type: 'null' - description: The version of this tool in the registry. Iterates when fields - like the description, author, etc. are updated. - title: Meta Version - name: - anyOf: - - type: string - - type: 'null' - description: The name of the tool. - title: Name - organization: - description: The organization that published the image. - title: Organization - type: string - toolclass: - $ref: '#/components/schemas/ToolClass' - url: - description: The URL for this tool in this registry. - examples: - - http://agora.broadinstitute.org/tools/123456 - title: Url - type: string - versions: - description: A list of versions for this tool. - items: - $ref: '#/components/schemas/ToolVersion' - title: Versions - type: array - required: - - url - - id - - organization - - toolclass - - versions - title: Tool - type: object - ToolClass: - properties: - description: - anyOf: - - type: string - - type: 'null' - description: A longer explanation of what this class is and what it can - accomplish. - title: Description - id: - anyOf: - - type: string - - type: 'null' - description: The unique identifier for the class. - title: Id - name: - anyOf: - - type: string - - type: 'null' - description: A short friendly name for the class. - title: Name - title: ToolClass - type: object - ToolVersion: - properties: - author: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: Contact information for the author of this version of the tool - in the registry. (More complex authorship information is handled by the - descriptor). - title: Author - containerfile: - anyOf: - - type: boolean - - type: 'null' - description: Reports if this tool has a containerfile available. (For Docker-based - tools, this would indicate the presence of a Dockerfile) - title: Containerfile - descriptor_type: - anyOf: - - items: - $ref: '#/components/schemas/DescriptorType' - type: array - - type: 'null' - description: The type (or types) of descriptors available. - title: Descriptor Type - descriptor_type_version: - anyOf: - - additionalProperties: - items: - $ref: '#/components/schemas/DescriptorTypeVersion' - type: array - type: object - - type: 'null' - description: A map providing information about the language versions used - in this tool. The keys should be the same values used in the `descriptor_type` - field, and the value should be an array of all the language versions used - for the given `descriptor_type`. Depending on the `descriptor_type` (e.g. - CWL) multiple version values may be used in a single tool. - examples: - - "{\n \"WDL\": [\"1.0\", \"1.0\"],\n \"CWL\": [\"v1.0.2\"],\n \"NFL\"\ - : [\"DSL2\"]\n}\n" - title: Descriptor Type Version - id: - description: An identifier of the version of this tool for this particular - tool registry. - examples: - - v1 - title: Id - type: string - images: - anyOf: - - items: - $ref: '#/components/schemas/ImageData' - type: array - - type: 'null' - description: All known docker images (and versions/hashes) used by this - tool. If the tool has to evaluate any of the docker images strings at - runtime, those ones cannot be reported here. - title: Images - included_apps: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: An array of IDs for the applications that are stored inside - this tool. - examples: - - https://bio.tools/tool/mytum.de/SNAP2/1 - - https://bio.tools/bioexcel_seqqc - title: Included Apps - is_production: - anyOf: - - type: boolean - - type: 'null' - description: This version of a tool is guaranteed to not change over time - (for example, a tool built from a tag in git as opposed to a branch). - A production quality tool is required to have a checksum - title: Is Production - meta_version: - anyOf: - - type: string - - type: 'null' - description: The version of this tool version in the registry. Iterates - when fields like the description, author, etc. are updated. - title: Meta Version - name: - anyOf: - - type: string - - type: 'null' - description: The name of the version. - title: Name - signed: - anyOf: - - type: boolean - - type: 'null' - description: Reports whether this version of the tool has been signed. - title: Signed - url: - description: The URL for this tool version in this registry. - examples: - - http://agora.broadinstitute.org/tools/123456/versions/1 - title: Url - type: string - verified: - anyOf: - - type: boolean - - type: 'null' - description: Reports whether this tool has been verified by a specific organization - or individual. - title: Verified - verified_source: - anyOf: - - items: - type: string - type: array - - type: 'null' - description: Source of metadata that can support a verified tool, such as - an email or URL. - title: Verified Source - required: - - url - - id - title: ToolVersion - type: object - UiChangePasswordRequest: - properties: - current: - title: Current - type: string - password: - title: Password - type: string - required: - - current - - password - title: UiChangePasswordRequest - type: object - UiLoginRequest: - properties: - login: - title: Login - type: string - password: - title: Password - type: string - session_csrf_token: - title: Session Csrf Token - type: string - required: - - session_csrf_token - - login - - password - title: UiLoginRequest - type: object - UiLoginResponse: - properties: {} - title: UiLoginResponse - type: object - UiLogoutRequest: - properties: - logout_all: - default: false - title: Logout All - type: boolean - session_csrf_token: - title: Session Csrf Token - type: string - required: - - session_csrf_token - title: UiLogoutRequest - type: object - UiLogoutResponse: - properties: {} - title: UiLogoutResponse - type: object - UiRegisterRequest: - properties: - bear_field: - title: Bear Field - type: string - email: - title: Email - type: string - password: - title: Password - type: string - username: - title: Username - type: string - required: - - email - - username - - password - - bear_field - title: UiRegisterRequest - type: object - UiRegisterResponse: - properties: - activation_error: - default: false - title: Activation Error - type: boolean - activation_sent: - default: false - title: Activation Sent - type: boolean - contact_email: - anyOf: - - type: string - - type: 'null' - title: Contact Email - email: - title: Email - type: string - required: - - email - title: UiRegisterResponse - type: object - UserV2: - properties: - id: - title: Id - type: string - is_admin: - title: Is Admin - type: boolean - username: - title: Username - type: string - required: - - id - - username - - is_admin - title: UserV2 - type: object - ValidRepostiroyUpdateMessage: - properties: - message: - title: Message - type: string - required: - - message - title: ValidRepostiroyUpdateMessage - type: object - ValidTool: - properties: - add_to_tool_panel: - title: Add To Tool Panel - type: boolean - description: - title: Description - type: string - guid: - title: Guid - type: string - id: - title: Id - type: string - name: - title: Name - type: string - requirements: - items: {} - title: Requirements - type: array - tests: - items: {} - title: Tests - type: array - tool_config: - title: Tool Config - type: string - tool_type: - title: Tool Type - type: string - version: - title: Version - type: string - version_string_cmd: - anyOf: - - type: string - - type: 'null' - title: Version String Cmd - required: - - add_to_tool_panel - - description - - guid - - id - - name - - requirements - - tests - - tool_config - - tool_type - - version - title: ValidTool - type: object - ValidationError: - properties: - loc: - items: - anyOf: - - type: string - - type: integer - title: Location - type: array - msg: - title: Message - type: string - type: - title: Error Type - type: string - required: - - loc - - msg - - type - title: ValidationError - type: object - Version: - properties: - api_version: - default: v1 - title: Api Version - type: string - version: - title: Version - type: string - version_major: - title: Version Major - type: string - required: - - version_major - - version - title: Version - type: object - securitySchemes: - APIKeyCookie: - in: cookie - name: galaxycommunitysession - type: apiKey - APIKeyHeader: - in: header - name: x-api-key - type: apiKey - APIKeyQuery: - in: query - name: key - type: apiKey -info: - description: This API allows you to manage the Tool Shed repositories. - license: - name: MIT - url: https://github.com/galaxyproject/galaxy/blob/dev/LICENSE.txt - title: Galaxy Tool Shed API - version: 0.1.0 -openapi: 3.1.0 -paths: - /api/authenticate/baseauth: - get: - operationId: authenticate__baseauth - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/APIKeyResponse' - description: Successful Response - summary: Returns returns an API key for authenticated user based on BaseAuth - headers. - tags: - - authenticate - - authenticate - /api/categories: - get: - description: index category - operationId: categories__index - responses: - '200': - content: - application/json: - schema: - items: - $ref: '#/components/schemas/Category' - title: Response Categories Index - type: array - description: Successful Response - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Index - tags: - - categories - - categories - post: - description: create a category - operationId: categories__create - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/CreateCategoryRequest' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/Category' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Create - tags: - - categories - - categories - /api/categories/{encoded_category_id}: - get: - description: show category - operationId: categories__show - parameters: - - description: The encoded database identifier of the category. - in: path - name: encoded_category_id - required: true - schema: - description: The encoded database identifier of the category. - title: Category ID - type: string - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/Category' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - summary: Show - tags: - - categories - - categories - /api/categories/{encoded_category_id}/repositories: - get: - description: display repositories by category - operationId: categories__repositories - parameters: - - description: The encoded database identifier of the category. - in: path - name: encoded_category_id - required: true - schema: - description: The encoded database identifier of the category. - title: Category ID - type: string - - in: query - name: installable - required: false - schema: - default: false - title: Installable? - type: boolean - - in: query - name: sort_key - required: false - schema: - default: name - title: Sort Key - type: string - - in: query - name: sort_order - required: false - schema: - default: asc - title: Sort Order - type: string - - in: query - name: page - required: false - schema: - anyOf: - - type: integer - - type: 'null' - title: Page - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/RepositoriesByCategory' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Repositories - tags: - - categories - - categories - /api/ga4gh/trs/v2/service-info: - get: - operationId: tools_trs_service_info - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/Service' - description: Successful Response - summary: Service Info - tags: - - tools - - tools - /api/ga4gh/trs/v2/toolClasses: - get: - operationId: tools__trs_tool_classes - responses: - '200': - content: - application/json: - schema: - items: - $ref: '#/components/schemas/ToolClass' - title: Response Tools Trs Tool Classes - type: array - description: Successful Response - summary: Tool Classes - tags: - - tools - - tools - /api/ga4gh/trs/v2/tools: - get: - operationId: tools__trs_index - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - summary: Trs Index - tags: - - tools - - tools - /api/ga4gh/trs/v2/tools/{tool_id}: - get: - operationId: tools__trs_get - parameters: - - description: See also https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs-tool-and-trs-tool-version-ids - in: path - name: tool_id - required: true - schema: - description: See also https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs-tool-and-trs-tool-version-ids - title: GA4GH TRS Tool ID - type: string - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/Tool' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Trs Get - tags: - - tools - - tools - /api/ga4gh/trs/v2/tools/{tool_id}/versions: - get: - operationId: tools__trs_get_versions - parameters: - - description: See also https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs-tool-and-trs-tool-version-ids - in: path - name: tool_id - required: true - schema: - description: See also https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs-tool-and-trs-tool-version-ids - title: GA4GH TRS Tool ID - type: string - responses: - '200': - content: - application/json: - schema: - items: - $ref: '#/components/schemas/ToolVersion' - title: Response Tools Trs Get Versions - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Trs Get Versions - tags: - - tools - - tools - /api/repositories: - get: - description: Get a list of repositories or perform a search. - operationId: repositories__index - parameters: - - in: query - name: q - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Search Query - - in: query - name: page - required: false - schema: - anyOf: - - type: integer - - type: 'null' - default: 1 - title: Page - - in: query - name: page_size - required: false - schema: - anyOf: - - type: integer - - type: 'null' - default: 10 - title: Page Size - - in: query - name: deleted - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: false - title: Deleted? - - in: query - name: owner - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Owner - - in: query - name: name - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Name - responses: - '200': - content: - application/json: - schema: - anyOf: - - $ref: '#/components/schemas/RepositorySearchResults' - - items: - $ref: '#/components/schemas/Repository' - type: array - title: Response Repositories Index - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Index - tags: - - repositories - - repositories - post: - description: create a new repository - operationId: repositories__create - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/CreateRepositoryRequest' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/Repository' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Create - tags: - - repositories - - repositories - /api/repositories/get_ordered_installable_revisions: - get: - description: Get an ordered list of the repository changeset revisions that - are installable - operationId: repositories__get_ordered_installable_revisions - parameters: - - in: query - name: owner - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Owner - - in: query - name: name - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Name - - in: query - name: tsr_id - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: TSR ID - responses: - '200': - content: - application/json: - schema: - items: - type: string - title: Response Repositories Get Ordered Installable Revisions - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - summary: Get Ordered Installable Revisions - tags: - - repositories - - repositories - /api/repositories/get_repository_revision_install_info: - get: - description: Get information used by the install client to install this repository. - operationId: repositories__legacy_install_info - parameters: - - description: Name of the target repository. - in: query - name: name - required: true - schema: - description: Name of the target repository. - title: Name - type: string - - description: Owner of the target repository. - in: query - name: owner - required: true - schema: - description: Owner of the target repository. - title: owner - type: string - - description: Changeset of the target repository. - in: query - name: changeset_revision - required: true - schema: - description: Changeset of the target repository. - title: changeset - type: string - responses: - '200': - content: - application/json: - schema: - items: {} - title: Response Repositories Legacy Install Info - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Legacy Install Info - tags: - - repositories - - repositories - /api/repositories/install_info: - get: - description: Get information used by the install client to install this repository. - operationId: repositories__install_info - parameters: - - description: Name of the target repository. - in: query - name: name - required: true - schema: - description: Name of the target repository. - title: Name - type: string - - description: Owner of the target repository. - in: query - name: owner - required: true - schema: - description: Owner of the target repository. - title: owner - type: string - - description: Changeset of the target repository. - in: query - name: changeset_revision - required: true - schema: - description: Changeset of the target repository. - title: changeset - type: string - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/InstallInfo' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Install Info - tags: - - repositories - - repositories - /api/repositories/reset_metadata_on_repository: - post: - description: reset metadata on a repository - operationId: repositories__reset_legacy - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ResetMetadataOnRepositoryResponse' - description: Successful Response - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Reset Metadata On Repository Legacy - tags: - - repositories - - repositories - /api/repositories/updates: - get: - operationId: repositories__update - parameters: - - in: query - name: owner - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Owner - - in: query - name: name - required: false - schema: - anyOf: - - type: string - - type: 'null' - title: Name - - in: query - name: changeset_revision - required: true - schema: - title: Changeset Revision - type: string - - in: query - name: hexlify - required: false - schema: - anyOf: - - type: boolean - - type: 'null' - default: true - title: Hexlify response - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - summary: Updates - tags: - - repositories - - repositories - /api/repositories/{encoded_repository_id}: - get: - operationId: repositories__show - parameters: - - description: The encoded database identifier of the repository. - in: path - name: encoded_repository_id - required: true - schema: - description: The encoded database identifier of the repository. - title: Repository ID - type: string - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/DetailedRepository' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - summary: Show - tags: - - repositories - - repositories - /api/repositories/{encoded_repository_id}/allow_push: - get: - operationId: repositories__show_allow_push - parameters: - - description: The encoded database identifier of the repository. - in: path - name: encoded_repository_id - required: true - schema: - description: The encoded database identifier of the repository. - title: Repository ID - type: string - responses: - '200': - content: - application/json: - schema: - items: - type: string - title: Response Repositories Show Allow Push - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Show Allow Push - tags: - - repositories - - repositories - /api/repositories/{encoded_repository_id}/allow_push/{username}: - delete: - operationId: repositories__remove_allow_push - parameters: - - description: The encoded database identifier of the repository. - in: path - name: encoded_repository_id - required: true - schema: - description: The encoded database identifier of the repository. - title: Repository ID - type: string - - description: The target username. - in: path - name: username - required: true - schema: - description: The target username. - title: Username - type: string - responses: - '200': - content: - application/json: - schema: - items: - type: string - title: Response Repositories Remove Allow Push - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Remove Allow Push - tags: - - repositories - - repositories - post: - operationId: repositories__add_allow_push - parameters: - - description: The encoded database identifier of the repository. - in: path - name: encoded_repository_id - required: true - schema: - description: The encoded database identifier of the repository. - title: Repository ID - type: string - - description: The target username. - in: path - name: username - required: true - schema: - description: The target username. - title: Username - type: string - responses: - '200': - content: - application/json: - schema: - items: - type: string - title: Response Repositories Add Allow Push - type: array - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Add Allow Push - tags: - - repositories - - repositories - /api/repositories/{encoded_repository_id}/changeset_revision: - post: - description: upload new revision to the repository - operationId: repositories__create_revision - parameters: - - description: The encoded database identifier of the repository. - in: path - name: encoded_repository_id - required: true - schema: - description: The encoded database identifier of the repository. - title: Repository ID - type: string - - description: Set commit message as a query parameter. - in: query - name: commit_message - required: false - schema: - anyOf: - - type: string - - type: 'null' - description: Set commit message as a query parameter. - title: Commit Message - requestBody: - content: - multipart/form-data: - schema: - allOf: - - $ref: '#/components/schemas/Body_repositories__create_revision' - title: Body - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/RepositoryUpdate' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Create Changeset Revision - tags: - - repositories - - repositories - /api/repositories/{encoded_repository_id}/deprecated: - delete: - operationId: repositories__unset_deprecated - parameters: - - description: The encoded database identifier of the repository. - in: path - name: encoded_repository_id - required: true - schema: - description: The encoded database identifier of the repository. - title: Repository ID - type: string - responses: - '204': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Unset Deprecated - tags: - - repositories - - repositories - put: - operationId: repositories__set_deprecated - parameters: - - description: The encoded database identifier of the repository. - in: path - name: encoded_repository_id - required: true - schema: - description: The encoded database identifier of the repository. - title: Repository ID - type: string - responses: - '204': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Set Deprecated - tags: - - repositories - - repositories - /api/repositories/{encoded_repository_id}/metadata: - get: - description: Get information about repository metadata - operationId: repositories__metadata - parameters: - - description: The encoded database identifier of the repository. - in: path - name: encoded_repository_id - required: true - schema: - description: The encoded database identifier of the repository. - title: Repository ID - type: string - - description: Include only downloadable repositories. - in: query - name: downloadable_only - required: false - schema: - default: true - description: Include only downloadable repositories. - title: downloadable_only - type: boolean - responses: - '200': - content: - application/json: - schema: - title: Response Repositories Metadata - type: object - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - summary: Metadata - tags: - - repositories - - repositories - /api/repositories/{encoded_repository_id}/permissions: - get: - operationId: repositories__permissions - parameters: - - description: The encoded database identifier of the repository. - in: path - name: encoded_repository_id - required: true - schema: - description: The encoded database identifier of the repository. - title: Repository ID - type: string - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/RepositoryPermissions' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Permissions - tags: - - repositories - - repositories - /api/repositories/{encoded_repository_id}/reset_metadata: - post: - description: reset metadata on a repository - operationId: repositories__reset - parameters: - - description: The encoded database identifier of the repository. - in: path - name: encoded_repository_id - required: true - schema: - description: The encoded database identifier of the repository. - title: Repository ID - type: string - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/ResetMetadataOnRepositoryResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Reset Metadata On Repository - tags: - - repositories - - repositories - /api/repositories/{encoded_repository_id}/revisions/{changeset_revision}/malicious: - delete: - operationId: repositories__unset_malicious - parameters: - - description: The encoded database identifier of the repository. - in: path - name: encoded_repository_id - required: true - schema: - description: The encoded database identifier of the repository. - title: Repository ID - type: string - - description: The changeset revision corresponding to the target revision of - the target repository. - in: path - name: changeset_revision - required: true - schema: - description: The changeset revision corresponding to the target revision - of the target repository. - title: Change Revision - type: string - responses: - '204': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Unset Malicious - tags: - - repositories - - repositories - put: - operationId: repositories__set_malicious - parameters: - - description: The encoded database identifier of the repository. - in: path - name: encoded_repository_id - required: true - schema: - description: The encoded database identifier of the repository. - title: Repository ID - type: string - - description: The changeset revision corresponding to the target revision of - the target repository. - in: path - name: changeset_revision - required: true - schema: - description: The changeset revision corresponding to the target revision - of the target repository. - title: Change Revision - type: string - responses: - '204': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Set Malicious - tags: - - repositories - - repositories - /api/repositories/{encoded_repository_id}/revisions/{changeset_revision}/readmes: - get: - description: fetch readmes for repository revision - operationId: repositories__readmes - parameters: - - description: The encoded database identifier of the repository. - in: path - name: encoded_repository_id - required: true - schema: - description: The encoded database identifier of the repository. - title: Repository ID - type: string - - description: The changeset revision corresponding to the target revision of - the target repository. - in: path - name: changeset_revision - required: true - schema: - description: The changeset revision corresponding to the target revision - of the target repository. - title: Change Revision - type: string - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/RepositoryRevisionReadmes' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - summary: Get Readmes - tags: - - repositories - - repositories - /api/tools: - get: - operationId: tools__index - parameters: - - in: query - name: q - required: true - schema: - title: Search Query - type: string - - in: query - name: page - required: false - schema: - default: 1 - title: Page - type: integer - - in: query - name: page_size - required: false - schema: - default: 10 - title: Page Size - type: integer - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Index - tags: - - tools - - tools - /api/tools/build_search_index: - put: - description: 'Not part of the stable API, just something to simplify - - bootstrapping tool sheds, scripting, testing, etc...' - operationId: tools__build_search_index - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/BuildSearchIndexResponse' - description: Successful Response - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Build Search Index - tags: - - tools - - tools - /api/users: - get: - description: index users - operationId: users__index - responses: - '200': - content: - application/json: - schema: - items: - $ref: '#/components/schemas/UserV2' - title: Response Users Index - type: array - description: Successful Response - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Index - tags: - - users - - users - post: - description: create a user - operationId: users__create - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/CreateUserRequest' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/UserV2' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Create - tags: - - users - - users - /api/users/current: - get: - description: show current user - operationId: users__current - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/UserV2' - description: Successful Response - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Current - tags: - - users - - users - /api/users/{encoded_user_id}: - get: - description: show a user - operationId: users__show - parameters: - - description: The encoded database identifier of the user. - in: path - name: encoded_user_id - required: true - schema: - description: The encoded database identifier of the user. - title: User ID - type: string - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/UserV2' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Show - tags: - - users - - users - /api/users/{encoded_user_id}/api_key: - delete: - operationId: users__delete_api_key - parameters: - - description: The encoded database identifier of the user. - in: path - name: encoded_user_id - required: true - schema: - description: The encoded database identifier of the user. - title: User ID - type: string - responses: - '204': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Delete the current API key of the user - tags: - - users - - users - get: - operationId: users__get_or_create_api_key - parameters: - - description: The encoded database identifier of the user. - in: path - name: encoded_user_id - required: true - schema: - description: The encoded database identifier of the user. - title: User ID - type: string - responses: - '200': - content: - application/json: - schema: - title: Response Users Get Or Create Api Key - type: string - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Return the user's API key - tags: - - users - - users - post: - operationId: users__create_api_key - parameters: - - description: The encoded database identifier of the user. - in: path - name: encoded_user_id - required: true - schema: - description: The encoded database identifier of the user. - title: User ID - type: string - responses: - '200': - content: - application/json: - schema: - title: Response Users Create Api Key - type: string - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Creates a new API key for the user - tags: - - users - - users - /api/version: - get: - operationId: configuration__version - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/Version' - description: Successful Response - summary: Version - tags: - - configuration - - configuration - /api_internal/change_password: - put: - description: reset a user - operationId: users__internal_change_password - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/UiChangePasswordRequest' - required: true - responses: - '204': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Change Password - tags: - - users - - users - /api_internal/login: - put: - description: login to web UI - operationId: users__internal_login - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/UiLoginRequest' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/UiLoginResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Internal Login - tags: - - users - - users - /api_internal/logout: - put: - description: logout of web UI - operationId: users__internal_logout - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/UiLogoutRequest' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/UiLogoutResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Internal Logout - tags: - - users - - users - /api_internal/register: - post: - description: register a user - operationId: users__internal_register - requestBody: - content: - application/json: - schema: - $ref: '#/components/schemas/UiRegisterRequest' - required: true - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/UiRegisterResponse' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - APIKeyCookie: [] - - APIKeyQuery: [] - - APIKeyHeader: [] - summary: Register - tags: - - users - - users - /api_internal/repositories/{encoded_repository_id}/metadata: - get: - description: Get information about repository metadata - operationId: repositories__internal_metadata - parameters: - - description: The encoded database identifier of the repository. - in: path - name: encoded_repository_id - required: true - schema: - description: The encoded database identifier of the repository. - title: Repository ID - type: string - - description: Include only downloadable repositories. - in: query - name: downloadable_only - required: false - schema: - default: true - description: Include only downloadable repositories. - title: downloadable_only - type: boolean - responses: - '200': - content: - application/json: - schema: - $ref: '#/components/schemas/RepositoryMetadata' - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - summary: Metadata Internal - tags: - - repositories - - repositories diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts index c66cb4c0675d..32c9e4e063a3 100644 --- a/client/src/api/schema/schema.ts +++ b/client/src/api/schema/schema.ts @@ -47,6 +47,13 @@ export interface paths { */ get: operations["dynamic_tool_confs_api_configuration_dynamic_tool_confs_get"]; }; + "/api/configuration/encode/{decoded_id}": { + /** + * Encode a given id + * @description Decode a given id. + */ + get: operations["encode_id_api_configuration_encode__decoded_id__get"]; + }; "/api/configuration/tool_lineages": { /** * Return tool lineages for tools that have them @@ -11518,6 +11525,38 @@ export interface operations { }; }; }; + encode_id_api_configuration_encode__decoded_id__get: { + /** + * Encode a given id + * @description Decode a given id. + */ + parameters: { + /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ + header?: { + "run-as"?: string | null; + }; + /** @description Decoded id to be encoded */ + path: { + decoded_id: number; + }; + }; + responses: { + /** @description Encoded id */ + 200: { + content: { + "application/json": { + [key: string]: string | undefined; + }; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; tool_lineages_api_configuration_tool_lineages_get: { /** * Return tool lineages for tools that have them diff --git a/lib/galaxy/managers/configuration.py b/lib/galaxy/managers/configuration.py index d15eb0332b6a..bb010dfd909d 100644 --- a/lib/galaxy/managers/configuration.py +++ b/lib/galaxy/managers/configuration.py @@ -18,7 +18,6 @@ from galaxy.managers.markdown_util import weasyprint_available from galaxy.schema import SerializationParams from galaxy.structured_app import StructuredApp -from galaxy.util import unicodify log = logging.getLogger(__name__)