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Refactor models enums to eliminate schema dependency on model layer. #16080

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May 13, 2023
Merged

Refactor models enums to eliminate schema dependency on model layer. #16080

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7edc84f
Refactor enum dependencies between schema and models.
jmchilton May 12, 2023
c040d83
Ooo... look it cleaned up schema.ts nicely also!
jmchilton May 12, 2023
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126 changes: 63 additions & 63 deletions client/src/schema/schema.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -2472,6 +2472,12 @@ export interface components {
* @description Represents a collection of elements contained in the dataset collection.
*/
DatasetCollectionContentElements: components["schemas"]["DCESummary"][];
/**
* DatasetCollectionPopulatedState
* @description An enumeration.
* @enum {string}
*/
DatasetCollectionPopulatedState: "new" | "ok" | "failed";
/**
* DatasetContentType
* @description For retrieving content from a structured dataset (e.g. HDF5)
Expand Down Expand Up @@ -2557,6 +2563,24 @@ export interface components {
* @enum {string}
*/
DatasetSourceType: "hda" | "ldda";
/**
* DatasetState
* @description An enumeration.
* @enum {string}
*/
DatasetState:
| "new"
| "upload"
| "queued"
| "running"
| "ok"
| "empty"
| "error"
| "paused"
| "setting_metadata"
| "failed_metadata"
| "deferred"
| "discarded";
/**
* DatasetStorageDetails
* @description Base model definition with common configuration used by all derived models.
Expand Down Expand Up @@ -2634,6 +2658,12 @@ export interface components {
*/
truncated: boolean;
};
/**
* DatasetValidatedState
* @description An enumeration.
* @enum {string}
*/
DatasetValidatedState: "unknown" | "invalid" | "ok";
/** DatatypeConverter */
DatatypeConverter: {
/**
Expand Down Expand Up @@ -3178,7 +3208,7 @@ export interface components {
* State
* @description The current state of this dataset.
*/
state: components["schemas"]["galaxy__model__Dataset__states"];
state: components["schemas"]["DatasetState"];
/** Tags */
tags: string;
/**
Expand Down Expand Up @@ -3684,7 +3714,7 @@ export interface components {
* State
* @description The current state of this dataset.
*/
state: components["schemas"]["galaxy__model__Dataset__states"];
state: components["schemas"]["DatasetState"];
tags: components["schemas"]["TagCollection"];
/**
* Type
Expand Down Expand Up @@ -3721,7 +3751,7 @@ export interface components {
* Validated State
* @description The state of the datatype validation for this dataset.
*/
validated_state: components["schemas"]["validated_states"];
validated_state: components["schemas"]["DatasetValidatedState"];
/**
* Validated State Message
* @description The message with details about the datatype validation result for this dataset.
Expand Down Expand Up @@ -3772,7 +3802,7 @@ export interface components {
* State
* @description The current state of this dataset.
*/
state: components["schemas"]["galaxy__model__Dataset__states"];
state: components["schemas"]["DatasetState"];
/** Tags */
tags: string[];
};
Expand Down Expand Up @@ -3840,7 +3870,7 @@ export interface components {
* State
* @description The current state of this dataset.
*/
state: components["schemas"]["galaxy__model__Dataset__states"];
state: components["schemas"]["DatasetState"];
tags: components["schemas"]["TagCollection"];
/**
* Type
Expand Down Expand Up @@ -3978,7 +4008,7 @@ export interface components {
* Populated State
* @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.
*/
populated_state: components["schemas"]["populated_states"];
populated_state: components["schemas"]["DatasetCollectionPopulatedState"];
/**
* Populated State Message
* @description Optional message with further information in case the population of the dataset collection failed.
Expand Down Expand Up @@ -4107,7 +4137,7 @@ export interface components {
* Populated State
* @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.
*/
populated_state: components["schemas"]["populated_states"];
populated_state: components["schemas"]["DatasetCollectionPopulatedState"];
/**
* Populated State Message
* @description Optional message with further information in case the population of the dataset collection failed.
Expand Down Expand Up @@ -4531,7 +4561,7 @@ export interface components {
* State
* @description The current state of the History based on the states of the datasets it contains.
*/
state: components["schemas"]["galaxy__model__Dataset__states"];
state: components["schemas"]["DatasetState"];
/**
* State Counts
* @description A dictionary keyed to possible dataset states and valued with the number of datasets in this history that have those states.
Expand Down Expand Up @@ -4683,7 +4713,7 @@ export interface components {
* Populated State
* @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.
*/
populated_state: components["schemas"]["populated_states"];
populated_state: components["schemas"]["DatasetCollectionPopulatedState"];
/**
* States
* @description A dictionary of job states and the number of jobs in that state.
Expand Down Expand Up @@ -4964,7 +4994,7 @@ export interface components {
* State
* @description Current state of the job.
*/
state: components["schemas"]["galaxy__model__Job__states"];
state: components["schemas"]["JobState"];
/**
* Tool ID
* @description Identifier of the tool that generated this job.
Expand Down Expand Up @@ -5003,6 +5033,27 @@ export interface components {
* @enum {string}
*/
JobSourceType: "Job" | "ImplicitCollectionJobs" | "WorkflowInvocation";
/**
* JobState
* @description An enumeration.
* @enum {string}
*/
JobState:
| "new"
| "resubmitted"
| "upload"
| "waiting"
| "queued"
| "running"
| "ok"
| "error"
| "failed"
| "paused"
| "deleting"
| "deleted"
| "stop"
| "stopped"
| "skipped";
/**
* JobStateSummary
* @description Base model definition with common configuration used by all derived models.
Expand All @@ -5025,7 +5076,7 @@ export interface components {
* Populated State
* @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.
*/
populated_state: components["schemas"]["populated_states"];
populated_state: components["schemas"]["DatasetCollectionPopulatedState"];
/**
* States
* @description A dictionary of job states and the number of jobs in that state.
Expand Down Expand Up @@ -7475,7 +7526,7 @@ export interface components {
* Populated State
* @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.
*/
populated_state: components["schemas"]["populated_states"];
populated_state: components["schemas"]["DatasetCollectionPopulatedState"];
/**
* States
* @description A dictionary of job states and the number of jobs in that state.
Expand Down Expand Up @@ -7615,57 +7666,6 @@ export interface components {
*/
namespace: string;
};
/**
* states
* @description An enumeration.
* @enum {string}
*/
galaxy__model__Dataset__states:
| "new"
| "upload"
| "queued"
| "running"
| "ok"
| "empty"
| "error"
| "paused"
| "setting_metadata"
| "failed_metadata"
| "deferred"
| "discarded";
/**
* states
* @description An enumeration.
* @enum {string}
*/
galaxy__model__Job__states:
| "new"
| "resubmitted"
| "upload"
| "waiting"
| "queued"
| "running"
| "ok"
| "error"
| "failed"
| "paused"
| "deleting"
| "deleted"
| "stop"
| "stopped"
| "skipped";
/**
* populated_states
* @description An enumeration.
* @enum {string}
*/
populated_states: "new" | "ok" | "failed";
/**
* validated_states
* @description An enumeration.
* @enum {string}
*/
validated_states: "unknown" | "invalid" | "ok";
};
responses: never;
parameters: never;
Expand Down
58 changes: 10 additions & 48 deletions lib/galaxy/model/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -129,6 +129,12 @@
from galaxy.model.orm.now import now
from galaxy.model.orm.util import add_object_to_object_session
from galaxy.objectstore import ObjectStore
from galaxy.schema.schema import (
DatasetCollectionPopulatedState,
DatasetState,
DatasetValidatedState,
JobState,
)
from galaxy.security import get_permitted_actions
from galaxy.security.idencoding import IdEncodingHelper
from galaxy.security.validate_user_input import validate_password_str
Expand Down Expand Up @@ -1299,22 +1305,7 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
_numeric_metric = JobMetricNumeric
_text_metric = JobMetricText

class states(str, Enum):
NEW = "new"
RESUBMITTED = "resubmitted"
UPLOAD = "upload"
WAITING = "waiting"
QUEUED = "queued"
RUNNING = "running"
OK = "ok"
ERROR = "error"
FAILED = "failed"
PAUSED = "paused"
DELETING = "deleting"
DELETED = "deleted"
STOPPING = "stop"
STOPPED = "stopped"
SKIPPED = "skipped"
states = JobState

terminal_states = [states.OK, states.ERROR, states.DELETED]
#: job states where the job hasn't finished and the model may still change
Expand Down Expand Up @@ -3739,31 +3730,8 @@ class Dataset(Base, StorableObject, Serializable):
back_populates="dataset",
)

class states(str, Enum):
NEW = "new"
UPLOAD = "upload"
QUEUED = "queued"
RUNNING = "running"
OK = "ok"
EMPTY = "empty"
ERROR = "error"
PAUSED = "paused"
SETTING_METADATA = "setting_metadata"
FAILED_METADATA = "failed_metadata"
# Non-deleted, non-purged datasets that don't have physical files.
# These shouldn't have objectstores attached -
# 'deferred' can be materialized for jobs using
# attached DatasetSource objects but 'discarded'
# cannot (e.g. imported histories). These should still
# be able to have history contents associated (normal HDAs?)
DEFERRED = "deferred"
DISCARDED = "discarded"

@classmethod
def values(self):
return self.__members__.values()

# failed_metadata is only valid as DatasetInstance state currently
states = DatasetState

non_ready_states = (states.NEW, states.UPLOAD, states.QUEUED, states.RUNNING, states.SETTING_METADATA)
ready_states = tuple(set(states.__members__.values()) - set(non_ready_states))
Expand Down Expand Up @@ -4190,10 +4158,7 @@ class DatasetInstance(UsesCreateAndUpdateTime, _HasTable):
purged: bool
creating_job_associations: List[Union[JobToOutputDatasetCollectionAssociation, JobToOutputDatasetAssociation]]

class validated_states(str, Enum):
UNKNOWN = "unknown"
INVALID = "invalid"
OK = "ok"
validated_states = DatasetValidatedState

def __init__(
self,
Expand Down Expand Up @@ -5963,10 +5928,7 @@ class DatasetCollection(Base, Dictifiable, UsesAnnotations, Serializable):
dict_collection_visible_keys = ["id", "collection_type"]
dict_element_visible_keys = ["id", "collection_type"]

class populated_states(str, Enum):
NEW = "new" # New dataset collection, unpopulated elements
OK = "ok" # Collection elements populated (HDAs may or may not have errors)
FAILED = "failed" # some problem populating state, won't be populated
populated_states = DatasetCollectionPopulatedState

def __init__(self, id=None, collection_type=None, populated=True, element_count=None):
self.id = id
Expand Down
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