Merge branch 'feature_stdout_live_reporting' of github.com:gecage952/…

…galaxy into feature_stdout_live_reporting

client/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@galaxyproject/galaxy-client",
-  "version": "23.1.1",
+  "version": "24.0.0",
   "description": "Galaxy client application build system",
   "keywords": [
     "galaxy"
@@ -43,6 +43,7 @@
     "@sentry/browser": "^7.74.1",
     "@types/jest": "^29.5.6",
     "@vueuse/core": "^10.5.0",
+    "@vueuse/math": "^10.9.0",
     "assert": "^2.1.0",
     "axios": "^1.6.2",
     "babel-runtime": "^6.26.0",

client/src/api/datasetCollections.ts

@@ -1,4 +1,4 @@
-import { CollectionEntry, DCESummary, HDCADetailed, isHDCA } from "@/api";
+import { CollectionEntry, DCESummary, HDCADetailed, HDCASummary, isHDCA } from "@/api";
 import { fetcher } from "@/api/schema";
 
 const DEFAULT_LIMIT = 50;
@@ -11,7 +11,16 @@ const getCollectionDetails = fetcher.path("/api/dataset_collections/{id}").metho
  */
 export async function fetchCollectionDetails(params: { id: string }): Promise<HDCADetailed> {
     const { data } = await getCollectionDetails({ id: params.id });
-    return data;
+    return data as HDCADetailed;
+}
+
+/**
+ * Fetches the details of a collection.
+ * @param params.id The ID of the collection (HDCA) to fetch.
+ */
+export async function fetchCollectionSummary(params: { id: string }): Promise<HDCASummary> {
+    const { data } = await getCollectionDetails({ id: params.id, view: "collection" });
+    return data as HDCASummary;
 }
 
 const getCollectionContents = fetcher

client/src/api/datasets.ts

@@ -1,6 +1,7 @@
+import axios from "axios";
 import type { FetchArgType } from "openapi-typescript-fetch";
 
-import { DatasetDetails } from "@/api";
+import { HDADetailed } from "@/api";
 import { components, fetcher } from "@/api/schema";
 import { withPrefix } from "@/utils/redirect";
 
@@ -11,7 +12,7 @@ type GetDatasetsQuery = Pick<GetDatasetsApiOptions, "limit" | "offset">;
 // custom interface for how we use getDatasets
 interface GetDatasetsOptions extends GetDatasetsQuery {
     sortBy?: string;
-    sortDesc?: string;
+    sortDesc?: boolean;
     query?: string;
 }
 
@@ -40,32 +41,28 @@ export const fetchDataset = fetcher.path("/api/datasets/{dataset_id}").method("g
 
 export const fetchDatasetStorage = fetcher.path("/api/datasets/{dataset_id}/storage").method("get").create();
 
-export async function fetchDatasetDetails(params: { id: string }): Promise<DatasetDetails> {
+export async function fetchDatasetDetails(params: { id: string }): Promise<HDADetailed> {
     const { data } = await fetchDataset({ dataset_id: params.id, view: "detailed" });
     // We know that the server will return a DatasetDetails object because of the view parameter
     // but the type system doesn't, so we have to cast it.
-    return data as unknown as DatasetDetails;
+    return data as unknown as HDADetailed;
 }
 
-const updateHistoryDataset = fetcher.path("/api/histories/{history_id}/contents/{type}s/{id}").method("put").create();
+const updateDataset = fetcher.path("/api/datasets/{dataset_id}").method("put").create();
 
-export async function undeleteHistoryDataset(historyId: string, datasetId: string) {
-    const { data } = await updateHistoryDataset({
-        history_id: historyId,
-        id: datasetId,
+export async function undeleteDataset(datasetId: string) {
+    const { data } = await updateDataset({
+        dataset_id: datasetId,
         type: "dataset",
         deleted: false,
     });
     return data;
 }
 
-const deleteHistoryDataset = fetcher
-    .path("/api/histories/{history_id}/contents/{type}s/{id}")
-    .method("delete")
-    .create();
+const deleteDataset = fetcher.path("/api/datasets/{dataset_id}").method("delete").create();
 
-export async function purgeHistoryDataset(historyId: string, datasetId: string) {
-    const { data } = await deleteHistoryDataset({ history_id: historyId, id: datasetId, type: "dataset", purge: true });
+export async function purgeDataset(datasetId: string) {
+    const { data } = await deleteDataset({ dataset_id: datasetId, purge: true });
     return data;
 }
 
@@ -92,3 +89,9 @@ export function getCompositeDatasetLink(historyDatasetId: string, path: string)
 
 export type DatasetExtraFiles = components["schemas"]["DatasetExtraFiles"];
 export const fetchDatasetExtraFiles = fetcher.path("/api/datasets/{dataset_id}/extra_files").method("get").create();
+
+export async function fetchDatasetAttributes(datasetId: string) {
+    const { data } = await axios.get(withPrefix(`/dataset/get_edit?dataset_id=${datasetId}`));
+
+    return data;
+}

client/src/api/histories.ts

@@ -12,3 +12,5 @@ export const updateHistoryItemsInBulk = fetcher
     .path("/api/histories/{history_id}/contents/bulk")
     .method("put")
     .create();
+export const sharing = fetcher.path("/api/histories/{history_id}/sharing").method("get").create();
+export const enableLink = fetcher.path("/api/histories/{history_id}/enable_link_access").method("put").create();

client/src/api/index.ts

@@ -7,18 +7,72 @@ import { components } from "@/api/schema";
  */
 export type HistorySummary = components["schemas"]["HistorySummary"];
 
-export interface HistorySummaryExtended extends HistorySummary {
+/**
+ * Contains minimal information about a History with additional content stats.
+ * This is a subset of information that can be relatively frequently updated after
+ * certain actions are performed on the history.
+ */
+export interface HistoryContentsStats {
+    id: string;
+    update_time: string;
     size: number;
     contents_active: components["schemas"]["HistoryActiveContentCounts"];
+}
+
+/**
+ * Contains summary information plus additional details about the contents and owner of a History.
+ * This is used by the client API to simplify the handling of History objects.
+ *
+ * Data returned by the API when requesting `?view=summary&keys=size,contents_active,user_id`.
+ */
+export interface HistorySummaryExtended extends HistorySummary, HistoryContentsStats {
     user_id: string;
 }
 
+type HistoryDetailedModel = components["schemas"]["HistoryDetailed"];
+
 /**
  * Contains additional details about a History.
+ *
+ * Data returned by the API when requesting `?view=detailed`.
+ */
+export interface HistoryDetailed extends HistoryDetailedModel {
+    // TODO: these fields are not present in the backend schema model `HistoryDetailedModel` but are serialized by the API
+    // when requesting ?view=detailed. We should consider adding them to the backend schema.
+    email_hash?: string;
+    empty: boolean;
+    hid_counter: number;
+}
+
+type HistoryDetailedCommon = Omit<
+    HistoryDetailed,
+    "username" | "state" | "state_ids" | "state_details" | "email_hash" | "empty"
+>;
+
+/**
+ * Alternative representation of history details used by the client API.
+ * Shares most of the fields with HistoryDetailed but not all and adds some additional fields.
+ *
+ * Data returned by the API when requesting `?view=dev-detailed`.
  */
-export type HistoryDetailed = components["schemas"]["HistoryDetailed"];
+export interface HistoryDevDetailed extends HistoryDetailedCommon {
+    contents_active: components["schemas"]["HistoryActiveContentCounts"];
+}
 
-export type AnyHistory = HistorySummary | HistorySummaryExtended | HistoryDetailed;
+/**
+ * Contains all available information about a History.
+ */
+export type HistoryExtended = HistoryDevDetailed & HistoryDetailed;
+
+/**
+ * Represents any amount of information about a History with the minimal being a HistorySummary.
+ */
+export type AnyHistory =
+    | HistorySummary
+    | HistorySummaryExtended
+    | HistoryDetailed
+    | HistoryDevDetailed
+    | HistoryExtended;
 
 /**
  * Contains minimal information about a HistoryContentItem.
@@ -28,12 +82,17 @@ export type HistoryContentItemBase = components["schemas"]["EncodedHistoryConten
 /**
  * Contains summary information about a HistoryDatasetAssociation.
  */
-export type DatasetSummary = components["schemas"]["HDASummary"];
+export type HDASummary = components["schemas"]["HDASummary"];
 
 /**
  * Contains additional details about a HistoryDatasetAssociation.
  */
-export type DatasetDetails = components["schemas"]["HDADetailed"];
+export type HDADetailed = components["schemas"]["HDADetailed"];
+
+/**
+ * Represents either an HDA or an HDCA with minimal information.
+ */
+export type HistoryItemSummary = HDASummary | HDCASummary;
 
 /**
  * Contains storage (object store, quota, etc..) details for a dataset.
@@ -43,7 +102,7 @@ export type DatasetStorageDetails = components["schemas"]["DatasetStorageDetails
 /**
  * Represents a HistoryDatasetAssociation with either summary or detailed information.
  */
-export type DatasetEntry = DatasetSummary | DatasetDetails;
+export type DatasetEntry = HDASummary | HDADetailed;
 
 /**
  * Contains summary information about a DCE (DatasetCollectionElement).
@@ -125,7 +184,7 @@ export function isCollectionElement(element: DCESummary): element is DCECollecti
 /**
  * Returns true if the given dataset entry is an instance of DatasetDetails.
  */
-export function hasDetails(entry: DatasetEntry): entry is DatasetDetails {
+export function hasDetails(entry: DatasetEntry): entry is HDADetailed {
     return "peek" in entry;
 }
 
@@ -174,5 +233,12 @@ export function userOwnsHistory(user: User | AnonymousUser | null, history: AnyH
 }
 
 function hasOwner(history: AnyHistory): history is HistorySummaryExtended {
-    return "user_id" in history;
+    return "user_id" in history && history.user_id !== null;
 }
+
+export type DatasetHash = components["schemas"]["DatasetHash"];
+
+export type DatasetTransform = {
+    action: "to_posix_lines" | "spaces_to_tabs" | "datatype_groom";
+    datatype_ext: "bam" | "qname_sorted.bam" | "qname_input_sorted.bam" | "isa-tab" | "isa-json";
+};

client/src/api/jobs.ts

@@ -2,9 +2,20 @@ import { components, fetcher } from "@/api/schema";
 
 export type JobDestinationParams = components["schemas"]["JobDestinationParams"];
 
+export const getJobDetails = fetcher.path("/api/jobs/{job_id}").method("get").create();
+
 export const jobLockStatus = fetcher.path("/api/job_lock").method("get").create();
 export const jobLockUpdate = fetcher.path("/api/job_lock").method("put").create();
 
 export const fetchJobDestinationParams = fetcher.path("/api/jobs/{job_id}/destination_params").method("get").create();
 
 export const jobsFetcher = fetcher.path("/api/jobs").method("get").create();
+
+export type ShowFullJobResponse = components["schemas"]["ShowFullJobResponse"];
+export type JobDetails = components["schemas"]["ShowFullJobResponse"] | components["schemas"]["EncodedJobDetails"];
+export const fetchJobDetails = fetcher.path("/api/jobs/{job_id}").method("get").create();
+
+export type JobInputSummary = components["schemas"]["JobInputSummary"];
+export const fetchJobCommonProblems = fetcher.path("/api/jobs/{job_id}/common_problems").method("get").create();
+
+export const postJobErrorReport = fetcher.path("/api/jobs/{job_id}/error").method("post").create();

client/src/api/notifications.preferences.ts

@@ -1,11 +1,18 @@
 import { type components, fetcher } from "@/api/schema";
 
-export type UserNotificationPreferences = components["schemas"]["UserNotificationPreferences"];
+type UserNotificationPreferences = components["schemas"]["UserNotificationPreferences"];
+
+export interface UserNotificationPreferencesExtended extends UserNotificationPreferences {
+    supportedChannels: string[];
+}
 
 const getNotificationsPreferences = fetcher.path("/api/notifications/preferences").method("get").create();
-export async function getNotificationsPreferencesFromServer() {
-    const { data } = await getNotificationsPreferences({});
-    return data;
+export async function getNotificationsPreferencesFromServer(): Promise<UserNotificationPreferencesExtended> {
+    const { data, headers } = await getNotificationsPreferences({});
+    return {
+        ...data,
+        supportedChannels: headers.get("supported-channels")?.split(",") ?? [],
+    };
 }
 
 type UpdateUserNotificationPreferencesRequest = components["schemas"]["UpdateUserNotificationPreferencesRequest"];

client/src/api/notifications.ts

@@ -25,7 +25,7 @@ export type NewSharedItemNotificationContentItemType =
 
 type UserNotificationUpdateRequest = components["schemas"]["UserNotificationUpdateRequest"];
 
-type NotificationCreateRequest = components["schemas"]["NotificationCreateRequest"];
+export type NotificationCreateRequest = components["schemas"]["NotificationCreateRequest"];
 
 type NotificationResponse = components["schemas"]["NotificationResponse"];