Merge branch 'dev' into topic/lint-whitespace-text

.github/ISSUE_TEMPLATE/bug_report.md

@@ -14,6 +14,10 @@ A clear and concise description of what the bug is.
 Galaxy Version: (check <galaxy_url>/api/version if you don't know)
 Commit: (run `git rev-parse HEAD` if you run this Galaxy server)
 
+**Browser and Operating System**
+Operating System: Windows, Linux, macOS
+Browser: Firefox, Chrome, Chrome-based, Safari
+
 **To Reproduce**
 Steps to reproduce the behavior:
 1. Go to '...'

Makefile

@@ -53,9 +53,9 @@ remove-unused-imports:  ## Remove unused imports in Python code base
 	$(IN_VENV) autoflake --in-place --remove-all-unused-imports --recursive --verbose lib/ test/
 
 pyupgrade:  ## Convert older code patterns to Python3.7/3.8 idiomatic ones
-	ack --type=python -f | grep -v '^lib/galaxy/schema/bco/\|^lib/galaxy/schema/drs/\|^lib/tool_shed_client/schema/trs\|^tools/\|^.venv/\|^.tox/\|^lib/galaxy/files/sources/\|^lib/galaxy/job_metrics/\|^lib/galaxy/objectstore/\|^lib/galaxy/tool_util/\|^lib/galaxy/util/\|^test/functional/tools/cwl_tools/' | xargs pyupgrade --py38-plus
-	ack --type=python -f | grep -v '^lib/galaxy/schema/bco/\|^lib/galaxy/schema/drs/\|^lib/tool_shed_client/schema/trs\|^tools/\|^.venv/\|^.tox/\|^lib/galaxy/files/sources/\|^lib/galaxy/job_metrics/\|^lib/galaxy/objectstore/\|^lib/galaxy/tool_util/\|^lib/galaxy/util/\|^test/functional/tools/cwl_tools/' | xargs auto-walrus
-	ack --type=python -f lib/galaxy/files/sources/ lib/galaxy/job_metrics/ lib/galaxy/objectstore/ lib/galaxy/tool_util/ lib/galaxy/util/ | xargs pyupgrade --py37-plus
+	ack --type=python -f | grep -v '^lib/galaxy/schema/bco/\|^lib/galaxy/schema/drs/\|^lib/tool_shed_client/schema/trs\|^tools/\|^.venv/\|^.tox/\|^lib/galaxy/exceptions/\|^lib/galaxy/job_metrics/\|^lib/galaxy/objectstore/\|^lib/galaxy/tool_util/\|^lib/galaxy/util/\|^test/functional/tools/cwl_tools/' | xargs pyupgrade --py38-plus
+	ack --type=python -f | grep -v '^lib/galaxy/schema/bco/\|^lib/galaxy/schema/drs/\|^lib/tool_shed_client/schema/trs\|^tools/\|^.venv/\|^.tox/\|^lib/galaxy/exceptions/\|^lib/galaxy/job_metrics/\|^lib/galaxy/objectstore/\|^lib/galaxy/tool_util/\|^lib/galaxy/util/\|^test/functional/tools/cwl_tools/' | xargs auto-walrus
+	ack --type=python -f lib/galaxy/exceptions/ lib/galaxy/job_metrics/ lib/galaxy/objectstore/ lib/galaxy/tool_util/ lib/galaxy/util/ | xargs pyupgrade --py37-plus
 
 docs-slides-ready:
 	test -f plantuml.jar ||  wget http://jaist.dl.sourceforge.net/project/plantuml/plantuml.jar

client/src/api/datasetCollections.ts

@@ -61,3 +61,9 @@ export const fetchCollectionAttributes = fetcher
     .path("/api/dataset_collections/{id}/attributes")
     .method("get")
     .create();
+
+const postCopyCollection = fetcher.path("/api/dataset_collections/{id}/copy").method("post").create();
+export async function copyCollection(id: string, dbkey: string): Promise<Record<string, never>> {
+    const { data } = await postCopyCollection({ id, dbkey });
+    return data;
+}

client/src/api/datasets.ts

@@ -6,12 +6,14 @@ import { withPrefix } from "@/utils/redirect";
 
 export const datasetsFetcher = fetcher.path("/api/datasets").method("get").create();
 
+export type HDASummary = components["schemas"]["HDASummary"];
+
 type GetDatasetsApiOptions = FetchArgType<typeof datasetsFetcher>;
 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;
 }
 
@@ -47,25 +49,21 @@ export async function fetchDatasetDetails(params: { id: string }): Promise<Datas
     return data as unknown as DatasetDetails;
 }
 
-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 undeleteHistoryDataset(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;
 }
 

client/src/api/histories.ts

@@ -8,3 +8,7 @@ export const undeleteHistory = fetcher.path("/api/histories/deleted/{history_id}
 export const undeleteHistories = fetcher.path("/api/histories/batch/undelete").method("put").create();
 export const publishedHistoriesFetcher = fetcher.path("/api/histories/published").method("get").create();
 export const historyFetcher = fetcher.path("/api/histories/{history_id}").method("get").create();
+export const updateHistoryItemsInBulk = fetcher
+    .path("/api/histories/{history_id}/contents/bulk")
+    .method("put")
+    .create();

client/src/api/index.ts

@@ -7,11 +7,19 @@ import { components } from "@/api/schema";
  */
 export type HistorySummary = components["schemas"]["HistorySummary"];
 
+export interface HistorySummaryExtended extends HistorySummary {
+    size: number;
+    contents_active: components["schemas"]["HistoryActiveContentCounts"];
+    user_id: string;
+}
+
 /**
  * Contains additional details about a History.
  */
 export type HistoryDetailed = components["schemas"]["HistoryDetailed"];
 
+export type AnyHistory = HistorySummary | HistorySummaryExtended | HistoryDetailed;
+
 /**
  * Contains minimal information about a HistoryContentItem.
  */
@@ -125,3 +133,46 @@ export function hasDetails(entry: DatasetEntry): entry is DatasetDetails {
  * Contains dataset metadata information.
  */
 export type MetadataFiles = components["schemas"]["MetadataFile"][];
+
+export function isHistorySummary(history: AnyHistory): history is HistorySummary {
+    return !("user_id" in history);
+}
+
+export function isHistorySummaryExtended(history: AnyHistory): history is HistorySummaryExtended {
+    return "contents_active" in history && "user_id" in history;
+}
+
+type QuotaUsageResponse = components["schemas"]["UserQuotaUsage"];
+
+export interface User extends QuotaUsageResponse {
+    id: string;
+    email: string;
+    tags_used: string[];
+    isAnonymous: false;
+    is_admin?: boolean;
+    username?: string;
+}
+
+export interface AnonymousUser {
+    isAnonymous: true;
+    username?: string;
+    is_admin?: false;
+}
+
+export type GenericUser = User | AnonymousUser;
+
+export function isRegisteredUser(user: User | AnonymousUser | null): user is User {
+    return !user?.isAnonymous;
+}
+
+export function userOwnsHistory(user: User | AnonymousUser | null, history: AnyHistory) {
+    return (
+        // Assuming histories without user_id are owned by the current user
+        (isRegisteredUser(user) && !hasOwner(history)) ||
+        (isRegisteredUser(user) && hasOwner(history) && user.id === history.user_id)
+    );
+}
+
+function hasOwner(history: AnyHistory): history is HistorySummaryExtended {
+    return "user_id" in history;
+}

client/src/api/invocations.ts

@@ -2,14 +2,16 @@ import axios from "axios";
 
 import { getAppRoot } from "@/onload";
 
-import { ApiResponse, fetcher } from "./schema";
+import { ApiResponse, components, fetcher } from "./schema";
+
+export type WorkflowInvocationElementView = components["schemas"]["WorkflowInvocationElementView"];
+export type WorkflowInvocationCollectionView = components["schemas"]["WorkflowInvocationCollectionView"];
+export type InvocationJobsSummary = components["schemas"]["InvocationJobsResponse"];
+export type InvocationStep = components["schemas"]["InvocationStep"];
 
 export const invocationsFetcher = fetcher.path("/api/invocations").method("get").create();
 
-// TODO: Replace these interfaces with real schema models after https://github.com/galaxyproject/galaxy/pull/16707 is merged
-export interface WorkflowInvocation {
-    id: string;
-}
+export type WorkflowInvocation = WorkflowInvocationElementView | WorkflowInvocationCollectionView;
 
 export interface WorkflowInvocationJobsSummary {
     id: string;