Merge branch 'dev' into interactivetoolssqlalchemy

.github/workflows/framework.yaml → .github/workflows/framework_tools.yaml

@@ -1,4 +1,4 @@
-name: Framework tests
+name: Tool framework tests
 on:
   push:
     paths-ignore:
@@ -64,9 +64,9 @@ jobs:
         uses: actions/cache@v4
         with:
           path: 'galaxy root/.venv'
-          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework-tools
       - name: Run tests
-        run: ./run_tests.sh --coverage --framework
+        run: ./run_tests.sh --coverage --framework-tools
         working-directory: 'galaxy root'
       - uses: codecov/codecov-action@v3
         with:

.github/workflows/framework_workflows.yaml

@@ -0,0 +1,79 @@
+name: Workflow framework tests
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+  schedule:
+    # Run at midnight UTC every Tuesday
+    - cron: '0 0 * * 2'
+env:
+  GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
+  GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.8']
+    services:
+      postgres:
+        image: postgres:13
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+      - if: github.event_name == 'schedule'
+        run: |
+          echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV
+          echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
+      - uses: actions/checkout@v4
+        with:
+          path: 'galaxy root'
+      - uses: actions/setup-node@v4
+        with:
+          node-version: '18.12.1'
+          cache: 'yarn'
+          cache-dependency-path: 'galaxy root/client/yarn.lock'
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
+      - name: Cache pip dir
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+      - name: Cache galaxy venv
+        uses: actions/cache@v4
+        with:
+          path: 'galaxy root/.venv'
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework-workflows
+      - name: Run tests
+        run: ./run_tests.sh --coverage --framework-workflows
+        working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v3
+        with:
+          flags: framework
+          working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v4
+        if: failure()
+        with:
+          name: Framework test results (${{ matrix.python-version }})
+          path: 'galaxy root/run_framework_workflows_tests.html'

client/.eslintrc.js

@@ -82,6 +82,11 @@ const baseRules = {
     "import/first": "error",
     "import/newline-after-import": "error",
     "import/no-duplicates": "error",
+
+    "@typescript-eslint/consistent-type-imports": [
+        "error",
+        { prefer: "type-imports", fixStyle: "inline-type-imports" },
+    ],
 };
 
 const baseExtends = [

client/package.json

@@ -89,7 +89,7 @@
     "pyre-to-regexp": "^0.0.6",
     "querystring-es3": "^0.2.1",
     "regenerator-runtime": "^0.14.0",
-    "requirejs": "2.3.6",
+    "requirejs": "2.3.7",
     "rxjs": "^7.8.1",
     "rxjs-spy": "^8.0.2",
     "rxjs-spy-devtools-plugin": "^0.0.4",

client/src/api/configTemplates.ts

@@ -1,4 +1,4 @@
-import type { components } from "@/api/schema/schema";
+import { type components } from "@/api/schema/schema";
 
 export type Instance =
     | components["schemas"]["UserFileSourceModel"]

client/src/api/datasetCollections.ts

@@ -1,4 +1,4 @@
-import { CollectionEntry, DCESummary, HDCADetailed, HDCASummary, isHDCA } from "@/api";
+import { type CollectionEntry, type DCESummary, type HDCADetailed, type HDCASummary, isHDCA } from "@/api";
 import { fetcher } from "@/api/schema";
 
 const DEFAULT_LIMIT = 50;

client/src/api/datasets.ts

@@ -1,8 +1,8 @@
 import axios from "axios";
-import type { FetchArgType } from "openapi-typescript-fetch";
+import { type FetchArgType } from "openapi-typescript-fetch";
 
-import { HDADetailed } from "@/api";
-import { components, fetcher } from "@/api/schema";
+import { type HDADetailed } from "@/api";
+import { type components, fetcher } from "@/api/schema";
 import { withPrefix } from "@/utils/redirect";
 
 export const datasetsFetcher = fetcher.path("/api/datasets").method("get").create();

client/src/api/groups.ts

@@ -1,6 +1,6 @@
 import axios from "axios";
 
-import { components, fetcher } from "@/api/schema";
+import { type components, fetcher } from "@/api/schema";
 
 type GroupModel = components["schemas"]["GroupModel"];
 export async function getAllGroups(): Promise<GroupModel[]> {

client/src/api/histories.archived.ts

@@ -1,4 +1,4 @@
-import type { FetchArgType } from "openapi-typescript-fetch";
+import { type FetchArgType } from "openapi-typescript-fetch";
 
 import { type components, fetcher } from "@/api/schema";
 

client/src/api/histories.export.ts

@@ -1,5 +1,4 @@
-import type { components } from "@/api/schema";
-import { fetcher } from "@/api/schema";
+import { type components, fetcher } from "@/api/schema";
 import {
     type ExportRecord,
     ExportRecordModel,

client/src/api/index.ts

@@ -1,6 +1,6 @@
 /** Contains type alias and definitions related to Galaxy API models. */
 
-import { components } from "@/api/schema";
+import { type components } from "@/api/schema";
 
 /**
  * Contains minimal information about a History.

client/src/api/invocations.ts

@@ -2,7 +2,7 @@ import axios from "axios";
 
 import { getAppRoot } from "@/onload";
 
-import { ApiResponse, components, fetcher } from "./schema";
+import { type ApiResponse, type components, fetcher } from "./schema";
 
 export type WorkflowInvocationElementView = components["schemas"]["WorkflowInvocationElementView"];
 export type WorkflowInvocationCollectionView = components["schemas"]["WorkflowInvocationCollectionView"];

client/src/api/jobs.ts

@@ -1,4 +1,4 @@
-import { components, fetcher } from "@/api/schema";
+import { type components, fetcher } from "@/api/schema";
 
 export type JobDestinationParams = components["schemas"]["JobDestinationParams"];
 

client/src/api/objectStores.ts

@@ -1,5 +1,5 @@
 import { fetcher } from "@/api/schema";
-import type { components } from "@/api/schema/schema";
+import { type components } from "@/api/schema/schema";
 
 export type UserConcreteObjectStore = components["schemas"]["UserConcreteObjectStoreModel"];
 

client/src/api/remoteFiles.ts

@@ -1,4 +1,4 @@
-import type { components } from "@/api/schema";
+import { type components } from "@/api/schema";
 import { fetcher } from "@/api/schema/fetcher";
 
 /** The browsing mode:

client/src/api/schema/__mocks__/fetcher.ts

@@ -1,4 +1,4 @@
-import type { paths } from "@/api/schema";
+import { type paths } from "@/api/schema";
 
 jest.mock("@/api/schema", () => ({
     fetcher: mockFetcher,

client/src/api/schema/fetcher.ts

@@ -1,12 +1,11 @@
-import type { ApiResponse, Middleware } from "openapi-typescript-fetch";
-import { Fetcher } from "openapi-typescript-fetch";
+import { type ApiResponse, Fetcher, type Middleware } from "openapi-typescript-fetch";
 
 import { getAppRoot } from "@/onload/loadConfig";
 import { rethrowSimple } from "@/utils/simple-error";
 
-import type { paths } from "./schema";
+import { type paths } from "./schema";
 
-export { ApiResponse };
+export { type ApiResponse };
 
 const rethrowSimpleMiddleware: Middleware = async (url, init, next) => {
     try {

client/src/api/schema/schema.ts

@@ -12397,6 +12397,26 @@ export interface components {
             visible?: boolean | null;
             [key: string]: unknown;
         };
+        /** UpdateHistoryPayload */
+        UpdateHistoryPayload: {
+            /** Annotation */
+            annotation?: string | null;
+            /** Deleted */
+            deleted?: boolean | null;
+            /** Genome Build */
+            genome_build?: string | null;
+            /** Importable */
+            importable?: boolean | null;
+            /** Name */
+            name?: string | null;
+            /** Preferred Object Store Id */
+            preferred_object_store_id?: string | null;
+            /** Published */
+            published?: boolean | null;
+            /** Purged */
+            purged?: boolean | null;
+            tags?: components["schemas"]["TagCollection"] | null;
+        };
         /** UpdateInstancePayload */
         UpdateInstancePayload: {
             /** Active */
@@ -12902,8 +12922,7 @@ export interface components {
              */
             content:
                 | components["schemas"]["MessageNotificationContent"]
-                | components["schemas"]["NewSharedItemNotificationContent"]
-                | components["schemas"]["BroadcastNotificationContent"];
+                | components["schemas"]["NewSharedItemNotificationContent"];
             /**
              * Create time
              * Format: date-time
@@ -13021,6 +13040,24 @@ export interface components {
             /** Total Disk Usage */
             total_disk_usage: number;
         };
+        /** UserUpdatePayload */
+        UserUpdatePayload: {
+            /**
+             * Active
+             * @description User is active
+             */
+            active?: boolean | null;
+            /**
+             * Preferred Object Store ID
+             * @description The ID of the object store that should be used to store new datasets in this history.
+             */
+            preferred_object_store_id?: string | null;
+            /**
+             * Username
+             * @description The name of the user.
+             */
+            username?: string | null;
+        };
         /** Visualization */
         Visualization: Record<string, never>;
         /** VisualizationSummary */
@@ -17571,7 +17608,7 @@ export interface operations {
         };
         requestBody: {
             content: {
-                "application/json": unknown;
+                "application/json": components["schemas"]["UpdateHistoryPayload"];
             };
         };
         responses: {
@@ -24967,7 +25004,7 @@ export interface operations {
         };
         requestBody: {
             content: {
-                "application/json": Record<string, never>;
+                "application/json": components["schemas"]["UserUpdatePayload"];
             };
         };
         responses: {

client/src/api/tags.ts

@@ -1,4 +1,4 @@
-import { components, fetcher } from "@/api/schema";
+import { type components, fetcher } from "@/api/schema";
 
 type TaggableItemClass = components["schemas"]["TaggableItemClass"];
 

client/src/api/workflows.ts

@@ -1,4 +1,4 @@
-import { components, fetcher } from "@/api/schema";
+import { type components, fetcher } from "@/api/schema";
 
 export type StoredWorkflowDetailed = components["schemas"]["StoredWorkflowDetailed"];
 

client/src/components/Citation/CitationItem.vue

@@ -4,7 +4,7 @@ import { faExternalLinkAlt } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { computed } from "vue";
 
-import { Citation } from ".";
+import { type Citation } from ".";
 
 library.add(faExternalLinkAlt);
 

client/src/components/Collections/common/CollectionEditView.vue

@@ -18,7 +18,7 @@ import localize from "@/utils/localization";
 import { prependPath } from "@/utils/redirect";
 import { errorMessageAsString } from "@/utils/simple-error";
 
-import { HistoryContentBulkOperationPayload, updateHistoryItemsBulk } from "./services";
+import { type HistoryContentBulkOperationPayload, updateHistoryItemsBulk } from "./services";
 
 import ChangeDatatypeTab from "@/components/Collections/common/ChangeDatatypeTab.vue";
 import DatabaseEditTab from "@/components/Collections/common/DatabaseEditTab.vue";

client/src/components/Common/ExportForm.vue

@@ -2,7 +2,7 @@
 import { BButton, BCol, BFormGroup, BFormInput, BRow } from "bootstrap-vue";
 import { computed, ref } from "vue";
 
-import { FilterFileSourcesOptions } from "@/api/remoteFiles";
+import { type FilterFileSourcesOptions } from "@/api/remoteFiles";
 import localize from "@/utils/localization";
 
 import FilesInput from "@/components/FilesDialog/FilesInput.vue";

client/src/components/Common/ExportRDMForm.test.ts

@@ -1,8 +1,8 @@
 import { getLocalVue } from "@tests/jest/helpers";
-import { mount, Wrapper } from "@vue/test-utils";
+import { mount, type Wrapper } from "@vue/test-utils";
 import flushPromises from "flush-promises";
 
-import { type BrowsableFilesSourcePlugin, CreatedEntry } from "@/api/remoteFiles";
+import { type BrowsableFilesSourcePlugin, type CreatedEntry } from "@/api/remoteFiles";
 import { mockFetcher } from "@/api/schema/__mocks__";
 
 import ExportRDMForm from "./ExportRDMForm.vue";

client/src/components/Common/ExportRDMForm.vue

@@ -3,10 +3,10 @@ import { BButton, BCard, BFormGroup, BFormInput, BFormRadio, BFormRadioGroup } f
 import { computed, ref } from "vue";
 
 import {
-    BrowsableFilesSourcePlugin,
-    CreatedEntry,
+    type BrowsableFilesSourcePlugin,
+    type CreatedEntry,
     createRemoteEntry,
-    FilterFileSourcesOptions,
+    type FilterFileSourcesOptions,
 } from "@/api/remoteFiles";
 import { useToast } from "@/composables/toast";
 import localize from "@/utils/localization";

client/src/components/Common/ExportRecordDOILink.vue

@@ -2,7 +2,7 @@
 import axios from "axios";
 import { ref, watch } from "vue";
 
-import { BrowsableFilesSourcePlugin } from "@/api/remoteFiles";
+import { type BrowsableFilesSourcePlugin } from "@/api/remoteFiles";
 import { useFileSources } from "@/composables/fileSources";
 
 import DOILink from "./DOILink.vue";

client/src/components/Common/ExportRecordDetails.vue

@@ -12,7 +12,7 @@ import { BAlert, BButton } from "bootstrap-vue";
 import { computed } from "vue";
 
 import type { ColorVariant } from ".";
-import { ExportRecord } from "./models/exportRecordModel";
+import { type ExportRecord } from "./models/exportRecordModel";
 
 import Heading from "@/components/Common/Heading.vue";
 import LoadingSpan from "@/components/LoadingSpan.vue";

client/src/components/Common/FilterMenu.test.ts

@@ -1,6 +1,6 @@
 import { createTestingPinia } from "@pinia/testing";
 import { getLocalVue } from "@tests/jest/helpers";
-import { mount, Wrapper } from "@vue/test-utils";
+import { mount, type Wrapper } from "@vue/test-utils";
 
 import { HistoryFilters } from "@/components/History/HistoryFilters";
 import { WorkflowFilters } from "@/components/Workflow/List/WorkflowFilters";