Merge branch 'dev' into name-validation

.ci/flake8_ignorelist.txt

@@ -11,6 +11,7 @@ database
 doc/build
 eggs
 lib/galaxy/web/proxy/js/node_modules
+lib/tool_shed/test/test_data/repos
 static/maps
 static/scripts
 test/functional/tools/cwl_tools/v1.?/

.flake8

@@ -7,3 +7,4 @@
 # W503 is line breaks before binary operators, which has been reversed in PEP 8.
 # D** are docstring linting - which we mostly ignore except D302. (Hopefully we will solve more over time).
 ignore = B008,E203,E402,E501,W503,D100,D101,D102,D103,D104,D105,D106,D107,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403,D412,D413
+exclude = lib/tool_shed/test/test_data/repos

.github/workflows/converter_tests.yaml

@@ -68,7 +68,7 @@ jobs:
       - name: Run tests
         run: |
           mapfile -t TOOL_ARRAY < tool_list.txt
-          planemo test --galaxy_python_version ${{ matrix.python-version }} --galaxy_root 'galaxy root' "${TOOL_ARRAY[@]}"
+          planemo test --biocontainers --galaxy_python_version ${{ matrix.python-version }} --galaxy_root 'galaxy root' "${TOOL_ARRAY[@]}"
       - uses: actions/upload-artifact@v3
         if: failure()
         with:

.github/workflows/dependencies.yaml

@@ -14,12 +14,12 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: ${{ matrix.python-version }}
-      - name: Cache pip dir
-        uses: actions/cache@v3
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
+          # poetry requires Python >=3.8, but lint requirements currently need
+          # to be generated with `pip freeze`` on the oldest Python version
+          # supported by Galaxy.
+          python-version: |
+            ${{ matrix.python-version }}
+            3.8
       - name: Update dependencies
         run: | 
           python -m venv .venv

.github/workflows/lint.yaml

@@ -20,6 +20,7 @@ jobs:
     name: Test
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
         python-version: ['3.7', '3.11']
     env:

.github/workflows/lint_openapi_schema.yml

@@ -51,6 +51,9 @@ jobs:
       - name: Build typescript schema
         run: make update-client-api-schema
         working-directory: 'galaxy root'
+      - name: Diff...
+        run: git diff
+        working-directory: 'galaxy root'
       - name: Check for changes
         run: |
           if [[ `git status --porcelain` ]]; then

.github/workflows/setup_selenium.yaml

@@ -5,4 +5,4 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install chromedriver
-        uses: mvdbeek/setup-chromedriver@chromedriver_puppeteer
+        uses: nanasess/setup-chromedriver@v2

.github/workflows/test_galaxy_packages_for_pulsar.yaml

@@ -0,0 +1,44 @@
+name: Test Galaxy packages for Pulsar
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.7']
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          path: 'galaxy root'
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Cache pip dir
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+      - name: Install Apptainer's singularity
+        uses: eWaterCycle/setup-apptainer@v2
+      - name: Install ffmpeg
+        run: sudo apt-get update && sudo apt-get -y install ffmpeg
+      - name: Install tox
+        run: pip install tox
+      - name: Run tests
+        run: tox -e test_galaxy_packages_for_pulsar
+        working-directory: 'galaxy root'

.github/workflows/toolshed.yaml

@@ -19,8 +19,11 @@ jobs:
     name: Test
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.7', '3.11']
+        shed-api: ['v1', 'v2']
+        test-install-client: ['galaxy_api', 'standalone']
     services:
       postgres:
         image: postgres:13
@@ -34,6 +37,11 @@ jobs:
       - uses: actions/checkout@v3
         with:
           path: 'galaxy root'
+      - uses: actions/setup-node@v3
+        with:
+          node-version: '18.12.1'
+          cache: 'yarn'
+          cache-dependency-path: 'galaxy root/client/yarn.lock'
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
@@ -52,11 +60,30 @@ jobs:
         with:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-toolshed
+      - name: Install dependencies
+        run: ./scripts/common_startup.sh --skip-client-build
+        working-directory: 'galaxy root'
+      - name: Build Frontend
+        run: |
+          . .venv/bin/activate
+          cd lib/tool_shed/webapp/frontend
+          yarn
+          make client
+        working-directory: 'galaxy root'
+      - name: Install playwright
+        run: |
+          . .venv/bin/activate
+          playwright install
+        working-directory: 'galaxy root'
       - name: Run tests
-        run: './run_tests.sh -toolshed'
+        run: ./run_tests.sh -toolshed
+        env:
+          TOOL_SHED_TEST_INSTALL_CLIENT: ${{ matrix.test-install-client }}
+          TOOL_SHED_API_VERSION: ${{ matrix.shed-api }}
+          TOOL_SHED_TEST_BROWSER: ${{ matrix.shed-api == 'v1' && 'twill' || 'playwright' }}
         working-directory: 'galaxy root'
       - uses: actions/upload-artifact@v3
         if: failure()
         with:
-          name: Toolshed test results (${{ matrix.python-version }})
+          name: Toolshed test results (${{ matrix.python-version }}, ${{ matrix.shed-api }}, ${{ matrix.test-install-client }})
           path: 'galaxy root/run_toolshed_tests.html'

.isort.cfg

@@ -10,5 +10,5 @@ profile=black
 reverse_relative=true
 skip_gitignore=true
 # Make isort run faster by skipping database
-skip_glob=database/*
+skip_glob=database/*,lib/tool_shed/test/test_data/repos/*
 src_paths=lib

.redocly.lint-ignore.yaml

@@ -14,3 +14,6 @@ _schema.yaml:
       #/paths/~1api~1histories~1{history_id}~1contents~1{history_content_id}~1metadata_file
     - '#/paths/~1api~1histories~1{history_id}~1contents~1{id}~1validate'
     - '#/paths/~1api~1histories~1{history_id}~1contents~1{type}s~1{id}'
+_shed_schema.yaml:
+  no-empty-servers:
+    - '#/openapi'

.vscode/shed.code-snippets

@@ -0,0 +1,41 @@
+{
+    "shedcomp": {
+        "prefix": "shed_component",
+        "body": [
+            "<script setup lang=\"ts\">",
+            "\t$0",
+            "</script>",
+            "<template>",
+            "</template>"
+        ],
+       "description": "outline of a tool shed component"
+    },
+    "shedpage": {
+        "prefix": "shed_page",
+        "body": [
+            "<script setup lang=\"ts\">",
+            "import PageContainer from \"@/components/PageContainer.vue\"",
+            "</script>",
+            "<template>",
+            "    <page-container>",
+            "        $0",
+            "    </page-container>",
+            "</template>"
+        ],
+       "description": "outline of a tool shed page"
+    },
+    "shedfetcher": {
+        "prefix": "shed_fetcher",
+        "body": [
+            "import { fetcher } from \"@/schema\"",
+            "const fetcher = fetcher.path(\"$1\").method(\"get\").create()"
+        ],
+        "description": "Import shed fetcher and instantiate with a path"
+    },
+    "shedrouter": {
+        "prefix": "shed_router",
+        "body": [
+            "import router from \"@/router\""
+        ]
+    }
+}

Makefile

@@ -139,7 +139,7 @@ release-bootstrap-history: ## bootstrap history for a new release
 update-lint-requirements:
 	./lib/galaxy/dependencies/update_lint_requirements.sh
 
-update-dependencies: update-lint-requirements ## update pinned and dev dependencies
+update-dependencies: update-lint-requirements ## update pinned, dev and typecheck dependencies
 	$(IN_VENV) ./lib/galaxy/dependencies/update.sh
 
 $(CWL_TARGETS):
@@ -182,17 +182,22 @@ endif
 
 build-api-schema:
 	$(IN_VENV) python scripts/dump_openapi_schema.py _schema.yaml
+	$(IN_VENV) python scripts/dump_openapi_schema.py --app shed _shed_schema.yaml
 
 remove-api-schema:
 	rm _schema.yaml
+	rm _shed_schema.yaml
 
 update-client-api-schema: client-node-deps build-api-schema
 	$(IN_VENV) cd client && node openapi_to_schema.mjs ../_schema.yaml > src/schema/schema.ts && npx prettier --write src/schema/schema.ts
+	$(IN_VENV) cd client && node openapi_to_schema.mjs ../_shed_schema.yaml > ../lib/tool_shed/webapp/frontend/src/schema/schema.ts && npx prettier --write ../lib/tool_shed/webapp/frontend/src/schema/schema.ts
 	$(MAKE) remove-api-schema
 
 lint-api-schema: build-api-schema
 	$(IN_VENV) npx --yes @redocly/cli lint _schema.yaml
+	$(IN_VENV) npx --yes @redocly/cli lint _shed_schema.yaml
 	$(IN_VENV) codespell -I .ci/ignore-spelling.txt _schema.yaml
+	$(IN_VENV) codespell -I .ci/ignore-spelling.txt _shed_schema.yaml
 	$(MAKE) remove-api-schema
 
 update-navigation-schema: client-node-deps
@@ -210,7 +215,10 @@ client-production: client-node-deps ## Rebuild client-side artifacts for a produ
 client-production-maps: client-node-deps ## Rebuild client-side artifacts for a production deployment with sourcemaps.
 	$(IN_VENV) cd client && $(NODE_ENV) yarn run build-production-maps
 
-client-format: client-node-deps ## Reformat client code
+client-lint-autofix: client-node-deps ## Automatically fix linting errors in client code
+	$(IN_VENV) cd client && yarn run eslint --quiet --fix
+
+client-format: client-node-deps client-lint-autofix ## Reformat client code, ensures autofixes are applied first
 	$(IN_VENV) cd client && yarn run format
 
 client-dev-server: client-node-deps ## Starts a webpack dev server for client development (HMR enabled)

client/package.json

@@ -15,7 +15,8 @@
   ],
   "browserslist": [
     "defaults",
-    "not op_mini all"
+    "not op_mini all",
+    "not ios_saf <= 15.0"
   ],
   "resolutions": {
     "chokidar": "3.5.3",

client/src/components/AboutGalaxy.vue

@@ -12,7 +12,7 @@ import ExternalLink from "@/components/ExternalLink.vue";
 import License from "@/components/License/License.vue";
 import UtcDate from "@/components/UtcDate.vue";
 
-const { config, isLoaded } = useConfig();
+const { config, isConfigLoaded } = useConfig();
 
 const clientBuildDate = __buildTimestamp__ || new Date().toISOString();
 const apiDocsLink = `${getAppRoot()}api/docs`;
@@ -27,7 +27,7 @@ const versionUserDocumentationUrl = computed(() => {
 </script>
 
 <template>
-    <div v-if="isLoaded" class="about-galaxy">
+    <div v-if="isConfigLoaded" class="about-galaxy">
         <Heading h1 :icon="['gxd', 'galaxyLogo']" size="xl">About This Galaxy</Heading>
         <div>
             <!-- Galaxy version (detailed), with a link to the release notes -->

client/src/components/ActivityBar/ActivityBar.test.js

@@ -1,7 +1,7 @@
 import { createTestingPinia } from "@pinia/testing";
 import { shallowMount } from "@vue/test-utils";
 import { PiniaVuePlugin } from "pinia";
-import { getLocalVue } from "tests/jest/helpers";
+import { dispatchEvent, getLocalVue } from "tests/jest/helpers";
 
 import { useConfig } from "@/composables/config";
 import { useActivityStore } from "@/stores/activityStore";
@@ -12,7 +12,7 @@ import mountTarget from "./ActivityBar.vue";
 jest.mock("composables/config");
 useConfig.mockReturnValue({
     config: {},
-    isLoaded: true,
+    isConfigLoaded: true,
 });
 
 jest.mock("vue-router/composables", () => ({
@@ -37,12 +37,6 @@ function testActivity(id, newOptions = {}) {
     return { ...defaultOptions, ...newOptions };
 }
 
-const createBubbledEvent = (type, props = {}) => {
-    const event = new Event(type, { bubbles: true });
-    Object.assign(event, props);
-    return event;
-};
-
 describe("ActivityBar", () => {
     let activityStore;
     let eventStore;
@@ -74,7 +68,7 @@ describe("ActivityBar", () => {
             name: "workflow-name",
         });
         const bar = wrapper.find("[data-description='activity bar']");
-        bar.element.dispatchEvent(createBubbledEvent("dragenter", { clientX: 0, clientY: 0 }));
+        dispatchEvent(bar, "dragenter");
         const emittedEvent = wrapper.emitted()["dragstart"][0][0];
         expect(emittedEvent.to).toBe("/workflows/run?id=workflow-id");
     });

client/src/components/ActivityBar/ActivityBar.vue

@@ -17,10 +17,10 @@ import NotificationItem from "./Items/NotificationItem.vue";
 import UploadItem from "./Items/UploadItem.vue";
 import ContextMenu from "@/components/Common/ContextMenu.vue";
 import FlexPanel from "@/components/Panels/FlexPanel.vue";
-import ToolBox from "@/components/Panels/ProviderAwareToolBox.vue";
+import ToolPanel from "@/components/Panels/ToolPanel.vue";
 import WorkflowBox from "@/components/Panels/WorkflowBox.vue";
 
-const { config } = useConfig();
+const { config, isConfigLoaded } = useConfig();
 
 const route = useRoute();
 const userStore = useUserStore();
@@ -193,7 +193,7 @@ function toggleContextMenu(evt: MouseEvent) {
             </b-nav>
             <b-nav vertical class="flex-nowrap p-1">
                 <NotificationItem
-                    v-if="!isAnonymous && config.enable_notification_system"
+                    v-if="!isAnonymous && isConfigLoaded && config.enable_notification_system"
                     id="activity-notifications"
                     icon="bell"
                     :is-active="isActiveRoute('/user/notifications')"
@@ -211,7 +211,7 @@ function toggleContextMenu(evt: MouseEvent) {
             </b-nav>
         </div>
         <FlexPanel v-if="isActiveSideBar('tools')" key="tools" side="left" :collapsible="false">
-            <ToolBox />
+            <ToolPanel />
         </FlexPanel>
         <FlexPanel v-else-if="isActiveSideBar('workflows')" key="workflows" side="left" :collapsible="false">
             <WorkflowBox />