Merge branch 'release_23.0' into dev

nsoranzo · May 14, 2023 · ab99721 · ab99721
2 parents ad5ca5c + a4266b8
commit ab99721
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Showing 103 changed files with 1,492 additions and 721 deletions.
diff --git a/.github/workflows/api.yaml b/.github/workflows/api.yaml
@@ -47,6 +47,11 @@ 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 }}

diff --git a/.github/workflows/converter_tests.yaml b/.github/workflows/converter_tests.yaml
@@ -31,6 +31,11 @@ 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'
       - name: Clone galaxyproject/galaxy-test-data
         uses: actions/checkout@v3
         with:

diff --git a/.github/workflows/cwl_conformance.yaml b/.github/workflows/cwl_conformance.yaml
@@ -38,6 +38,11 @@ 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 }}

diff --git a/.github/workflows/first_startup.yaml b/.github/workflows/first_startup.yaml
@@ -29,6 +29,11 @@ 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'
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
@@ -48,11 +53,6 @@ jobs:
         with:
           path: .tox
           key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-first-startup
-      - uses: actions/setup-node@v3
-        with:
-          node-version: '18.12.1'
-          cache: 'yarn'
-          cache-dependency-path: 'galaxy root/client/yarn.lock'
       - name: Install tox
         run: pip install tox
       - name: run tests

diff --git a/.github/workflows/framework.yaml b/.github/workflows/framework.yaml
@@ -43,6 +43,11 @@ 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 }}

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
@@ -71,6 +71,11 @@ 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 }}

diff --git a/.github/workflows/osx_startup.yaml b/.github/workflows/osx_startup.yaml
@@ -22,6 +22,11 @@ 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'
       - name: Get full Python version
         id: full-python-version
         shell: bash

diff --git a/.github/workflows/performance.yaml b/.github/workflows/performance.yaml
@@ -42,6 +42,11 @@ 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 }}

diff --git a/.github/workflows/reports_startup.yaml b/.github/workflows/reports_startup.yaml
@@ -26,6 +26,11 @@ 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'
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
@@ -45,11 +50,6 @@ jobs:
         with:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-reports-startup
-      - uses: actions/setup-node@v3
-        with:
-          node-version: '18.12.1'
-          cache: 'yarn'
-          cache-dependency-path: 'galaxy root/client/yarn.lock'
       - name: Install tox
         run: pip install tox
       - name: Run tests

diff --git a/.github/workflows/selenium.yaml b/.github/workflows/selenium.yaml
@@ -46,6 +46,11 @@ 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: ${{ matrix.python-version }}
@@ -63,11 +68,6 @@ jobs:
         with:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-selenium
-      - uses: actions/setup-node@v3
-        with:
-          node-version: '18.12.1'
-          cache: 'yarn'
-          cache-dependency-path: 'galaxy root/client/yarn.lock'
       - uses: nanasess/setup-chromedriver@v1
       - name: Run tests
         run: ./run_tests.sh --coverage -selenium lib/galaxy_test/selenium -- --num-shards=3 --shard-id=${{ matrix.chunk }}

diff --git a/.github/workflows/unit-postgres.yaml b/.github/workflows/unit-postgres.yaml
@@ -36,6 +36,11 @@ 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 }}

diff --git a/.github/workflows/unit.yaml b/.github/workflows/unit.yaml
@@ -28,6 +28,11 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
+      - uses: actions/setup-node@v3
+        with:
+          node-version: '18.12.1'
+          cache: 'yarn'
+          cache-dependency-path: 'galaxy root/client/yarn.lock'
       - name: Get full Python version
         id: full-python-version
         shell: bash

diff --git a/client/src/components/History/Content/GenericItem.vue b/client/src/components/History/Content/GenericItem.vue
@@ -3,37 +3,39 @@
         <loading-span v-if="loading" message="Loading dataset" />
         <div v-else>
             <ContentItem
-                :id="item.hid"
+                :id="item.hid ?? item.element_index + 1"
                 add-highlight-btn
                 is-history-item
-                :item="item"
-                :name="item.name"
+                :item="item?.object || item"
+                :name="item.name || item.element_identifier"
                 :expand-dataset="expandDataset"
-                :is-dataset="item.history_content_type == 'dataset'"
+                :is-dataset="item.history_content_type == 'dataset' || item.element_type == 'hda'"
                 @update:expand-dataset="expandDataset = $event"
                 @view-collection="viewCollection = !viewCollection"
                 @delete="onDelete(item)"
                 @toggleHighlights="onHighlight(item)"
                 @undelete="onUndelete(item)"
                 @unhide="onUnhide(item)" />
             <div v-if="viewCollection">
-                <GenericElement :dsc="item" />
+                <GenericElement :dsc="item?.object || item" />
             </div>
         </div>
     </component>
 </template>
 
 <script>
 import LoadingSpan from "components/LoadingSpan";
-import { DatasetCollectionProvider, DatasetProvider } from "components/providers";
-import { deleteContent, updateContentFields } from "components/History/model/queries";
+import { DatasetCollectionProvider, DatasetProvider } from "@/components/providers";
+import { DatasetCollectionElementProvider } from "@/components/providers/storeProviders";
+import { deleteContent, updateContentFields } from "@/components/History/model/queries";
 import ContentItem from "./ContentItem";
 import GenericElement from "./GenericElement";
 import { mapActions } from "pinia";
 import { useHistoryStore } from "@/stores/historyStore";
 
 export default {
     components: {
+        DatasetCollectionElementProvider,
         ContentItem,
         GenericElement,
         DatasetProvider,
@@ -58,7 +60,16 @@ export default {
     },
     computed: {
         providerComponent() {
-            return this.itemSrc == "hda" ? "DatasetProvider" : "DatasetCollectionProvider";
+            switch (this.itemSrc) {
+                case "hda":
+                    return "DatasetProvider";
+                case "hdca":
+                    return "DatasetCollectionProvider";
+                case "dce":
+                    return "DatasetCollectionElementProvider";
+                default:
+                    throw Error(`Unknown element src ${this.itemSrc}`);
+            }
         },
     },
     methods: {

diff --git a/client/src/components/History/CurrentHistory/HistoryOperations/SelectionOperations.vue b/client/src/components/History/CurrentHistory/HistoryOperations/SelectionOperations.vue
@@ -343,8 +343,8 @@ export default {
             // have to hide the source items if that was requested
             if (modalResult.hide_source_items) {
                 this.$emit("hide-selection", this.contentSelection);
-                this.$emit("reset-selection");
             }
+            this.$emit("reset-selection");
         },
     },
 };

diff --git a/client/src/components/History/Export/HistoryExport.test.ts b/client/src/components/History/Export/HistoryExport.test.ts
@@ -19,7 +19,13 @@ const mockGetExportRecords = getExportRecords as jest.MockedFunction<typeof getE
 mockGetExportRecords.mockResolvedValue([]);
 
 const FAKE_HISTORY_ID = "fake-history-id";
+const FAKE_HISTORY = {
+    id: FAKE_HISTORY_ID,
+    name: "fake-history-name",
+};
+
 const REMOTE_FILES_API_ENDPOINT = new RegExp("/api/remote_files/plugins");
+const GET_HISTORY_ENDPOINT = new RegExp(`/api/histories/${FAKE_HISTORY_ID}`);
 
 type FilesSourcePluginList = components["schemas"]["FilesSourcePlugin"][];
 const REMOTE_FILES_API_RESPONSE: FilesSourcePluginList = [
@@ -50,12 +56,19 @@ describe("HistoryExport.vue", () => {
     beforeEach(async () => {
         axiosMock = new MockAdapter(axios);
         axiosMock.onGet(REMOTE_FILES_API_ENDPOINT).reply(200, []);
+        axiosMock.onGet(GET_HISTORY_ENDPOINT).reply(200, FAKE_HISTORY);
     });
 
     afterEach(() => {
         axiosMock.restore();
     });
 
+    it("should render the history name", async () => {
+        const wrapper = await mountHistoryExport();
+
+        expect(wrapper.find("#history-name").text()).toBe(FAKE_HISTORY.name);
+    });
+
     it("should render export options", async () => {
         const wrapper = await mountHistoryExport();