Merge pull request #23142 from mvdbeek/fix-flaky-testa

Stabilize flaky integration and UI tests

Author: davelopez

.github/workflows/integration.yaml

@@ -25,8 +25,57 @@ concurrency:
   cancel-in-progress: true
 permissions: {}
 jobs:
+  prepare-mulled-cache:
+    name: Prepare mulled resolution cache
+    runs-on: ubuntu-latest
+    steps:
+      - name: Select weekly cache
+        run: echo "MULLED_CACHE_WEEK=$(date -u +%G-%V)" >> "$GITHUB_ENV"
+      - name: Restore Biocontainers repository index
+        id: restore-mulled-cache
+        uses: actions/cache/restore@v6.1.0
+        with:
+          key: biocontainers-repository-index-${{ env.MULLED_CACHE_WEEK }}
+          path: '${{ runner.temp }}/mulled-resolution-seed'
+      - name: Check out Galaxy for mulled-cache
+        if: steps.restore-mulled-cache.outputs.cache-hit != 'true'
+        uses: actions/checkout@v7.0.0
+        with:
+          path: 'galaxy cache source'
+          persist-credentials: false
+      - name: Fetch Biocontainers repository index
+        id: fetch-mulled-cache
+        if: steps.restore-mulled-cache.outputs.cache-hit != 'true'
+        continue-on-error: true
+        env:
+          SEED_DIRECTORY: '${{ runner.temp }}/mulled-resolution-seed'
+        run: |
+          python3 'galaxy cache source/lib/galaxy/tool_util/deps/mulled/mulled_cache.py' \
+              --namespace biocontainers \
+              --output "$SEED_DIRECTORY/biocontainers.json"
+      - name: Save Biocontainers repository index
+        if: steps.restore-mulled-cache.outputs.cache-hit != 'true' && steps.fetch-mulled-cache.outcome == 'success'
+        uses: actions/cache/save@v6.1.0
+        with:
+          key: biocontainers-repository-index-${{ env.MULLED_CACHE_WEEK }}
+          path: '${{ runner.temp }}/mulled-resolution-seed'
+      - name: Create fallback seed
+        if: steps.fetch-mulled-cache.outcome == 'failure'
+        env:
+          SEED_DIRECTORY: '${{ runner.temp }}/mulled-resolution-seed'
+        run: |
+          mkdir -p "$SEED_DIRECTORY"
+          echo '{"namespace":"biocontainers","repositories":[]}' > "$SEED_DIRECTORY/biocontainers.json"
+      - name: Upload mulled resolution cache seed
+        uses: actions/upload-artifact@v7
+        with:
+          name: mulled-resolution-cache-seed
+          path: '${{ runner.temp }}/mulled-resolution-seed/biocontainers.json'
+          retention-days: 1
+
   test:
     name: Test
+    needs: prepare-mulled-cache
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -63,9 +112,18 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Install Python
         run: uv python install
+      - name: Download mulled resolution cache seed
+        uses: actions/download-artifact@v8
+        with:
+          name: mulled-resolution-cache-seed
+          path: '${{ runner.temp }}/mulled-resolution-seed'
       - name: Install Apptainer's singularity
         uses: './galaxy root/.github/actions/install_apptainer'
       - name: Run tests
+        env:
+          GALAXY_TEST_MULLED_RESOLUTION_CACHE_SEED: '${{ runner.temp }}/mulled-resolution-seed/biocontainers.json'
+          GALAXY_CONFIG_OVERRIDE_MULLED_RESOLUTION_CACHE_DATA_DIR: '${{ runner.temp }}/mulled-resolution-cache/data'
+          GALAXY_CONFIG_OVERRIDE_MULLED_RESOLUTION_CACHE_LOCK_DIR: '${{ runner.temp }}/mulled-resolution-cache/locks'
         run: |
           . .ci/minikube-test-setup/start_services.sh
           ./run_tests.sh --coverage -integration test/integration -- --num-shards=4 --shard-id=${{ matrix.chunk }}

client/packages/api-client/src/schema/schema.ts

@@ -20647,7 +20647,7 @@ export interface components {
             /** Version */
             version: string | null;
             /** Xrefs */
-            xrefs: components["schemas"]["XrefDict-Output"][];
+            xrefs: components["schemas"]["XrefDict"][];
         };
         /** ParsedWorkbook */
         ParsedWorkbook: {
@@ -26412,7 +26412,7 @@ export interface components {
              */
             version: string;
             /** xrefs */
-            xrefs?: components["schemas"]["XrefDict-Input"][] | null;
+            xrefs?: components["schemas"]["XrefDict"][] | null;
         };
         /**
          * UserToolSource
@@ -26519,7 +26519,7 @@ export interface components {
              */
             version: string;
             /** xrefs */
-            xrefs?: components["schemas"]["XrefDict-Output"][] | null;
+            xrefs?: components["schemas"]["XrefDict"][] | null;
         };
         /** UserUpdatePayload */
         UserUpdatePayload: {
@@ -27695,19 +27695,12 @@ export interface components {
             target_uri: string;
         };
         /** XrefDict */
-        "XrefDict-Input": {
+        XrefDict: {
             /** type */
             type: string;
             /** value */
             value: string;
         };
-        /** XrefDict */
-        "XrefDict-Output": {
-            /** Type */
-            type: string;
-            /** Value */
-            value: string;
-        };
         /** XrefItem */
         XrefItem: {
             /**
@@ -28330,7 +28323,7 @@ export interface components {
              */
             version?: string | null;
             /** xrefs */
-            xrefs?: components["schemas"]["XrefDict-Input"][] | null;
+            xrefs?: components["schemas"]["XrefDict"][] | null;
         };
         /**
          * YamlToolTest

client/src/components/AvailableDatatypes/AvailableDatatypes.vue

@@ -13,7 +13,7 @@ const filter = ref("");
 const filterFields: Array<keyof DetailedDatatypes> = ["extension"];
 
 const { datatypes } = useDetailedDatatypes();
-const filteredDatatypes = useFilterObjectArray(datatypes, filter, filterFields);
+const { filtered: filteredDatatypes } = useFilterObjectArray(datatypes, filter, filterFields);
 
 const fields: TableField[] = [
     {

client/src/components/Form/Elements/FormSelect.vue

@@ -58,7 +58,10 @@ const emit = defineEmits<{
 }>();
 
 const filter = ref("");
-const filteredOptions = useFilterObjectArray(() => props.options, filter, ["label", ["value", "tags"]]);
+const { filtered: filteredOptions, pending: filterPending } = useFilterObjectArray(() => props.options, filter, [
+    "label",
+    ["value", "tags"],
+]);
 
 // Debounced upward emit so consumers (e.g. ``FormData`` paginating against the
 // backend) can refetch on typing without firing on every keystroke. The local
@@ -241,6 +244,7 @@ function isSelected(item: SelectValue): boolean {
             v-if="hasOptions"
             :id="id"
             v-model="currentValue"
+            :data-filter-pending="filterPending ? 'true' : undefined"
             :allow-empty="optional || multiple"
             :aria-expanded="ariaExpanded"
             :close-on-select="!multiple"
@@ -258,7 +262,10 @@ function isSelected(item: SelectValue): boolean {
             @open="onOpen"
             @close="onClose">
             <template v-slot:option="{ option }">
-                <div class="d-flex align-items-center justify-content-between">
+                <!-- Replace recycled option content when its identity changes. -->
+                <div
+                    :key="`${option.label}:${String(option.value)}`"
+                    class="d-flex align-items-center justify-content-between">
                     <div>
                         <span>{{ option.label }}</span>
                         <StatelessTags

client/src/components/ToolsList/ToolsListTable.vue

@@ -42,9 +42,8 @@ async function loadTools(offset: number, limit: number): Promise<{ items: Tool[]
     return { items, total: props.tools.length };
 }
 
-// Force ScrollList remount when tools change (e.g. after search),
-// ensuring loadTools is called again to await help data for new results.
-const toolsKey = computed(() => `${props.tools.length}-${props.tools[0]?.id}`);
+// Remount ScrollList when its result set changes so it reloads help data.
+const toolsKey = computed(() => JSON.stringify(props.tools.map((tool) => tool.id)));
 </script>
 
 <template>

client/src/components/Workflow/Editor/Node.vue

@@ -20,6 +20,7 @@
             :class="headerClass"
             @pointerdown.exact="onPointerDown"
             @pointerup.exact="onPointerUp"
+            @dblclick.exact="onDoubleClick"
             @click.shift.capture.prevent.stop="toggleSelected"
             @keyup.enter="makeActive">
             <b-button-group class="float-right">
@@ -104,6 +105,7 @@
             class="node-error m-0 rounded-0 rounded-bottom"
             @pointerdown.exact="onPointerDown"
             @pointerup.exact="onPointerUp"
+            @dblclick.exact="onDoubleClick"
             @click.shift.capture.prevent.stop="toggleSelected">
             {{ errors }}
         </b-alert>
@@ -114,6 +116,7 @@
             :class="{ 'cursor-pointer': isInvocation || isPopulatedInput }"
             @pointerdown.exact="onPointerDown"
             @pointerup.exact="onPointerUp"
+            @dblclick.exact="onDoubleClick"
             @click.shift.capture.prevent.stop="toggleSelected"
             @keyup.enter="makeActive">
             <NodeInput
@@ -352,10 +355,8 @@ function onDragConnector(dragPosition: TerminalPosition, terminal: OutputTermina
 
 const mouseMovementThreshold = 9;
 const singleClickTimeout = 800;
-const doubleClickTimeout = 500;
 
 let mouseDownTime = 0;
-let doubleClickTime = 0;
 
 let movementDistance = 0;
 let lastPosition: XYPosition | null = null;
@@ -381,15 +382,19 @@ function onPointerUp(e: PointerEvent) {
         makeActive();
     }
 
-    const timeBetweenClicks = mouseUpTime - doubleClickTime;
+    lastPosition = null;
+    movementDistance = 0;
+}
+
+function onDoubleClick(e: MouseEvent) {
+    const path = composedPartialPath(e);
+    const unclickable = path.every((target) => !isClickable(target as Element));
 
-    if (timeBetweenClicks < doubleClickTimeout) {
-        inspectorStore.setMaximized(props.step, true);
+    if (!unclickable) {
+        return;
     }
 
-    doubleClickTime = Date.now();
-    lastPosition = null;
-    movementDistance = 0;
+    inspectorStore.setMaximized(props.step, true);
 }
 
 function onMoveTo(position: XYPosition) {

client/src/components/admin/RoleForm.test.js

@@ -21,7 +21,7 @@ vi.mock("vue-router/composables", () => ({
 vi.mock("@/composables/filter/filter.js", () => {
     const { ref } = require("vue");
     return {
-        useFilterObjectArray: () => ref([]),
+        useFilterObjectArray: () => ({ filtered: ref([]), pending: ref(false) }),
     };
 });
 

client/src/composables/__mocks__/filter.ts

@@ -1,5 +1,5 @@
 import { toValue } from "@vueuse/core";
-import { computed, type Ref } from "vue";
+import { computed, ref } from "vue";
 
 import type { useFilterObjectArray as UseFilterObjectArray } from "@/composables/filter";
 
@@ -8,6 +8,6 @@ vi.mock("@/composables/filter", () => ({
     useFilterObjectArray,
 }));
 
-export const useFilterObjectArray: typeof UseFilterObjectArray = (array): Ref<any[]> => {
-    return computed(() => toValue(array));
-};
+export const useFilterObjectArray = ((array) => {
+    return { filtered: computed(() => toValue(array)), pending: ref(false) };
+}) as typeof UseFilterObjectArray;

client/src/composables/filter/filter.d.ts

@@ -12,4 +12,4 @@ export declare function useFilterObjectArray<O extends object, K extends keyof O
     array: MaybeRefOrGetter<Array<O>>,
     filter: MaybeRefOrGetter<string>,
     objectFields: MaybeRefOrGetter<Array<K | string[]>>,
-): Ref<O[]>;
+): { filtered: Ref<O[]>; pending: Ref<boolean> };

client/src/composables/filter/filter.js

@@ -7,8 +7,14 @@ export function useFilterObjectArray(array, filter, objectFields, asRegex = fals
     const filtered = ref([]);
     filtered.value = toValue(array);
 
+    // Track the latest request so consumers never act on an intermediate result.
+    const pending = ref(true);
+    let sentSeq = 0;
+
     const post = (message) => {
-        worker.postMessage(message);
+        sentSeq += 1;
+        pending.value = true;
+        worker.postMessage({ ...message, seq: sentSeq });
     };
 
     watch(
@@ -44,14 +50,15 @@ export function useFilterObjectArray(array, filter, objectFields, asRegex = fals
     worker.onmessage = (e) => {
         const message = e.data;
 
-        if (message.type === "result") {
+        if (message.type === "result" && message.seq === sentSeq) {
             filtered.value = message.filtered;
+            pending.value = false;
         }
     };
 
     onScopeDispose(() => {
         worker.terminate();
     });
 
-    return filtered;
+    return { filtered, pending };
 }