Merge 25.1 into dev

.github/release-drafter.yml

@@ -0,0 +1,83 @@
+# Release Drafter Configuration for Galaxy
+# Implements YY.N.P versioning scheme using existing Galaxy labels
+#
+# IMPORTANT: Galaxy's versioning scheme is YY.N.P where:
+# - YY = Two-digit year (25 for 2025)
+# - N = Feature release number (0, 1, 2... - typically 2-3 per year)
+# - P = Patch/point release number (0, 1, 2, 3...)
+#
+# Year transitions (24→25) must be handled manually when creating releases.
+
+name-template: 'Galaxy $RESOLVED_VERSION'
+tag-template: 'v$RESOLVED_VERSION'
+
+# Categories for organizing release notes using existing Galaxy labels
+categories:
+  - title: '🎉 Major Changes'
+    labels:
+      - 'major'
+      - 'highlight'
+  - title: '🚀 New Features'
+    labels:
+      - 'kind/feature'
+  - title: '🔧 Enhancements'
+    labels:
+      - 'kind/enhancement'
+  - title: '🐛 Bug Fixes'
+    labels:
+      - 'kind/bug'
+  - title: '🔒 Security Updates'
+    labels:
+      - 'area/security'
+  - title: '⚡ Performance'
+    labels:
+      - 'area/performance'
+  - title: '🧰 Refactoring'
+    labels:
+      - 'kind/refactoring'
+  - title: '📚 Documentation'
+    labels:
+      - 'area/documentation'
+  - title: '🔧 Admin & Configuration'
+    labels:
+      - 'area/admin'
+      - 'area/configuration'
+  - title: '🛠️ API Changes'
+    labels:
+      - 'area/API'
+  - title: '🧪 Testing'
+    labels:
+      - 'area/testing'
+      - 'area/testing/api'
+      - 'area/testing/integration'
+      - 'area/testing/selenium'
+  - title: '🏗️ Infrastructure & Dependencies'
+    labels:
+      - 'area/dependencies'
+      - 'area/client-build'
+
+# Exclude certain labels from release notes
+exclude-labels:
+  - 'triage'
+  - 'procedures'
+  - 'planning'
+  - 'merge'
+  - 'status/needs feedback'
+  - 'status/planning'
+
+# Template for each change line
+change-template: '- $TITLE @$AUTHOR (#$NUMBER)'
+
+# Characters to escape in titles
+change-title-escapes: '\<*_&'
+
+# Version is read from lib/galaxy/version.py by the workflow
+# No version-resolver needed since Galaxy manages versions manually
+
+# Template for the release body
+template: |
+  ## Changes in $RESOLVED_VERSION
+
+  $CHANGES
+
+  **Full Changelog**: https://github.com/$OWNER/$REPOSITORY/compare/$PREVIOUS_TAG...v$RESOLVED_VERSION

.github/workflows/build_container_image.yaml

@@ -43,7 +43,7 @@ jobs:
         id: buildargs
         run: |
             echo "gitcommit=$(git rev-parse HEAD)" >> $GITHUB_OUTPUT 
-            echo "builddate=$(date -u +'%Y-%m-%dT%H:%M:%SZ')"
+            echo "builddate=$(date -u +'%Y-%m-%dT%H:%M:%SZ')"  >> $GITHUB_OUTPUT
 
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3

.github/workflows/release-drafter.yml

@@ -0,0 +1,43 @@
+name: Release Drafter
+
+on:
+  push:
+    branches:
+      - dev
+      - master
+      - 'release_*'
+  pull_request_target:
+    types: [opened, reopened, synchronize]
+
+permissions:
+  contents: read
+
+jobs:
+  update_release_draft:
+    permissions:
+      contents: write
+      pull-requests: write
+    if: github.repository == 'galaxyproject/galaxy'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: dev
+          sparse-checkout: |
+            lib/galaxy/version.py
+
+      - name: Read Galaxy version
+        id: galaxy-version
+        run: |
+          # Extract VERSION_MAJOR from version.py (e.g., "25.1")
+          VERSION_MAJOR=$(grep '^VERSION_MAJOR' lib/galaxy/version.py | cut -d'"' -f2)
+          RELEASE_VERSION="${VERSION_MAJOR}.0"
+          echo "version=${RELEASE_VERSION}" >> $GITHUB_OUTPUT
+          echo "Galaxy release version: ${RELEASE_VERSION}"
+
+      - uses: release-drafter/release-drafter@v6
+        with:
+          config-name: release-drafter.yml
+          version: ${{ steps.galaxy-version.outputs.version }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.k8s_ci.Dockerfile

@@ -150,12 +150,14 @@ RUN set -xe; \
         locales \
         vim-tiny \
         nano-tiny \
+        netcat-openbsd \
         curl \
         procps \
         less \
         bzip2 \
         tini \
         nodejs \
+        wget \
     && update-alternatives --install /usr/bin/nano nano /bin/nano-tiny 0 \
     && update-alternatives --install /usr/bin/vim vim /usr/bin/vim.tiny 0 \
     && echo "set nocompatible\nset backspace=indent,eol,start" >> /usr/share/vim/vimrc.tiny \

client/src/components/Collections/ListWizard.vue

@@ -19,6 +19,7 @@ import { showHid } from "./common/useCollectionCreator";
 import type { WhichListBuilder } from "./ListWizard/types";
 import { useAutoPairing } from "./usePairing";
 
+import LoadingSpan from "../LoadingSpan.vue";
 import ListCollectionCreator from "./ListCollectionCreator.vue";
 import WhichBuilder from "./ListWizard/WhichBuilder.vue";
 import PairedOrUnpairedListCollectionCreator from "./PairedOrUnpairedListCollectionCreator.vue";
@@ -199,16 +200,22 @@ function onRuleState(newRuleState: boolean) {
 <template>
     <div v-if="currentHistoryId">
         <div v-if="creationError">
-            <BAlert variant="danger">
+            <BAlert variant="danger" show>
                 {{ creationError }}
             </BAlert>
         </div>
         <div v-if="collectionCreated">
             <BAlert variant="success" show> Collection created and it has been added to your history. </BAlert>
         </div>
-        <div v-else-if="!selectedItems">Loading...</div>
+        <div v-else-if="!selectedItems">
+            <BAlert variant="info" show>
+                <LoadingSpan />
+            </BAlert>
+        </div>
         <div v-else-if="selectedItems.length == 0">
-            <p>Select datasets from history panel to use the Galaxy list building wizard.</p>
+            <BAlert variant="info" show>
+                Select datasets from the history panel to use the Galaxy list building wizard.
+            </BAlert>
         </div>
         <GenericWizard v-else :use="wizard" :is-busy="isBusy" :submit-button-label="buildButtonLabel" @submit="submit">
             <div v-if="wizard.isCurrent('which-builder')">

client/src/components/Collections/ListWizard/WhichBuilder.vue

@@ -34,7 +34,7 @@ function toggleAdvanced() {
                     <b>Flat List</b>
                 </BCardTitle>
                 <div>
-                    This options creates a simple flat list of files. If your data isn't nested and does not contained
+                    This option creates a simple flat list of files. If your data isn't nested and does not contained
                     paired datasets, this is the the option to choose.
                 </div>
             </BCard>
@@ -47,8 +47,8 @@ function toggleAdvanced() {
                     <b>List of Paired Datasets</b>
                 </BCardTitle>
                 <div>
-                    This options creates a uniform list of paired datasets, use this option if all of your data should
-                    be paired off.
+                    This option creates a uniform list of paired datasets, use this option if all of your data should be
+                    paired off.
                 </div>
             </BCard>
             <BCard

client/src/components/Collections/wizard/WhichWorkbookCollectionType.vue

@@ -26,8 +26,8 @@ defineProps<Props>();
                     <b>Flat List</b>
                 </BCardTitle>
                 <div>
-                    This options creates a simple flat list of files. If your data isn't nested and does not contained
-                    paired datasets, this is the the option to choose.
+                    This option creates a simple flat list of files. If your data isn't nested and does not contained
+                    paired datasets, this is the option to choose.
                 </div>
             </BCard>
             <BCard
@@ -39,8 +39,8 @@ defineProps<Props>();
                     <b>List of Paired Datasets</b>
                 </BCardTitle>
                 <div>
-                    This options creates a uniform list of paired datasets, use this option if all of your data should
-                    be paired off.
+                    This option creates a uniform list of paired datasets, use this option if all of your data should be
+                    paired off.
                 </div>
             </BCard>
         </BCardGroup>

client/src/components/Common/Wizard/GenericWizard.vue

@@ -344,6 +344,11 @@ const bodyStyle = computed(() => {
         .card-header {
             border-radius: 0;
         }
+
+        &:hover {
+            border-color: lighten($brand-primary, 20%);
+            cursor: pointer;
+        }
     }
 }
 </style>

client/src/components/History/CurrentCollection/CollectionOperations.vue

@@ -22,6 +22,10 @@ const showCollectionDetailsUrl = computed(() =>
 );
 const disableDownload = props.dsc.populated_state !== "ok";
 
+const hasSampleSheet = computed(() => {
+    return props.dsc.collection_type && props.dsc.collection_type.startsWith("sample_sheet");
+});
+
 const sheetUrl = computed(() => {
     return `${getAppRoot()}collection/${props.dsc.id}/sheet`;
 });
@@ -68,7 +72,7 @@ function onDownload() {
                     <span>Run Job Again</span>
                 </b-button>
                 <b-button
-                    v-if="sheetUrl"
+                    v-if="hasSampleSheet && sheetUrl"
                     class="rounded-0 text-decoration-none"
                     size="sm"
                     variant="link"

client/src/components/History/CurrentHistory/HistoryOperations/SelectionOperations.vue

@@ -303,7 +303,14 @@ export default {
             const { setSelectedItems } = useCollectionBuilderItemSelection();
             const selection = Array.from(this.contentSelection.values());
             setSelectedItems(selection);
-            this.$router.push({ path: `/collection/new_list?advanced=${advanced}` });
+
+            if (this.$route.path === "/collection/new_list") {
+                // vue-router 4 supports a native force push with clean URLs, but we're using a __vkey__
+                // bit as a workaround to allow the builder to be invoked consecutively
+                this.$router.push({ path: `/collection/new_list?advanced=${advanced}` }, { force: true });
+            } else {
+                this.$router.push(`/collection/new_list?advanced=${advanced}`);
+            }
         },
         // Selected content manipulation, hide/show/delete/purge
         hideSelected() {

client/src/components/Upload/DefaultBox.vue

@@ -76,9 +76,7 @@ const queue = ref(createUploadQueue());
 const selectedItemsForModal = ref<HDASummary[]>([]);
 
 const counterNonRunning = computed(() => counterAnnounce.value + counterSuccess.value + counterError.value);
-const creatingPairedType = computed(
-    () => props.isCollection && ["list:paired", "paired"].includes(collectionType.value),
-);
+const creatingPairedType = computed(() => props.isCollection && collectionType.value === "list:paired");
 const enableBuild = computed(
     () =>
         !isRunning.value &&

client/src/components/Upload/utils.js

@@ -14,7 +14,6 @@ export const AUTO_EXTENSION = {
 };
 export const COLLECTION_TYPES = [
     { id: "list", text: "List" },
-    { id: "paired", text: "Pair" },
     { id: "list:paired", text: "List of Pairs" },
 ];
 export const DEFAULT_DBKEY = "?";

client/src/composables/resourceWatcher.test.ts

@@ -228,7 +228,7 @@ describe("useResourceWatcher", () => {
             expect(mockAddEventListener).toHaveBeenCalledWith("visibilitychange", expect.any(Function));
         });
 
-        it("should restart watching with short interval when app becomes visible", async () => {
+        it("should switch to short interval when app becomes visible without restarting watcher", async () => {
             const { startWatchingResource } = useResourceWatcher(mockWatchHandler);
 
             startWatchingResource();
@@ -242,22 +242,22 @@ describe("useResourceWatcher", () => {
             mockDocument.visibilityState = "hidden";
             visibilityChangeHandler();
 
-            // Clear the handler calls from the visibility change restart
+            // Clear the handler calls
             mockWatchHandler.mockClear();
 
             // Simulate app becoming visible again
             mockDocument.visibilityState = "visible";
             visibilityChangeHandler();
 
-            // Should immediately call the handler (from startWatchingResource)
+            // Should NOT immediately call the handler (watcher already running, no restart)
             await flushPromises();
-            expect(mockWatchHandler).toHaveBeenCalledTimes(1);
+            expect(mockWatchHandler).toHaveBeenCalledTimes(0);
 
-            // Should continue with short polling interval
+            // But should continue with short polling interval on next scheduled poll
             jest.advanceTimersByTime(3000);
             await flushPromises();
 
-            expect(mockWatchHandler).toHaveBeenCalledTimes(2);
+            expect(mockWatchHandler).toHaveBeenCalledTimes(1);
         });
     });
 
@@ -494,25 +494,25 @@ describe("useResourceWatcher", () => {
             mockDocument.visibilityState = "hidden";
             visibilityChangeHandler();
 
-            // Change to visible - this restarts the watcher
+            // Change to visible - this changes currentPollingInterval back to short but doesn't restart
             mockDocument.visibilityState = "visible";
             visibilityChangeHandler();
             await flushPromises();
-            expect(mockWatchHandler).toHaveBeenCalledTimes(2); // + 1 from becoming visible
+            expect(mockWatchHandler).toHaveBeenCalledTimes(1); // No additional call from becoming visible
 
-            // Change to hidden again - this changes currentPollingInterval but doesn't restart timer
-            mockDocument.visibilityState = "hidden";
-            visibilityChangeHandler();
-
-            // The timer that was started when becoming visible is still running with short interval
+            // The timer continues with the short interval
             jest.advanceTimersByTime(3000);
             await flushPromises();
-            expect(mockWatchHandler).toHaveBeenCalledTimes(3); // + 1 from short interval timer
+            expect(mockWatchHandler).toHaveBeenCalledTimes(2); // + 1 from short interval timer
+
+            // Change to hidden again
+            mockDocument.visibilityState = "hidden";
+            visibilityChangeHandler();
 
-            // Now the next timer should be using the long interval
+            // The next timer should use the long interval
             jest.advanceTimersByTime(10000);
             await flushPromises();
-            expect(mockWatchHandler).toHaveBeenCalledTimes(4); // + 1 from long interval timer
+            expect(mockWatchHandler).toHaveBeenCalledTimes(3); // + 1 from long interval timer
         });
     });
 });

client/src/composables/resourceWatcher.ts

@@ -111,7 +111,7 @@ export function useResourceWatcher<T = unknown>(
     function updateThrottle() {
         if (document.visibilityState === "visible") {
             currentPollingInterval = shortPollingInterval;
-            startWatchingResource();
+            startWatchingResourceIfNeeded();
         } else {
             currentPollingInterval = enableBackgroundPolling ? longPollingInterval : undefined;
         }

client/src/entry/analysis/router-push.js

@@ -15,7 +15,16 @@ export function patchRouterPush(VueRouter) {
         // add key to location to force component refresh
         const { title, force, preventWindowManager } = options;
         if (force) {
-            location = addSearchParams(location, { __vkey__: Date.now() });
+            // since location can either be string or object, we need to pass the string url to addSearchParams
+            if (typeof location === "string") {
+                location = addSearchParams(location, { __vkey__: Date.now() });
+            } else if (typeof location === "object") {
+                // convert to string version addSearchParams can handle
+                let url = this.resolve(location).href;
+                url = addSearchParams(url, { __vkey__: Date.now() });
+                // convert back to object version
+                location = this.resolve(url).route;
+            }
         }
         // verify if confirmation is required
         if (this.confirmation) {