Merge branch 'dev' into lint-output-filter

.github/workflows/api.yaml

@@ -18,6 +18,7 @@ env:
   GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
   GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
   GALAXY_CONFIG_SQLALCHEMY_WARN_20: '1'
+  GALAXY_TEST_REQUIRE_ALL_NEEDED_TOOLS: '1'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true

.github/workflows/dependencies.yaml

@@ -8,18 +8,17 @@ jobs:
     name: Update dependencies
     if: github.repository_owner == 'galaxyproject'
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ['3.8']
     steps:
       - uses: actions/checkout@v4
+      # Install Python 3.8 for update_lint_requirements.sh
+      # Install Python 3.9 (as default) to allow `uv lock` to generate metadata for rucio-clients
       - uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: |
+            3.8
+            3.9
       - name: Update dependencies
-        run: | 
-          python -m venv .venv
-          make update-dependencies
+        run: make update-dependencies
       - name: Create pull request
         uses: peter-evans/create-pull-request@v6
         with:

.github/workflows/first_startup.yaml

@@ -23,7 +23,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     defaults:
       run:
         shell: bash -l {0}

.github/workflows/lint.yaml

@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     env:
       LINT_PATH: 'lib/galaxy/dependencies/pinned-lint-requirements.txt'
       TYPE_PATH: 'lib/galaxy/dependencies/pinned-typecheck-requirements.txt'

.github/workflows/lint_openapi_schema.yml

@@ -20,7 +20,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     steps:
       - uses: actions/checkout@v4
         with:

.github/workflows/osx_startup.yaml

@@ -21,7 +21,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     defaults:
       run:
         shell: bash -l {0}

.github/workflows/reports_startup.yaml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     defaults:
       run:
         shell: bash -l {0}

.github/workflows/test_galaxy_packages.yaml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     steps:
       - uses: actions/checkout@v4
         with:

.github/workflows/toolshed.yaml

@@ -21,7 +21,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
         shed-api: ['v1', 'v2']
         test-install-client: ['galaxy_api', 'standalone']
     services:

.github/workflows/unit.yaml

@@ -20,7 +20,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     steps:
       - uses: actions/checkout@v4
         with:

client/package.json

@@ -62,6 +62,7 @@
     "dom-to-image": "^2.6.0",
     "dompurify": "^3.0.6",
     "dumpmeta-webpack-plugin": "^0.2.0",
+    "echarts": "^5.5.1",
     "elkjs": "^0.8.2",
     "file-saver": "^2.0.5",
     "flush-promises": "^1.0.2",
@@ -100,7 +101,11 @@
     "tus-js-client": "^3.1.1",
     "underscore": "^1.13.6",
     "util": "^0.12.5",
+    "vega": "^5.30.0",
+    "vega-embed": "^6.26.0",
+    "vega-lite": "^5.21.0",
     "vue": "^2.7.14",
+    "vue-echarts": "^7.0.3",
     "vue-infinite-scroll": "^2.0.2",
     "vue-multiselect": "^2.1.7",
     "vue-observe-visibility": "^1.0.0",

client/src/api/schema/schema.ts

@@ -2594,6 +2594,23 @@ export interface paths {
         patch?: never;
         trace?: never;
     };
+    "/api/invocations/{invocation_id}/metrics": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        /** Get Invocation Metrics */
+        get: operations["get_invocation_metrics_api_invocations__invocation_id__metrics_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
+    };
     "/api/invocations/{invocation_id}/prepare_store_download": {
         parameters: {
             query?: never;
@@ -8753,6 +8770,11 @@ export interface components {
              * @description The email of the user that owns this job. Only the owner of the job and administrators can see this value.
              */
             user_email?: string | null;
+            /**
+             * User Id
+             * @description User ID of user that ran this job
+             */
+            user_id?: string | null;
         };
         /** EncodedJobParameterHistoryItem */
         EncodedJobParameterHistoryItem: {
@@ -16177,6 +16199,11 @@ export interface components {
              * @description The email of the user that owns this job. Only the owner of the job and administrators can see this value.
              */
             user_email?: string | null;
+            /**
+             * User Id
+             * @description User ID of user that ran this job
+             */
+            user_id?: string | null;
         };
         /**
          * Src
@@ -18317,6 +18344,49 @@ export interface components {
                 [key: string]: number;
             };
         };
+        /**
+         * WorkflowJobMetric
+         * @example {
+         *       "name": "start_epoch",
+         *       "plugin": "core",
+         *       "raw_value": "1614261340.0000000",
+         *       "title": "Job Start Time",
+         *       "value": "2021-02-25 14:55:40"
+         *     }
+         */
+        WorkflowJobMetric: {
+            /**
+             * Name
+             * @description The name of the metric variable.
+             */
+            name: string;
+            /**
+             * Plugin
+             * @description The instrumenter plugin that generated this metric.
+             */
+            plugin: string;
+            /**
+             * Raw Value
+             * @description The raw value of the metric as a string.
+             */
+            raw_value: string;
+            /** Step Index */
+            step_index: number;
+            /** Step Label */
+            step_label: string | null;
+            /**
+             * Title
+             * @description A descriptive title for this metric.
+             */
+            title: string;
+            /** Tool Id */
+            tool_id: string;
+            /**
+             * Value
+             * @description The textual representation of the metric value.
+             */
+            value: string;
+        };
         /** WorkflowLandingRequest */
         WorkflowLandingRequest: {
             /** Request State */
@@ -27021,6 +27091,50 @@ export interface operations {
             };
         };
     };
+    get_invocation_metrics_api_invocations__invocation_id__metrics_get: {
+        parameters: {
+            query?: never;
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The encoded database identifier of the Invocation. */
+                invocation_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["WorkflowJobMetric"][];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
     prepare_store_download_api_invocations__invocation_id__prepare_store_download_post: {
         parameters: {
             query?: never;

client/src/components/Help/terms.yml

@@ -106,3 +106,8 @@ galaxy:
       failed: |
         This state indicates there was a problem scheduling the workflow invocation. No additional datasets
         or jobs will be created for this workflow invocation.
+  upload:
+    galaxyUploadUtil: |
+      A utility for uploading files to a Galaxy server from the command line. Use ``galaxy-upload`` to upload
+      file(s) to a Galaxy server, and ``galaxy-history-search``, a helper utility to find Galaxy histories
+      to pass to the ``galaxy-upload`` command.

client/src/components/History/Content/Dataset/DatasetActions.vue

@@ -47,7 +47,7 @@ const showRerun = computed(() => {
 });
 const showVisualizations = computed(() => {
     // TODO: Check hasViz, if visualizations are activated in the config
-    return !props.item.purged && ["ok", "failed_metadata", "error"].includes(props.item.state);
+    return !props.item.purged && ["ok", "failed_metadata", "error", "deferred"].includes(props.item.state);
 });
 const reportErrorUrl = computed(() => {
     return prependPath(props.itemUrls.reportError!);

client/src/components/JobInformation/JobInformation.vue

@@ -5,7 +5,7 @@ import { JobDetailsProvider } from "components/providers/JobProvider";
 import UtcDate from "components/UtcDate";
 import { NON_TERMINAL_STATES } from "components/WorkflowInvocationState/util";
 import { formatDuration, intervalToDuration } from "date-fns";
-import { computed, ref } from "vue";
+import { computed, ref, watch } from "vue";
 
 import { GalaxyApi } from "@/api";
 import { rethrowSimple } from "@/utils/simple-error";
@@ -14,7 +14,7 @@ import DecodedId from "../DecodedId.vue";
 import CodeRow from "./CodeRow.vue";
 
 const job = ref(null);
-const invocationId = ref(null);
+const invocationId = ref(undefined);
 
 const props = defineProps({
     job_id: {
@@ -42,9 +42,6 @@ const metadataDetail = ref({
 
 function updateJob(newJob) {
     job.value = newJob;
-    if (newJob) {
-        fetchInvocation(newJob.id);
-    }
 }
 
 function filterMetadata(jobMessages) {
@@ -58,9 +55,9 @@ function filterMetadata(jobMessages) {
     });
 }
 
-async function fetchInvocation(jobId) {
+async function fetchInvocationForJob(jobId) {
     if (jobId) {
-        const { data: invocation, error } = await GalaxyApi().GET("/api/invocations", {
+        const { data: invocations, error } = await GalaxyApi().GET("/api/invocations", {
             params: {
                 query: { job_id: jobId },
             },
@@ -70,9 +67,29 @@ async function fetchInvocation(jobId) {
             rethrowSimple(error);
         }
 
-        invocationId.value = invocation.id;
+        if (invocations.length) {
+            return invocations[0];
+        }
+
+        return null;
     }
 }
+
+// Fetches the invocation for the given job id to get the associated invocation id
+watch(
+    () => props.job_id,
+    async (newId, oldId) => {
+        if (newId && (invocationId.value === undefined || newId !== oldId)) {
+            const invocation = await fetchInvocationForJob({ jobId: newId });
+            if (invocation) {
+                invocationId.value = invocation.id;
+            } else {
+                invocationId.value = null;
+            }
+        }
+    },
+    { immediate: true }
+);
 </script>
 
 <template>

client/src/components/Libraries/LibraryFolder/LibraryFolder.vue

@@ -384,7 +384,7 @@ export default {
                     this.sortBy,
                     this.sortDesc,
                     this.perPage,
-                    (this.currentPage - 1) * this.perPage,
+                    (this.currentPage ? this.currentPage - 1 : 0) * this.perPage,
                     this.searchText
                 )
                 .then((response) => {

client/src/components/Panels/utilities.ts

@@ -15,6 +15,7 @@ import levenshteinDistance from "@/utils/levenshtein";
 const FILTER_KEYS = {
     id: ["id", "tool_id"],
     panel_section_name: ["section", "panel_section_name"],
+    labels: ["label", "labels", "tag"],
 };
 const STRING_REPLACEMENTS: string[] = [" ", "-", "\\(", "\\)", "'", ":", `"`];
 const MINIMUM_DL_LENGTH = 5; // for Demerau-Levenshtein distance
@@ -286,7 +287,14 @@ export function searchToolsByKeys(
                 if (key === "combined") {
                     actualValue = `${tool.name.trim()} ${tool.description.trim()}`.toLowerCase();
                 } else {
-                    actualValue = (tool[key as keyof Tool] as string)?.trim().toLowerCase();
+                    const toolVal = tool[key as keyof Tool];
+                    if (typeof toolVal === "string") {
+                        actualValue = toolVal.trim().toLowerCase();
+                    } else if (Array.isArray(toolVal)) {
+                        actualValue = toolVal.join(" ").trim().toLowerCase();
+                    } else if (typeof toolVal === "number") {
+                        actualValue = toolVal.toString().trim().toLowerCase();
+                    }
                 }
 
                 // get all (space separated) words in actualValue for tool (for DL)