Merge branch 'release_24.2' into dev

client/src/components/WorkflowInvocationState/WorkflowInvocationMetrics.vue

@@ -1,5 +1,5 @@
 <script setup lang="ts">
-import { BButtonGroup, BCol, BContainer, BRow } from "bootstrap-vue";
+import { BAlert, BButtonGroup, BCol, BContainer, BRow } from "bootstrap-vue";
 import type { VisualizationSpec } from "vega-embed";
 import { computed, ref, watch } from "vue";
 import { type ComputedRef } from "vue";
@@ -8,16 +8,16 @@ import { type components, GalaxyApi } from "@/api";
 import { getAppRoot } from "@/onload/loadConfig";
 import { errorMessageAsString } from "@/utils/simple-error";
 
+import LoadingSpan from "../LoadingSpan.vue";
 import HelpText from "@/components/Help/HelpText.vue";
 
 const VegaWrapper = () => import("./VegaWrapper.vue");
 
-const props = defineProps({
-    invocationId: {
-        type: String,
-        required: true,
-    },
-});
+interface Props {
+    invocationId: string;
+    notTerminal?: boolean;
+}
+const props = defineProps<Props>();
 
 const groupBy = ref<"tool_id" | "step_id">("tool_id");
 const timing = ref<"seconds" | "minutes" | "hours">("seconds");
@@ -44,7 +44,11 @@ async function fetchMetrics() {
     }
 }
 
-watch(props, () => fetchMetrics(), { immediate: true });
+watch(
+    () => props.invocationId,
+    () => fetchMetrics(),
+    { immediate: true }
+);
 
 function itemToX(item: components["schemas"]["WorkflowJobMetric"]) {
     if (groupBy.value === "tool_id") {
@@ -380,6 +384,9 @@ const groupByInTitles = computed(() => {
 
 <template>
     <div>
+        <BAlert v-if="props.notTerminal" variant="warning" show>
+            <LoadingSpan message="Metrics will update and change as the workflow progresses." />
+        </BAlert>
         <BContainer>
             <BRow align-h="end" class="mb-2">
                 <BButtonGroup>

client/src/components/WorkflowInvocationState/WorkflowInvocationState.test.ts

@@ -16,6 +16,7 @@ const selectors = {
     bAlertStub: "balert-stub",
     spanElement: "span",
     invocationReportTab: '[titleitemclass="invocation-report-tab"]',
+    invocationExportTab: '[titleitemclass="invocation-export-tab"]',
     fullPageHeading: "anonymous-stub[h1='true']",
 };
 
@@ -177,16 +178,20 @@ describe("WorkflowInvocationState check invocation and job terminal states", ()
     });
 });
 
-describe("WorkflowInvocationState check 'Report' tab disabled state and header", () => {
-    it("determines that 'Report' tab is disabled for non-terminal invocation", async () => {
+describe("WorkflowInvocationState check 'Report' and 'Export' tab disabled state and header", () => {
+    it("for non-terminal invocation", async () => {
         const wrapper = await mountWorkflowInvocationState("non-terminal-id");
         const reportTab = wrapper.find(selectors.invocationReportTab);
         expect(reportTab.attributes("disabled")).toBe("true");
+        const exportTab = wrapper.find(selectors.invocationExportTab);
+        expect(exportTab.attributes("disabled")).toBe("true");
     });
-    it("determines that 'Report' tab is not disabled for terminal invocation", async () => {
+    it("for terminal invocation", async () => {
         const wrapper = await mountWorkflowInvocationState(invocationData.id);
         const reportTab = wrapper.find(selectors.invocationReportTab);
         expect(reportTab.attributes("disabled")).toBeUndefined();
+        const exportTab = wrapper.find(selectors.invocationExportTab);
+        expect(exportTab.attributes("disabled")).toBeUndefined();
     });
 });
 

client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue

@@ -67,22 +67,22 @@ watch(
 );
 
 const workflowStore = useWorkflowStore();
-const reportTabDisabled = computed(
+const tabsDisabled = computed(
     () =>
         !invocationStateSuccess.value ||
         !invocation.value ||
         !workflowStore.getStoredWorkflowByInstanceId(invocation.value.workflow_id)
 );
 
-/** Tooltip message for the report tab when it is disabled */
-const disabledReportTooltip = computed(() => {
+/** Tooltip message for the a tab when it is disabled */
+const disabledTabTooltip = computed(() => {
     const state = invocationState.value;
     if (state != "scheduled") {
-        return `This workflow is not currently scheduled. The current state is ${state}. Once the workflow is fully scheduled and jobs have complete this option will become available.`;
+        return `This workflow is not currently scheduled. The current state is ${state}. Once the workflow is fully scheduled and jobs have complete any disabled tabs will become available.`;
     } else if (runningCount.value != 0) {
-        return `The workflow invocation still contains ${runningCount.value} running job(s). Once these jobs have completed this option will become available.`;
+        return `The workflow invocation still contains ${runningCount.value} running job(s). Once these jobs have completed any disabled tabs will become available.`;
     } else {
-        return "Steps for this workflow are still running. A report will be available once complete.";
+        return "Steps for this workflow are still running. Any disabled tabs will be available once complete.";
     }
 });
 
@@ -332,45 +332,43 @@ async function onCancel() {
             </BTab> -->
             <BTab
                 v-if="!props.isSubworkflow"
+                title="Report"
                 title-item-class="invocation-report-tab"
-                :disabled="reportTabDisabled"
+                :disabled="tabsDisabled"
                 :lazy="reportLazy"
                 :active.sync="reportActive">
-                <template v-slot:title>
-                    <span>Report</span>
-                    <BBadge
-                        v-if="reportTabDisabled"
-                        v-b-tooltip.hover.noninteractive
-                        :title="disabledReportTooltip"
-                        variant="warning">
-                        <FontAwesomeIcon :icon="faExclamation" />
-                    </BBadge>
-                </template>
                 <InvocationReport v-if="invocationStateSuccess" :invocation-id="invocation.id" />
             </BTab>
-            <BTab title="Export" title-item-class="invocation-export-tab" lazy>
+            <BTab title="Export" title-item-class="invocation-export-tab" :disabled="tabsDisabled" lazy>
                 <div v-if="invocationAndJobTerminal">
                     <WorkflowInvocationExportOptions :invocation-id="invocation.id" />
                 </div>
-                <BAlert v-else variant="info" show>
-                    <LoadingSpan message="Waiting to complete invocation" />
-                </BAlert>
             </BTab>
             <BTab title="Metrics" :lazy="true">
-                <WorkflowInvocationMetrics :invocation-id="invocation.id"></WorkflowInvocationMetrics>
+                <WorkflowInvocationMetrics :invocation-id="invocation.id" :not-terminal="!invocationAndJobTerminal" />
             </BTab>
             <template v-slot:tabs-end>
-                <BButton
-                    v-if="!props.isFullPage && !invocationAndJobTerminal"
-                    v-b-tooltip.noninteractive.hover
-                    class="ml-auto my-1"
-                    title="Cancel scheduling of workflow invocation"
-                    data-description="cancel invocation button"
-                    size="sm"
-                    @click="onCancel">
-                    <FontAwesomeIcon :icon="faTimes" fixed-width />
-                    Cancel Workflow
-                </BButton>
+                <div class="ml-auto d-flex align-items-center">
+                    <BBadge
+                        v-if="tabsDisabled"
+                        v-b-tooltip.hover.noninteractive
+                        class="mr-1"
+                        :title="disabledTabTooltip"
+                        variant="primary">
+                        <FontAwesomeIcon :icon="faExclamation" />
+                    </BBadge>
+                    <BButton
+                        v-if="!props.isFullPage && !invocationAndJobTerminal"
+                        v-b-tooltip.noninteractive.hover
+                        class="my-1"
+                        title="Cancel scheduling of workflow invocation"
+                        data-description="cancel invocation button"
+                        size="sm"
+                        @click="onCancel">
+                        <FontAwesomeIcon :icon="faTimes" fixed-width />
+                        Cancel Workflow
+                    </BButton>
+                </div>
             </template>
         </BTabs>
     </div>
@@ -387,9 +385,10 @@ async function onCancel() {
 
 <style lang="scss">
 // To show the tooltip on the disabled report tab badge
-.invocation-report-tab {
+.invocation-report-tab,
+.invocation-export-tab {
     .nav-link.disabled {
-        pointer-events: auto !important;
+        background-color: #e9edf0;
     }
 }
 </style>

lib/galaxy_test/selenium/test_workflow_run.py

@@ -37,6 +37,7 @@ class TestWorkflowRun(SeleniumTestCase, UsesHistoryItemAssertions, RunsWorkflows
     def test_workflow_export_file_rocrate(self):
         self._setup_simple_invocation_for_export_testing()
         invocations = self.components.invocations
+        self.workflow_run_wait_for_ok(hid=2)
         invocations.export_tab.wait_for_and_click()
         self.screenshot("invocation_export_formats")
         invocations.export_output_format(type="ro-crate").wait_for_and_click()
@@ -60,6 +61,7 @@ def test_workflow_export_file_rocrate(self):
     def test_workflow_export_file_native(self):
         self._setup_simple_invocation_for_export_testing()
         invocations = self.components.invocations
+        self.workflow_run_wait_for_ok(hid=2)
         invocations.export_tab.wait_for_and_click()
         self.screenshot("invocation_export_formats")
         invocations.export_output_format(type="default-file").wait_for_and_click()

packages/app/HISTORY.rst

@@ -4,13 +4,13 @@ History
 .. to_doc
 
 ---------
-24.2.dev0
+25.0.dev0
 ---------
 
 
 
 -------------------
-24.1.3 (2024-10-25)
+24.1.4 (2024-12-11)
 -------------------
 
 
@@ -27,6 +27,72 @@ Bug fixes
 * Add input extra files to `get_input_fnames` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18462 <https://github.com/galaxyproject/galaxy/pull/18462>`_
 * Return generic message for password reset email by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#18479 <https://github.com/galaxyproject/galaxy/pull/18479>`_
 * Increase API robustness to invalid requests, improve compressed data serving by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18494 <https://github.com/galaxyproject/galaxy/pull/18494>`_
+* Don't call job_runner.stop_job on jobs in new state by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18495 <https://github.com/galaxyproject/galaxy/pull/18495>`_
+* Prevent job submission if input collection element is deleted by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18517 <https://github.com/galaxyproject/galaxy/pull/18517>`_
+* Strip unicode null from tool stdio by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18527 <https://github.com/galaxyproject/galaxy/pull/18527>`_
+* Fix map over calculation for runtime inputs  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18535 <https://github.com/galaxyproject/galaxy/pull/18535>`_
+* Fix for not-null in 'column_list' object by `@hujambo-dunia <https://github.com/hujambo-dunia>`_ in `#18553 <https://github.com/galaxyproject/galaxy/pull/18553>`_
+* Also fail ``ensure_dataset_on_disk`` if dataset is in new state by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18559 <https://github.com/galaxyproject/galaxy/pull/18559>`_
+* Fix sqlalchemy statement in tooltagmanager reset output by `@dannon <https://github.com/dannon>`_ in `#18591 <https://github.com/galaxyproject/galaxy/pull/18591>`_
+* Set minimum weasyprint version by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18606 <https://github.com/galaxyproject/galaxy/pull/18606>`_
+* Improve relabel identifiers message when number of columns is not 2 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18634 <https://github.com/galaxyproject/galaxy/pull/18634>`_
+* Fix extract workflow from history when implicit collection has no jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18661 <https://github.com/galaxyproject/galaxy/pull/18661>`_
+* Make sure we set file size also for purged outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18681 <https://github.com/galaxyproject/galaxy/pull/18681>`_
+* File source and object store instance api fixes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18685 <https://github.com/galaxyproject/galaxy/pull/18685>`_
+* Fix change datatype PJA on expression tool data outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18691 <https://github.com/galaxyproject/galaxy/pull/18691>`_
+* Fill in missing help for cross product tools. by `@jmchilton <https://github.com/jmchilton>`_ in `#18698 <https://github.com/galaxyproject/galaxy/pull/18698>`_
+* Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18731 <https://github.com/galaxyproject/galaxy/pull/18731>`_
+* Catch and display exceptions when importing malformatted yaml workflows by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18734 <https://github.com/galaxyproject/galaxy/pull/18734>`_
+* Fix infinitely delayed workflow scheduling if skipped step creates HDCA by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18751 <https://github.com/galaxyproject/galaxy/pull/18751>`_
+* Fix directory get or create logic by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18752 <https://github.com/galaxyproject/galaxy/pull/18752>`_
+* Fix job summary for optional unset job data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18754 <https://github.com/galaxyproject/galaxy/pull/18754>`_
+* Allow to change only the description of a quota by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18775 <https://github.com/galaxyproject/galaxy/pull/18775>`_
+* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
+* Fix unspecified ``oidc_endpoint`` variable overwriting specified ``redirect_url`` by `@bgruening <https://github.com/bgruening>`_ in `#18818 <https://github.com/galaxyproject/galaxy/pull/18818>`_
+* Fix wrong celery_app config on job and workflow handlers by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18819 <https://github.com/galaxyproject/galaxy/pull/18819>`_
+* Fix ``named cursor is not valid anymore`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18825 <https://github.com/galaxyproject/galaxy/pull/18825>`_
+* Tighten TRS url check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18841 <https://github.com/galaxyproject/galaxy/pull/18841>`_
+* Fix Workflow index bookmark filter by `@itisAliRH <https://github.com/itisAliRH>`_ in `#18842 <https://github.com/galaxyproject/galaxy/pull/18842>`_
+* Skip metric collection if job working directory doesn't exist by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18845 <https://github.com/galaxyproject/galaxy/pull/18845>`_
+* Extend on disk checks to running, queued and error states by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18846 <https://github.com/galaxyproject/galaxy/pull/18846>`_
+* Raise MessageException instead of assertions on rerun problems by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18858 <https://github.com/galaxyproject/galaxy/pull/18858>`_
+* Fix data_column ref to nested collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18875 <https://github.com/galaxyproject/galaxy/pull/18875>`_
+* Fix loading very old workflows with data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18876 <https://github.com/galaxyproject/galaxy/pull/18876>`_
+* Access tool data table filters in workflow building mode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18900 <https://github.com/galaxyproject/galaxy/pull/18900>`_
+* Fix username used in invocation report by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18932 <https://github.com/galaxyproject/galaxy/pull/18932>`_
+* Disable locking when opening h5 files, add missing ``with`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18976 <https://github.com/galaxyproject/galaxy/pull/18976>`_
+* Fix job search statement building by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19010 <https://github.com/galaxyproject/galaxy/pull/19010>`_
+* Put cached jobs back into queue on handler restart by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19012 <https://github.com/galaxyproject/galaxy/pull/19012>`_
+* Fix various invocation export issues by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19215 <https://github.com/galaxyproject/galaxy/pull/19215>`_
+* Create harmonized collections from correct tool outputs by `@wm75 <https://github.com/wm75>`_ in `#19222 <https://github.com/galaxyproject/galaxy/pull/19222>`_
+
+============
+Enhancements
+============
+
+* Include workflow invocation id in exception logs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18594 <https://github.com/galaxyproject/galaxy/pull/18594>`_
+* Implemented the generic OIDC backend from python-social-auth into Gal… by `@Edmontosaurus <https://github.com/Edmontosaurus>`_ in `#18670 <https://github.com/galaxyproject/galaxy/pull/18670>`_
+* Collect job metrics also when job failed by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18809 <https://github.com/galaxyproject/galaxy/pull/18809>`_
+* prevent "missing refresh_token" errors by supporting <extra_scopes> also with Keycloak backend by `@ljocha <https://github.com/ljocha>`_ in `#18826 <https://github.com/galaxyproject/galaxy/pull/18826>`_
+
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18428 <https://github.com/galaxyproject/galaxy/pull/18428>`_
+* Update mercurial to non-yanked 6.7.4 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18434 <https://github.com/galaxyproject/galaxy/pull/18434>`_
+* Fix dropped when_expression on step upgrade by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18446 <https://github.com/galaxyproject/galaxy/pull/18446>`_
+* Improve workflow-related exception reporting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18447 <https://github.com/galaxyproject/galaxy/pull/18447>`_
+* Fix subwofklow tags serialization type by `@arash77 <https://github.com/arash77>`_ in `#18456 <https://github.com/galaxyproject/galaxy/pull/18456>`_
+* by `@laperlej <https://github.com/laperlej>`_ in `#18459 <https://github.com/galaxyproject/galaxy/pull/18459>`_
+* Add input extra files to `get_input_fnames` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18462 <https://github.com/galaxyproject/galaxy/pull/18462>`_
+* Return generic message for password reset email by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#18479 <https://github.com/galaxyproject/galaxy/pull/18479>`_
+* Increase API robustness to invalid requests, improve compressed data serving by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18494 <https://github.com/galaxyproject/galaxy/pull/18494>`_
 * Prevent job submission if input collection element is deleted by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18517 <https://github.com/galaxyproject/galaxy/pull/18517>`_
 * Strip unicode null from tool stdio by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18527 <https://github.com/galaxyproject/galaxy/pull/18527>`_
 * Fix map over calculation for runtime inputs  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18535 <https://github.com/galaxyproject/galaxy/pull/18535>`_

packages/auth/HISTORY.rst

@@ -4,11 +4,17 @@ History
 .. to_doc
 
 ---------
-24.2.dev0
+25.0.dev0
 ---------
 
 
 
+-------------------
+24.1.4 (2024-12-11)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 24.1.3 (2024-10-25)
 -------------------