Merge branch 'release_24.2' into dev

2026-10-25 00:12:08 +08:00 · 2024-12-10 21:17:36 +00:00
parent a354124d83 9e266d454e
commit bbed4a85f8
30 changed files with 388 additions and 184 deletions
@@ -2,26 +2,28 @@ name: Update PR title

 on:
  pull_request_target:
-    types: [opened, edited]
-    branches:
-      - "release_**"
+    types: [opened, edited, reopened]

 jobs:
  update-title:
+    if: github.event.action != 'edited' || github.event.changes.base.ref.from != ''
    runs-on: ubuntu-latest
    permissions:
      pull-requests: write
    steps:
-      - uses: actions/checkout@v4
      - name: Update PR title
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          PR_NUMBER: ${{ github.event.pull_request.number }}
          TARGET_BRANCH: "${{ github.base_ref }}"
          PR_TITLE: "${{ github.event.pull_request.title }}"
+          REPO: "${{ github.repository }}"
        run: |
-          VERSION=$(echo $TARGET_BRANCH | grep -oP '\d+\.\d+')
-          if [[ -n "$VERSION" && ! "$PR_TITLE" =~ ^\[$VERSION\] ]]; then
-            NEW_TITLE="[$VERSION] $PR_TITLE"
-            gh pr edit $PR_NUMBER --title "$NEW_TITLE"
+          VERSION=$(echo $TARGET_BRANCH | grep -oP '^release_\K\d+.\d+$' || true)
+          NEW_TITLE=$(echo "$PR_TITLE" | sed -E "s/\[[0-9]+\.[0-9]+\] //")
+          if [[ -n "$VERSION" ]]; then
+            NEW_TITLE="[$VERSION] $NEW_TITLE"
+          fi
+          if [[ "$NEW_TITLE" != "$PR_TITLE" ]]; then
+            gh pr edit $PR_NUMBER --repo "$REPO" --title "$NEW_TITLE"
          fi
@@ -4,9 +4,9 @@
 import { BProgress, BProgressBar } from "bootstrap-vue";

 interface Props {
-    total: number;
+    total?: number;
    note: string;
-    loading: boolean;
+    loading?: boolean;
    okCount?: number;
    runningCount?: number;
    newCount?: number;
@@ -118,7 +118,7 @@ const showHelpForum = computed(() => isConfigLoaded.value && config.value.enable

 <template>
    <div class="position-relative">
-        <div class="underlay sticky-top" />
+        <div class="ui-form-header-underlay sticky-top" />
        <div class="tool-header sticky-top bg-secondary px-2 py-1 rounded">
            <div class="d-flex justify-content-between">
                <div class="py-1 d-flex flex-wrap flex-gapx-1">
@@ -209,19 +209,6 @@ const showHelpForum = computed(() => isConfigLoaded.value && config.value.enable
 </template>

 <style lang="scss" scoped>
-@import "scss/theme/blue.scss";
-
-.underlay::after {
-    content: "";
-    display: block;
-    position: absolute;
-    top: -$margin-h;
-    left: -0.5rem;
-    right: -0.5rem;
-    height: 50px;
-    background: linear-gradient($white 75%, change-color($white, $alpha: 0));
-}
-
 .fa-wrench {
    cursor: unset;
 }
@@ -308,7 +308,7 @@ export default {
            ensureParametersSet();
            stateStore.activeNodeId = null;
            activityBar.value?.setActiveSideBar("workflow-editor-attributes");
-            if (args.highlight) {
+            if (args?.highlight) {
                this.highlightAttribute = args.highlight;
            }
        }
@@ -327,6 +327,7 @@ Examples of RDM repositories include [Zenodo](https://zenodo.org/), [Invenio RDM
                    <BCard
                        v-for="plugin in exportPlugins"
                        :key="plugin.id"
+                        :data-invocation-export-type="plugin.id"
                        class="wizard-selection-card"
                        :border-variant="exportData.exportPluginFormat === plugin.id ? 'primary' : 'default'"
                        @click="exportData.exportPluginFormat = plugin.id">
@@ -350,6 +351,7 @@ Examples of RDM repositories include [Zenodo](https://zenodo.org/), [Invenio RDM
                    <BCard
                        v-for="target in exportDestinationTargets"
                        :key="target.destination"
+                        :data-invocation-export-destination="target.destination"
                        :border-variant="exportData.destination === target.destination ? 'primary' : 'default'"
                        :header-bg-variant="exportData.destination === target.destination ? 'primary' : 'default'"
                        :header-text-variant="exportData.destination === target.destination ? 'white' : 'default'"
@@ -34,8 +34,6 @@ interface Props {
    workflow: Workflow;
    /** Whether the invocation is terminal */
    isTerminal: boolean;
-    /** Whether the invocation is scheduled */
-    isScheduled: boolean;
    /** The zoom level for the graph */
    zoom?: number;
    /** Whether to show the minimap */
@@ -1,6 +1,7 @@
 <template>
    <div>
-        <div v-if="isConfigLoaded">
+        <div class="ui-form-header-underlay sticky-top" />
+        <div v-if="isConfigLoaded" class="sticky-top">
            <BAlert v-if="!canRunOnHistory" variant="warning" show>
                <span v-localize>
                    The workflow cannot run because the current history is immutable. Please select a different history
@@ -66,17 +66,13 @@ const localVue = getLocalVue();
 * @param version The version of the component to mount (`run_form` or `invocation` view)
 * @param ownsWorkflow Whether the user owns the workflow associated with the invocation
 * @param unimportableWorkflow Whether the workflow import should fail
- * @returns The wrapper object, and the mockRouter object
+ * @returns The wrapper object
 */
 async function mountWorkflowNavigationTitle(
    version: "run_form" | "invocation",
    ownsWorkflow = true,
    unimportableWorkflow = false
 ) {
-    const mockRouter = {
-        push: jest.fn(),
-    };
-
    let workflowId: string;
    let invocation;
    if (version === "invocation") {
@@ -96,9 +92,6 @@ async function mountWorkflowNavigationTitle(
            workflowId,
        },
        localVue,
-        mocks: {
-            $router: mockRouter,
-        },
        pinia: createTestingPinia(),
    });

@@ -107,7 +100,7 @@ async function mountWorkflowNavigationTitle(
        username: ownsWorkflow ? WORKFLOW_OWNER : OTHER_USER,
    });

-    return { wrapper, mockRouter };
+    return { wrapper };
 }

 describe("WorkflowNavigationTitle renders", () => {
@@ -116,10 +109,9 @@ describe("WorkflowNavigationTitle renders", () => {

        const heading = wrapper.find(SELECTORS.WORKFLOW_HEADING);
        expect(heading.text()).toContain(`Invoked Workflow: ${SAMPLE_WORKFLOW.name}`);
-        expect(heading.text()).toContain(`(version: ${SAMPLE_WORKFLOW.version + 1})`);
+        expect(heading.text()).toContain(`(Version: ${SAMPLE_WORKFLOW.version + 1})`);

-        const actionsGroup = wrapper.find(SELECTORS.ACTIONS_BUTTON_GROUP);
-        const runButton = actionsGroup.find(SELECTORS.ROUTE_TO_RUN_BUTTON);
+        const runButton = wrapper.find(SELECTORS.ROUTE_TO_RUN_BUTTON);
        expect(runButton.attributes("title")).toContain("Rerun");
        expect(runButton.attributes("title")).toContain(SAMPLE_WORKFLOW.name);
    });
@@ -129,24 +121,19 @@ describe("WorkflowNavigationTitle renders", () => {

        const heading = wrapper.find(SELECTORS.WORKFLOW_HEADING);
        expect(heading.text()).toContain(`Workflow: ${SAMPLE_WORKFLOW.name}`);
-        expect(heading.text()).toContain(`(version: ${SAMPLE_WORKFLOW.version + 1})`);
+        expect(heading.text()).toContain(`(Version: ${SAMPLE_WORKFLOW.version + 1})`);

-        const actionsGroup = wrapper.find(SELECTORS.ACTIONS_BUTTON_GROUP);
-        const runButton = actionsGroup.find(SELECTORS.EXECUTE_WORKFLOW_BUTTON);
+        const runButton = wrapper.find(SELECTORS.EXECUTE_WORKFLOW_BUTTON);
        expect(runButton.attributes("title")).toContain("Run");
    });

    it("edit button if user owns the workflow", async () => {
        async function findAndClickEditButton(version: "invocation" | "run_form") {
-            const { wrapper, mockRouter } = await mountWorkflowNavigationTitle(version);
+            const { wrapper } = await mountWorkflowNavigationTitle(version);
            const actionsGroup = wrapper.find(SELECTORS.ACTIONS_BUTTON_GROUP);

            const editButton = actionsGroup.find(SELECTORS.EDIT_WORKFLOW_BUTTON);
-            await editButton.trigger("click");
-            await flushPromises();
-
-            expect(mockRouter.push).toHaveBeenCalledTimes(1);
-            expect(mockRouter.push).toHaveBeenCalledWith(
+            expect(editButton.attributes("to")).toBe(
                `/workflows/edit?id=${SAMPLE_WORKFLOW.id}&version=${SAMPLE_WORKFLOW.version}`
            );
        }
@@ -5,7 +5,6 @@ import { BAlert, BButton, BButtonGroup } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
 import { computed, ref } from "vue";
 import { RouterLink } from "vue-router";
-import { useRouter } from "vue-router/composables";

 import { isRegisteredUser } from "@/api";
 import type { WorkflowInvocationElementView } from "@/api/invocations";
@@ -21,8 +20,6 @@ import AsyncButton from "../Common/AsyncButton.vue";
 import ButtonSpinner from "../Common/ButtonSpinner.vue";
 import WorkflowRunButton from "./WorkflowRunButton.vue";

-const router = useRouter();
-
 interface Props {
    invocation?: WorkflowInvocationElementView;
    workflowId: string;
@@ -98,16 +95,14 @@ const workflowImportTitle = computed(() => {

        <BAlert v-if="error" variant="danger" show>{{ error }}</BAlert>

-        <div class="position-relative">
-            <div v-if="workflow" class="ui-portlet-section">
-                <div class="d-flex portlet-header align-items-center">
+        <div class="position-relative mb-2">
+            <div v-if="workflow" class="bg-secondary px-2 py-1 rounded">
+                <div class="d-flex align-items-center flex-gapx-1">
                    <div class="flex-grow-1" data-description="workflow heading">
-                        <div class="px-1">
-                            <FontAwesomeIcon :icon="faSitemap" />
-                            <b class="mx-1">
-                                {{ props.invocation ? "Invoked " : "" }}Workflow: {{ getWorkflowName() }}
-                            </b>
-                            <i>(version: {{ workflow.version + 1 }})</i>
+                        <div>
+                            <FontAwesomeIcon :icon="faSitemap" fixed-width />
+                            <b> {{ props.invocation ? "Invoked " : "" }}Workflow: {{ getWorkflowName() }} </b>
+                            <span>(Version: {{ workflow.version + 1 }})</span>
                        </div>
                    </div>
                    <BButtonGroup>
@@ -122,7 +117,7 @@ const workflowImportTitle = computed(() => {
                            "
                            variant="link"
                            :disabled="workflow.deleted"
-                            @click="router.push(`/workflows/edit?id=${workflow.id}&version=${workflow.version}`)">
+                            :to="`/workflows/edit?id=${workflow.id}&version=${workflow.version}`">
                            <FontAwesomeIcon :icon="faEdit" fixed-width />
                        </BButton>
                        <AsyncButton
@@ -138,30 +133,30 @@ const workflowImportTitle = computed(() => {
                        </AsyncButton>

                        <slot name="workflow-title-actions" />
-
-                        <ButtonSpinner
-                            v-if="!props.invocation"
-                            id="run-workflow"
-                            data-description="execute workflow button"
-                            :wait="runWaiting"
-                            :disabled="runDisabled"
-                            size="sm"
-                            title="Run"
-                            @onClick="emit('on-execute')" />
-                        <WorkflowRunButton
-                            v-else
-                            :id="workflow.id"
-                            data-description="route to workflow run button"
-                            variant="link"
-                            :title="
-                                !workflow.deleted
-                                    ? `<b>Rerun</b><br>${getWorkflowName()}`
-                                    : 'This workflow has been deleted.'
-                            "
-                            :disabled="workflow.deleted"
-                            full
-                            :version="workflow.version" />
                    </BButtonGroup>
+                    <ButtonSpinner
+                        v-if="!props.invocation"
+                        id="run-workflow"
+                        data-description="execute workflow button"
+                        :wait="runWaiting"
+                        :disabled="runDisabled"
+                        size="sm"
+                        title="Run Workflow"
+                        @onClick="emit('on-execute')" />
+                    <WorkflowRunButton
+                        v-else
+                        :id="workflow.id"
+                        data-description="route to workflow run button"
+                        variant="link"
+                        :title="
+                            !workflow.deleted
+                                ? `<b>Rerun</b><br>${getWorkflowName()}`
+                                : 'This workflow has been deleted.'
+                        "
+                        :disabled="workflow.deleted"
+                        force
+                        full
+                        :version="workflow.version" />
                </div>
            </div>
            <div v-if="props.success" class="donemessagelarge">
@@ -1,4 +1,5 @@
-import { mount } from "@vue/test-utils";
+import { mount, type Wrapper } from "@vue/test-utils";
+import flushPromises from "flush-promises";
 import { getLocalVue } from "tests/jest/helpers";

 import { generateRandomString } from "./testUtils";
@@ -11,22 +12,69 @@ const WORKFLOW_ID = generateRandomString();
 const WORKFLOW_VERSION = 1;
 const WORKFLOW_RUN_BUTTON_SELECTOR = `[data-workflow-run="${WORKFLOW_ID}"]`;

-async function mountWorkflowRunButton(props?: { id: string; version: number; full?: boolean }) {
+function getPath() {
+    return `/workflows/run?id=${WORKFLOW_ID}&version=${WORKFLOW_VERSION}`;
+}
+
+async function mountWorkflowRunButton(
+    props?: { id: string; version: number; full?: boolean; force?: boolean },
+    currentPath?: string
+) {
+    const mockRouter = {
+        push: jest.fn(),
+        afterEach: jest.fn(),
+        currentRoute: {
+            fullPath: currentPath || getPath(),
+        },
+    };
+
    const wrapper = mount(WorkflowRunButton as object, {
        propsData: { ...props },
        localVue,
+        mocks: {
+            $router: mockRouter,
+        },
    });

-    return { wrapper };
+    return { wrapper, mockRouter };
+}
+
+async function clickButton(button: Wrapper<Vue>) {
+    // Remove the href and target attributes to prevent navigation error
+    // This is done because the `BButton` has a `:to` prop as well as an `@click` event
+    button.element.setAttribute("href", "javascript:void(0)");
+    button.element.setAttribute("target", "");
+
+    await button.trigger("click");
+    await flushPromises();
 }

 describe("WorkflowRunButton.vue", () => {
-    it("should render button with icon and route", async () => {
-        const { wrapper } = await mountWorkflowRunButton({ id: WORKFLOW_ID, version: WORKFLOW_VERSION });
+    it("should render button with icon and route to it", async () => {
+        const { wrapper, mockRouter } = await mountWorkflowRunButton({ id: WORKFLOW_ID, version: WORKFLOW_VERSION });

        const button = wrapper.find(WORKFLOW_RUN_BUTTON_SELECTOR);
        expect(button.attributes("title")).toBe("Run workflow");
        expect(button.text()).toBe("");
-        expect(button.attributes("href")).toBe(`/workflows/run?id=${WORKFLOW_ID}&version=${WORKFLOW_VERSION}`);
+        expect(button.attributes("href")).toBe(getPath());
+
+        await clickButton(button);
+
+        // Check that router.push was called with the correct arguments
+        expect(mockRouter.push).toHaveBeenCalledWith(getPath());
+    });
+
+    it("should force route if on the same path", async () => {
+        const { wrapper, mockRouter } = await mountWorkflowRunButton(
+            { id: WORKFLOW_ID, version: WORKFLOW_VERSION, force: true },
+            getPath()
+        );
+
+        const button = wrapper.find(WORKFLOW_RUN_BUTTON_SELECTOR);
+
+        await clickButton(button);
+
+        // Check that router.push was called with the correct arguments
+        expect(mockRouter.push).toHaveBeenCalledWith(getPath(), { force: true });
    });
 });
@@ -3,6 +3,7 @@ import { faPlay } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BButton } from "bootstrap-vue";
 import { computed } from "vue";
+import { useRoute, useRouter } from "vue-router/composables";

 interface Props {
    id: string;
@@ -20,13 +21,22 @@ const props = withDefaults(defineProps<Props>(), {
    variant: "primary",
 });

+const route = useRoute();
+const router = useRouter();
+
 const runPath = computed(
    () => `/workflows/run?id=${props.id}${props.version !== undefined ? `&version=${props.version}` : ""}`
 );

-function forceRunPath() {
-    if (props.force) {
-        window.open(runPath.value);
+function routeToPath() {
+    if (props.force && route.fullPath === runPath.value) {
+        // vue-router 4 supports a native force push with clean URLs,
+        // but we're using a __vkey__ bit as a workaround
+        // Only conditionally force to keep urls clean most of the time.
+        // @ts-ignore - monkeypatched router, drop with migration.
+        router.push(runPath.value, { force: true });
+    } else {
+        router.push(runPath.value);
    }
 }
 </script>
@@ -42,7 +52,7 @@ function forceRunPath() {
        class="text-decoration-none"
        :disabled="disabled"
        :to="runPath"
-        @click="forceRunPath">
+        @click="routeToPath">
        <FontAwesomeIcon :icon="faPlay" fixed-width />

        <span v-if="full" v-localize>Run</span>
@@ -1,5 +1,5 @@
 <template>
-    <div ref="chartContainer" class="chart" :style="style"></div>
+    <div ref="chartContainer" :style="style"></div>
 </template>

 <script setup lang="ts">
@@ -9,15 +9,18 @@ import { computed, onBeforeUnmount, onMounted, ref, watch } from "vue";

 export interface VisSpec {
    spec: VisualizationSpec;
-    width: string;
+    fillWidth?: boolean;
 }

 const props = withDefaults(defineProps<VisSpec>(), {
-    width: "100%",
+    fillWidth: true,
 });

 const style = computed(() => {
-    return { width: props.width };
+    if (props.fillWidth) {
+        return { width: "100%" };
+    }
+    return {};
 });

 const chartContainer = ref<HTMLDivElement | null>(null);
@@ -49,8 +52,3 @@ onBeforeUnmount(() => {
    }
 });
 </script>
-
-<style scoped>
-.chart {
-}
-</style>
@@ -275,18 +275,9 @@ function itemToPieChartSpec(item: piechartData) {
                type: "nominal",
                legend: {
                    type: "symbol",
-                    title: "", // should be item.category_title but it doesn't align right so just hide it
-                    direction: "vertical",
-                    titleAlign: "right",
-                    padding: 10,
-                    // rowPadding: 3,
-                    labelOffset: 40,
-                    // symbolOffset: 50,
-                    labelLimit: 120,
-                    // labelAlign: 'center',
-                    columnPadding: 5,
-                    // clipHeight: 20,
-                    titleOrient: "top",
+                    title: item.category_title,
+                    titleFontSize: 16,
+                    labelFontSize: 14,
                },
            },
            tooltip: [
@@ -381,6 +372,10 @@ function getTimingInTitle(timing: string): string {
 const timingInTitles = computed(() => {
    return getTimingInTitle(timing.value);
 });
+
+const groupByInTitles = computed(() => {
+    return attributeToLabel[groupBy.value];
+});
 </script>

 <template>
@@ -393,22 +388,22 @@ const timingInTitles = computed(() => {
                        <b-dropdown-item @click="timing = 'minutes'">{{ getTimingInTitle("minutes") }}</b-dropdown-item>
                        <b-dropdown-item @click="timing = 'hours'">{{ getTimingInTitle("hours") }}</b-dropdown-item>
                    </b-dropdown>
-                    <b-dropdown right text="Group By: Tool">
+                    <b-dropdown right :text="'Group By: ' + groupByInTitles">
                        <b-dropdown-item @click="groupBy = 'tool_id'">Tool</b-dropdown-item>
                        <b-dropdown-item @click="groupBy = 'step_id'">Workflow Step</b-dropdown-item>
                    </b-dropdown>
                </BButtonGroup>
            </BRow>
            <BRow>
-                <BCol v-if="wallclockAggregate && wallclockAggregate.values">
+                <BCol v-if="wallclockAggregate && wallclockAggregate.values" class="text-center">
                    <h2 class="h-l truncate text-center">
                        Aggregate
                        <HelpText :for-title="true" uri="galaxy.jobs.metrics.walltime" text="Runtime Time" /> (in
                        {{ timingInTitles }})
                    </h2>
-                    <VegaWrapper :spec="itemToPieChartSpec(wallclockAggregate)" />
+                    <VegaWrapper :spec="itemToPieChartSpec(wallclockAggregate)" :fill-width="false" />
                </BCol>
-                <BCol v-if="allocatedCoreTimeAggregate && allocatedCoreTimeAggregate.values">
+                <BCol v-if="allocatedCoreTimeAggregate && allocatedCoreTimeAggregate.values" class="text-center">
                    <h2 class="h-l truncate text-center">
                        Aggregate
                        <HelpText
@@ -417,14 +412,14 @@ const timingInTitles = computed(() => {
                            text="Allocated Core Time" />
                        (in {{ timingInTitles }})
                    </h2>
-                    <VegaWrapper :spec="itemToPieChartSpec(allocatedCoreTimeAggregate)" />
+                    <VegaWrapper :spec="itemToPieChartSpec(allocatedCoreTimeAggregate)" :fill-width="false" />
                </BCol>
            </BRow>
            <BRow v-for="({ spec, item }, key) in metrics" :key="key">
                <BCol>
                    <h2 class="h-l truncate text-center">
                        <span v-if="item.helpTerm">
-                            <HelpText :for-title="true" :uri="item.helpTerm" :text="key" />
+                            <HelpText :for-title="true" :uri="item.helpTerm" :text="`${key}`" />
                        </span>
                        <span v-else>
                            {{ key }}
@@ -15,7 +15,6 @@ import InvocationMessage from "@/components/WorkflowInvocationState/InvocationMe
 interface Props {
    invocation: WorkflowInvocationElementView;
    invocationAndJobTerminal: boolean;
-    invocationSchedulingTerminal: boolean;
    isFullPage?: boolean;
    isSubworkflow?: boolean;
 }
@@ -62,7 +61,6 @@ const uniqueMessages = computed(() => {
                :invocation="invocation"
                :workflow="workflow"
                :is-terminal="invocationAndJobTerminal"
-                :is-scheduled="invocationSchedulingTerminal"
                :is-full-page="isFullPage"
                :show-minimap="isFullPage" />
        </div>
@@ -10,7 +10,6 @@ import { useInvocationStore } from "@/stores/invocationStore";
 import { useWorkflowStore } from "@/stores/workflowStore";
 import { errorMessageAsString } from "@/utils/simple-error";

-import { cancelWorkflowScheduling } from "./services";
 import {
    errorCount as jobStatesSummaryErrorCount,
    isTerminal,
@@ -53,6 +52,7 @@ const stepStatesInterval = ref<any>(undefined);
 const jobStatesInterval = ref<any>(undefined);
 const invocationLoaded = ref(false);
 const errorMessage = ref<string | null>(null);
+const cancellingInvocation = ref(false);

 // after the report tab is first activated, no longer lazy-render it from then on
 const reportActive = ref(false);
@@ -199,6 +199,16 @@ watch(

 const storeId = computed(() => (invocation.value ? `invocation-${invocation.value.id}` : undefined));

+watch(
+    () => invocationSchedulingTerminal.value,
+    async (newVal, oldVal) => {
+        if (oldVal && !newVal) {
+            // If the invocation was terminal and now is not, start polling again
+            await pollStepStatesUntilTerminal();
+        }
+    }
+);
+
 onUnmounted(() => {
    clearTimeout(stepStatesInterval.value);
    clearTimeout(jobStatesInterval.value);
@@ -219,11 +229,16 @@ async function pollJobStatesUntilTerminal() {
 function onError(e: any) {
    console.error(e);
 }
-function onCancel() {
-    emit("invocation-cancelled");
-}
-function cancelWorkflowSchedulingLocal() {
-    cancelWorkflowScheduling(props.invocationId).then(onCancel).catch(onError);
+async function onCancel() {
+    try {
+        cancellingInvocation.value = true;
+        await invocationStore.cancelWorkflowScheduling(props.invocationId);
+    } catch (e) {
+        onError(e);
+    } finally {
+        emit("invocation-cancelled");
+        cancellingInvocation.value = false;
+    }
 }
 </script>

@@ -243,6 +258,7 @@ function cancelWorkflowSchedulingLocal() {
                    size="sm"
                    class="text-decoration-none"
                    variant="link"
+                    :disabled="cancellingInvocation || invocationState == 'cancelling'"
                    @click="onCancel">
                    <FontAwesomeIcon :icon="faSquare" fixed-width />
                    Cancel
@@ -301,9 +317,7 @@ function cancelWorkflowSchedulingLocal() {
                    :invocation="invocation"
                    :is-full-page="props.isFullPage"
                    :invocation-and-job-terminal="invocationAndJobTerminal"
-                    :invocation-scheduling-terminal="invocationSchedulingTerminal"
-                    :is-subworkflow="isSubworkflow"
-                    @invocation-cancelled="cancelWorkflowSchedulingLocal" />
+                    :is-subworkflow="isSubworkflow" />
            </BTab>
            <BTab v-if="!isSubworkflow" title="Steps" lazy>
                <WorkflowInvocationSteps
@@ -334,7 +348,7 @@ function cancelWorkflowSchedulingLocal() {
                </template>
                <InvocationReport v-if="invocationStateSuccess" :invocation-id="invocation.id" />
            </BTab>
-            <BTab title="Export" lazy>
+            <BTab title="Export" title-item-class="invocation-export-tab" lazy>
                <div v-if="invocationAndJobTerminal">
                    <WorkflowInvocationExportOptions :invocation-id="invocation.id" />
                </div>
@@ -1,14 +0,0 @@
-import axios from "axios";
-import { getRootFromIndexLink } from "onload";
-
-const getUrl = (path) => getRootFromIndexLink() + path;
-
-export function getInvocationJobsSummary(invocationId) {
-    const url = getUrl(`api/invocations/${invocationId}/jobs_summary`);
-    return axios.get(url);
-}
-
-export function cancelWorkflowScheduling(invocationId) {
-    const url = getUrl(`api/invocations/${invocationId}`);
-    return axios.delete(url);
-}
@@ -69,7 +69,7 @@ export const statePlaceholders: Record<string, string> = {
 };

 /** Only one job needs to be in one of these states for the graph step to be in that state */
-const SINGLE_INSTANCE_STATES = ["error", "running", "paused"];
+const SINGLE_INSTANCE_STATES = ["error", "running", "paused", "deleting"];
 /** All jobs need to be in one of these states for the graph step to be in that state */
 const ALL_INSTANCES_STATES = ["deleted", "skipped", "new", "queued"];

@@ -293,6 +293,9 @@ export function useInvocationGraph(
    function getStepStateFromJobStates(jobStates: string[]): GraphStep["state"] | undefined {
        for (const state of SINGLE_INSTANCE_STATES) {
            if (jobStates.includes(state)) {
+                if (state === "deleting") {
+                    return "deleted";
+                }
                return state as GraphStep["state"];
            }
        }
@@ -42,8 +42,24 @@ export const useInvocationStore = defineStore("invocationStore", () => {
        return data;
    }

-    const { getItemById: getInvocationById, fetchItemById: fetchInvocationForId } =
-        useKeyedCache<WorkflowInvocation>(fetchInvocationDetails);
+    async function cancelWorkflowScheduling(invocationId: string) {
+        const { data, error } = await GalaxyApi().DELETE("/api/invocations/{invocation_id}", {
+            params: {
+                path: { invocation_id: invocationId },
+            },
+        });
+        if (error) {
+            rethrowSimple(error);
+        }
+        storedInvocations.value[invocationId] = data;
+        return data;
+    }
+
+    const {
+        getItemById: getInvocationById,
+        fetchItemById: fetchInvocationForId,
+        storedItems: storedInvocations,
+    } = useKeyedCache<WorkflowInvocation>(fetchInvocationDetails);

    const { getItemById: getInvocationJobsSummaryById, fetchItemById: fetchInvocationJobsSummaryForId } =
        useKeyedCache<InvocationJobsSummary>(fetchInvocationJobsSummary);
@@ -58,6 +74,7 @@ export const useInvocationStore = defineStore("invocationStore", () => {
        fetchInvocationJobsSummaryForId,
        getInvocationStepById,
        fetchInvocationStepById,
+        cancelWorkflowScheduling,
        graphStepsByStoreId,
    };
 });
@@ -195,6 +195,17 @@ $ui-margin-horizontal-large: $margin-v * 2;
    }
 }

+.ui-form-header-underlay::after {
+    content: "";
+    display: block;
+    position: absolute;
+    top: -$margin-h;
+    left: -0.5rem;
+    right: -0.5rem;
+    height: 50px;
+    background: linear-gradient($white 75%, change-color($white, $alpha: 0));
+}
+
 // popovers
 .popover {
    max-width: 70%;
@@ -891,6 +891,12 @@ invocations:
    step_job_details: '[data-step="${order_index}"] .invocation-step-job-details'
    step_job_information: '[data-step="${order_index}"] .invocation-step-job-details .info_data_table'
    step_job_information_tool_id: '[data-step="${order_index}"] .invocation-step-job-details .info_data_table #galaxy-tool-id'
+    export_tab: '.invocation-export-tab'
+    export_output_format: '[data-invocation-export-type="${type}"] .card-body'
+    export_destination: '[data-invocation-export-destination="${destination}"] .card-body'
+    wizard_next_button: '.wizard-actions .go-next-btn'
+    wizard_export_button: '.wizard-actions .go-next-btn.btn-primary'
+    export_download_link: '.download-link'

 tour:
  popover:
@@ -620,7 +620,7 @@ class WorkflowContentsManager(UsesAnnotations):
        import_options = ImportOptions()
        import_options.deduplicate_subworkflows = True
        as_dict = python_to_workflow(as_dict, galaxy_interface, workflow_directory=None, import_options=import_options)
-        raw_description = RawWorkflowDescription(as_dict, path)
+        raw_description = RawWorkflowDescription(as_dict)
        created_workflow = self.build_workflow_from_raw_description(trans, raw_description, WorkflowCreateOptions())
        return created_workflow.workflow

@@ -959,8 +959,9 @@ class WorkflowContentsManager(UsesAnnotations):
        return wf_dict

    def _sync_stored_workflow(self, trans, stored_workflow):
-        workflow_path = stored_workflow.from_path
-        self.store_workflow_to_path(workflow_path, stored_workflow, stored_workflow.latest_workflow, trans=trans)
+        if trans.user_is_admin:
+            workflow_path = stored_workflow.from_path
+            self.store_workflow_to_path(workflow_path, stored_workflow, stored_workflow.latest_workflow, trans=trans)

    def store_workflow_artifacts(self, directory, filename_base, workflow, **kwd):
        modern_workflow_path = os.path.join(directory, f"{filename_base}.gxwf.yml")
@@ -2655,7 +2655,7 @@ class PostJobAction(Base, RepresentById):
    workflow_step_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow_step.id"), index=True)
    action_type: Mapped[str] = mapped_column(String(255))
    output_name: Mapped[Optional[str]] = mapped_column(String(255))
-    action_arguments: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
+    _action_arguments: Mapped[Optional[Dict[str, Any]]] = mapped_column("action_arguments", MutableJSONType)
    workflow_step: Mapped[Optional["WorkflowStep"]] = relationship(
        back_populates="post_job_actions",
        primaryjoin=(lambda: WorkflowStep.id == PostJobAction.workflow_step_id),
@@ -2668,6 +2668,18 @@ class PostJobAction(Base, RepresentById):
        self.workflow_step = workflow_step
        ensure_object_added_to_session(self, object_in_session=workflow_step)

+    @property
+    def action_arguments(self):
+        if self.action_type in ("HideDatasetAction", "DeleteIntermediatesAction") and self._action_arguments is True:
+            # Fix up broken workflows resulting from imports with gxformat2 <= 0.20.0
+            return {}
+        else:
+            return self._action_arguments
+
+    @action_arguments.setter
+    def action_arguments(self, value: Dict[str, Any]):
+        self._action_arguments = value
+

 class PostJobActionAssociation(Base, RepresentById):
    __tablename__ = "post_job_action_association"
@@ -7016,11 +7028,6 @@ class HistoryDatasetCollectionAssociation(
        primaryjoin=copied_from_history_dataset_collection_association_id == id,
        remote_side=[id],
        uselist=False,
-        back_populates="copied_to_history_dataset_collection_association",
-    )
-    copied_to_history_dataset_collection_association = relationship(
-        "HistoryDatasetCollectionAssociation",
-        back_populates="copied_from_history_dataset_collection_association",
    )
    implicit_input_collections: Mapped[List["ImplicitlyCreatedDatasetCollectionInput"]] = relationship(
        primaryjoin=(
@@ -999,14 +999,16 @@ class ModelImportStore(metaclass=abc.ABCMeta):
            # sense.
            hdca_copied_from_sinks = object_import_tracker.hdca_copied_from_sinks
            if copied_from_object_key in object_import_tracker.hdcas_by_key:
-                hdca.copied_from_history_dataset_collection_association = object_import_tracker.hdcas_by_key[
-                    copied_from_object_key
-                ]
+                source_hdca = object_import_tracker.hdcas_by_key[copied_from_object_key]
+                if source_hdca is not hdca:
+                    # We may not have the copied source, in which case the first included HDCA in the chain
+                    # acts as the source, so here we make sure we don't create a cycle.
+                    hdca.copied_from_history_dataset_collection_association = source_hdca
            else:
                if copied_from_object_key in hdca_copied_from_sinks:
-                    hdca.copied_from_history_dataset_collection_association = object_import_tracker.hdcas_by_key[
-                        hdca_copied_from_sinks[copied_from_object_key]
-                    ]
+                    source_hdca = object_import_tracker.hdcas_by_key[hdca_copied_from_sinks[copied_from_object_key]]
+                    if source_hdca is not hdca:
+                        hdca.copied_from_history_dataset_collection_association = source_hdca
                else:
                    hdca_copied_from_sinks[copied_from_object_key] = dataset_collection_key

@@ -1072,7 +1074,7 @@ class ModelImportStore(metaclass=abc.ABCMeta):
            for step_attrs in invocation_attrs["steps"]:
                imported_invocation_step = model.WorkflowInvocationStep()
                imported_invocation_step.workflow_invocation = imported_invocation
-                ensure_object_added_to_session(imported_invocation, session=self.sa_session)
+                ensure_object_added_to_session(imported_invocation_step, session=self.sa_session)
                attach_workflow_step(imported_invocation_step, step_attrs)
                restore_times(imported_invocation_step, step_attrs)
                imported_invocation_step.action = step_attrs["action"]
@@ -1926,12 +1928,14 @@ class DirectoryModelExportStore(ModelExportStore):
        self.export_files = export_files
        self.included_datasets: Dict[model.DatasetInstance, Tuple[model.DatasetInstance, bool]] = {}
        self.dataset_implicit_conversions: Dict[model.DatasetInstance, model.ImplicitlyConvertedDatasetAssociation] = {}
-        self.included_collections: List[Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation]] = []
+        self.included_collections: Dict[
+            Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation],
+            Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation],
+        ] = {}
        self.included_libraries: List[model.Library] = []
        self.included_library_folders: List[model.LibraryFolder] = []
        self.included_invocations: List[model.WorkflowInvocation] = []
        self.collection_datasets: Set[int] = set()
-        self.collections_attrs: List[Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation]] = []
        self.dataset_id_to_path: Dict[int, Tuple[Optional[str], Optional[str]]] = {}

        self.job_output_dataset_associations: Dict[int, Dict[str, model.DatasetInstance]] = {}
@@ -2298,8 +2302,7 @@ class DirectoryModelExportStore(ModelExportStore):
    def add_dataset_collection(
        self, collection: Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation]
    ) -> None:
-        self.collections_attrs.append(collection)
-        self.included_collections.append(collection)
+        self.included_collections[collection] = collection

    def add_implicit_conversion_dataset(
        self,
@@ -2362,7 +2365,7 @@ class DirectoryModelExportStore(ModelExportStore):

        collections_attrs_filename = os.path.join(export_directory, ATTRS_FILENAME_COLLECTIONS)
        with open(collections_attrs_filename, "w") as collections_attrs_out:
-            collections_attrs_out.write(to_json(self.collections_attrs))
+            collections_attrs_out.write(to_json(self.included_collections.values()))

        conversions_attrs_filename = os.path.join(export_directory, ATTRS_FILENAME_CONVERSIONS)
        with open(conversions_attrs_filename, "w") as conversions_attrs_out:
@@ -2383,12 +2386,12 @@ class DirectoryModelExportStore(ModelExportStore):
            #

            # Get all jobs associated with included HDAs.
-            jobs_dict: Dict[str, model.Job] = {}
+            jobs_dict: Dict[int, model.Job] = {}
            implicit_collection_jobs_dict = {}

            def record_job(job):
-                if not job:
-                    # No viable job.
+                if not job or job.id in jobs_dict:
+                    # No viable job or job already recorded.
                    return

                jobs_dict[job.id] = job
@@ -2414,10 +2417,11 @@ class DirectoryModelExportStore(ModelExportStore):
                    )
                job_hda = hda
                while job_hda.copied_from_history_dataset_association:  # should this check library datasets as well?
+                    # record job (if one exists) even if dataset was copied
+                    # copy could have been created manually through UI/API or using database operation tool,
+                    # in which case we have a relevant job to export.
+                    record_associated_jobs(job_hda)
                    job_hda = job_hda.copied_from_history_dataset_association
-                if not job_hda.creating_job_associations:
-                    # No viable HDA found.
-                    continue

                record_associated_jobs(job_hda)

@@ -738,7 +738,7 @@ class BuildMulledDockerContainerResolver(CliContainerResolver):
            "namespace": namespace,
            "hash_func": self.hash_func,
            "command": "build-and-test",
-            "use_mamba": True,
+            "use_mamba": False,
        }
        self._mulled_kwds["channels"] = default_mulled_conda_channels_from_env() or self._get_config_option(
            "mulled_channels", DEFAULT_CHANNELS
@@ -789,7 +789,7 @@ class BuildMulledSingularityContainerResolver(SingularityCliContainerResolver):
            "namespace": "local",
            "singularity": True,
            "singularity_image_dir": self.cache_directory.path,
-            "use_mamba": True,
+            "use_mamba": False,
        }
        self.involucro_context = InvolucroContext(**self._involucro_context_kwds)
        auto_init = self._get_config_option("involucro_auto_init", True)
@@ -894,12 +894,14 @@ class InputsSelectOptionsDefinesOptions(Linter):
            # TODO check if input param is present for from_dataset
            from_dataset = options.get("from_dataset", None)
            from_data_table = options.get("from_data_table", None)
+            from_url = options.get("from_url", None)

            if (
                from_file is None
                and from_parameter is None
                and from_dataset is None
                and from_data_table is None
+                and from_url is None
                and not filter_adds_options
            ):
                lint_ctx.error(
@@ -3875,14 +3875,13 @@ class HarmonizeTool(DatabaseOperationTool):
        final_sorted_identifiers = [
            element.element_identifier for element in elements1 if element.element_identifier in old_elements2_dict
        ]
-        # Raise Exception if it is empty
        if len(final_sorted_identifiers) == 0:
            # Create empty collections:
            output_collections.create_collection(
-                next(iter(self.outputs.values())), "output1", elements={}, propagate_hda_tags=False
+                self.outputs["output1"], "output1", elements={}, propagate_hda_tags=False
            )
            output_collections.create_collection(
-                next(iter(self.outputs.values())), "output2", elements={}, propagate_hda_tags=False
+                self.outputs["output2"], "output2", elements={}, propagate_hda_tags=False
            )
            return

@@ -3900,7 +3899,7 @@ class HarmonizeTool(DatabaseOperationTool):
            self._add_datasets_to_history(history, new_elements.values())
            # Create collections:
            output_collections.create_collection(
-                next(iter(self.outputs.values())), output_label, elements=new_elements, propagate_hda_tags=False
+                self.outputs[output_label], output_label, elements=new_elements, propagate_hda_tags=False
            )

        # Create outputs:
@@ -171,6 +171,37 @@
            <output_collection name="output1" type="list" count="0"/>
            <output_collection name="output2" type="list" count="0"/>
        </test>
+        <!-- test that collection types get propagated to outputs correctly -->
+        <test>
+            <param name="input1">
+                <collection type="list">
+                    <element name="element_1" value="simple_line.txt" />
+                </collection>
+            </param>
+            <param name="input2">
+                <collection type="list:paired">
+                    <element name="element_1">
+                        <collection type="paired">
+                            <element name="forward" value="1.fastqsanger" ftype="fastqsanger" />
+                            <element name="reverse" value="1.fastqsanger" ftype="fastqsanger" />
+                         </collection>
+                    </element>
+                </collection>
+            </param>
+            <output_collection name="output1" type="list" count="1">
+                <element name="element_1">
+                    <assert_contents>
+                        <has_text_matching expression="^This is a line of text.\n$" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="output2" type="list:paired" count="1">
+                <element name="element_1">
+                    <element name="forward" file="1.fastqsanger" ftype="fastqsanger" />
+                    <element name="reverse" file="1.fastqsanger" ftype="fastqsanger" />
+                </element>
+            </output_collection>
+        </test>
    </tests>
    <help><![CDATA[

@@ -1911,6 +1911,8 @@ class BaseWorkflowPopulator(BasePopulator):
                invocations = self.history_invocations(history_id)
                if len(invocations) == expected_invocation_count:
                    return True
+                elif len(invocations) > expected_invocation_count:
+                    raise AssertionError("More than the expect number of invocations found in workflow")

            wait_on(invocation_count, f"{expected_invocation_count} history invocations")
        for invocation in self.history_invocations(history_id):
@@ -32,6 +32,52 @@ from .framework import (
 class TestWorkflowRun(SeleniumTestCase, UsesHistoryItemAssertions, RunsWorkflows):
    ensure_registered = True

+    @selenium_test
+    @managed_history
+    def test_workflow_export_file_rocrate(self):
+        self._setup_simple_invocation_for_export_testing()
+        invocations = self.components.invocations
+        invocations.export_tab.wait_for_and_click()
+        self.screenshot("invocation_export_formats")
+        invocations.export_output_format(type="ro-crate").wait_for_and_click()
+        invocations.wizard_next_button.wait_for_and_click()
+        download_option = invocations.export_destination(destination="download")
+        download_option.wait_for_present()
+        self.screenshot("invocation_export_rocrate_destinations")
+        download_option.wait_for_and_click()
+        invocations.wizard_next_button.wait_for_and_click()
+        export_button = invocations.wizard_export_button
+        export_button.wait_for_present()
+        self.screenshot("invocation_export_rocrate_download_options")
+        export_button.wait_for_and_click()
+        self.sleep_for(self.wait_types.UX_TRANSITION)
+        self.screenshot("invocation_export_crate_preparing_download")
+        invocations.export_download_link.wait_for_present()
+        self.screenshot("invocation_export_crate_download_ready")
+
+    @selenium_test
+    @managed_history
+    def test_workflow_export_file_native(self):
+        self._setup_simple_invocation_for_export_testing()
+        invocations = self.components.invocations
+        invocations.export_tab.wait_for_and_click()
+        self.screenshot("invocation_export_formats")
+        invocations.export_output_format(type="default-file").wait_for_and_click()
+        invocations.wizard_next_button.wait_for_and_click()
+        download_option = invocations.export_destination(destination="download")
+        download_option.wait_for_present()
+        self.screenshot("invocation_export_native_destinations")
+        download_option.wait_for_and_click()
+        invocations.wizard_next_button.wait_for_and_click()
+        export_button = invocations.wizard_export_button
+        export_button.wait_for_present()
+        self.screenshot("invocation_export_native_download_options")
+        export_button.wait_for_and_click()
+        self.sleep_for(self.wait_types.UX_TRANSITION)
+        self.screenshot("invocation_export_native_preparing_download")
+        invocations.export_download_link.wait_for_present()
+        self.screenshot("invocation_export_native_download_ready")
+
    @selenium_test
    @managed_history
    def test_simple_execution(self):
@@ -376,3 +422,13 @@ steps: {}
        assert initial_value == "", initial_value
        input_element.clear()
        input_element.send_keys(value)
+
+    def _setup_simple_invocation_for_export_testing(self):
+        # precondition: refresh history
+        self.perform_upload(self.get_filename("1.fasta"))
+        self.wait_for_history()
+        self.workflow_run_open_workflow(WORKFLOW_SIMPLE_CAT_TWICE)
+        self.workflow_run_submit()
+        history_id = self.current_history_id()
+        self.workflow_populator.wait_for_history_workflows(history_id, expected_invocation_count=1)
+        return self.workflow_populator.history_invocations(history_id)[0]
@@ -17,6 +17,7 @@ from galaxy_test.api.test_workflows import RunsWorkflowFixtures
 from galaxy_test.base import api_asserts
 from galaxy_test.base.api import UsesCeleryTasks
 from galaxy_test.base.populators import (
+    DatasetCollectionPopulator,
    DatasetPopulator,
    RunJobsSummary,
    WorkflowPopulator,
@@ -27,6 +28,7 @@ from galaxy_test.driver.integration_util import IntegrationTestCase

 class TestWorkflowTasksIntegration(PosixFileSourceSetup, IntegrationTestCase, UsesCeleryTasks, RunsWorkflowFixtures):
    dataset_populator: DatasetPopulator
+    dataset_collection_populator: DatasetCollectionPopulator
    framework_tool_and_types = True

    @classmethod
@@ -37,6 +39,7 @@ class TestWorkflowTasksIntegration(PosixFileSourceSetup, IntegrationTestCase, Us
    def setUp(self):
        super().setUp()
        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+        self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor)
        self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
        self._write_file_fixtures()

@@ -124,6 +127,47 @@ class TestWorkflowTasksIntegration(PosixFileSourceSetup, IntegrationTestCase, Us
            invocation_details = self._export_and_import_workflow_invocation(summary, use_uris)
            self._rerun_imported_workflow(summary, invocation_details)

+    def test_export_import_invocation_with_copied_hdca_and_database_operation_tool(self):
+        with self.dataset_populator.test_history() as history_id:
+            self.dataset_collection_populator.create_list_in_history(history_id=history_id, wait=True).json()
+            new_history = self.dataset_populator.copy_history(history_id=history_id).json()
+            copied_collection = self.dataset_populator.get_history_collection_details(new_history["id"])
+            workflow_id = self.workflow_populator.upload_yaml_workflow(
+                """class: GalaxyWorkflow
+inputs:
+  input:
+    type: collection
+    collection_type: list
+steps:
+  extract_dataset:
+    tool_id: __EXTRACT_DATASET__
+    in:
+      input:
+        source: input
+"""
+            )
+            inputs = {"input": {"src": "hdca", "id": copied_collection["id"]}}
+            workflow_request = {"history": f"hist_id={new_history['id']}", "inputs_by": "name", "inputs": inputs}
+            invocation = self.workflow_populator.invoke_workflow_raw(
+                workflow_id, workflow_request, assert_ok=True
+            ).json()
+            invocation_id = invocation["id"]
+            self.workflow_populator.wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id)
+            jobs = self.workflow_populator.get_invocation_jobs(invocation_id)
+            summary = RunJobsSummary(
+                history_id=history_id,
+                workflow_id=workflow_id,
+                invocation_id=invocation["id"],
+                inputs=inputs,
+                jobs=jobs,
+                invocation=invocation,
+                workflow_request=workflow_request,
+            )
+            imported_invocation_details = self._export_and_import_workflow_invocation(summary)
+            original_contents = self.dataset_populator.get_history_contents(new_history["id"])
+            contents = self.dataset_populator.get_history_contents(imported_invocation_details["history_id"])
+            assert len(contents) == len(original_contents) == 5
+
    def _export_and_import_workflow_invocation(
        self, summary: RunJobsSummary, use_uris: bool = True, model_store_format="tgz"
    ) -> Dict[str, Any]: