Merge branch 'release_24.1' into usegalaxy

client/src/api/schema/schema.ts

@@ -8555,6 +8555,11 @@ export interface components {
              * @default false
              */
             use_cached_job?: boolean | null;
+            /**
+             * Version
+             * @description The version of the workflow to invoke.
+             */
+            version?: number | null;
         };
         /**
          * ItemTagsCreatePayload

client/src/components/Form/FormElement.vue

@@ -3,9 +3,12 @@ import { library } from "@fortawesome/fontawesome-svg-core";
 import { faCaretSquareDown, faCaretSquareUp } from "@fortawesome/free-regular-svg-icons";
 import { faArrowsAltH, faExclamation, faTimes } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { sanitize } from "dompurify";
 import type { ComputedRef } from "vue";
 import { computed, ref, useAttrs } from "vue";
 
+import { linkify } from "@/utils/utils";
+
 import type { FormParameterAttributes, FormParameterTypes, FormParameterValue } from "./parameterTypes";
 
 import FormBoolean from "./Elements/FormBoolean.vue";
@@ -181,7 +184,9 @@ const isOptional = computed(() => !isRequired.value && attrs.value["optional"] !
         :class="{ alert: hasAlert, 'alert-info': hasAlert }">
         <div v-if="hasAlert" class="ui-form-error">
             <FontAwesomeIcon class="mr-1" icon="fa-exclamation" />
-            <span class="ui-form-error-text" v-html="props.error || props.warning" />
+            <span
+                class="ui-form-error-text"
+                v-html="linkify(sanitize(props.error || props.warning, { USE_PROFILES: { html: true } }))" />
         </div>
 
         <div class="ui-form-title">

client/src/components/Sharing/Embeds/WorkflowEmbed.vue

@@ -6,8 +6,8 @@ import { useDebounce } from "@vueuse/core";
 import { BButton, BFormCheckbox, BFormInput, BInputGroup, BInputGroupAppend } from "bootstrap-vue";
 import { computed, reactive, ref } from "vue";
 
-import { getAppRoot } from "@/onload/loadConfig";
 import { copy } from "@/utils/clipboard";
+import { getFullAppUrl } from "@/utils/utils";
 
 import ZoomControl from "@/components/Workflow/Editor/ZoomControl.vue";
 import WorkflowPublished from "@/components/Workflow/Published/WorkflowPublished.vue";
@@ -39,13 +39,8 @@ function onChangePosition(event: Event, xy: "x" | "y") {
     }
 }
 
-const root = computed(() => {
-    const port = window.location.port ? `:${window.location.port}` : "";
-    return `${window.location.protocol}//${window.location.hostname}${port}${getAppRoot()}`;
-});
-
 const embedUrl = computed(() => {
-    let url = `${root.value}published/workflow?id=${props.id}&embed=true`;
+    let url = getFullAppUrl(`published/workflow?id=${props.id}&embed=true`);
     url += `&buttons=${settings.buttons}`;
     url += `&about=${settings.about}`;
     url += `&heading=${settings.heading}`;

client/src/components/Sharing/SharingPage.vue

@@ -9,6 +9,7 @@ import { getGalaxyInstance } from "@/app";
 import { useToast } from "@/composables/toast";
 import { getAppRoot } from "@/onload/loadConfig";
 import { errorMessageAsString } from "@/utils/simple-error";
+import { getFullAppUrl } from "@/utils/utils";
 
 import type { Item, ShareOption } from "./item";
 
@@ -52,11 +53,6 @@ const item = ref<Item>({
     extra: defaultExtra(),
 });
 
-const itemRoot = computed(() => {
-    const port = window.location.port ? `:${window.location.port}` : "";
-    return `${window.location.protocol}//${window.location.hostname}${port}${getAppRoot()}`;
-});
-
 const itemUrl = reactive({
     prefix: "",
     slug: "",
@@ -68,7 +64,7 @@ watch(
         if (value) {
             const index = value.lastIndexOf("/");
 
-            itemUrl.prefix = itemRoot.value + value.substring(0, index + 1);
+            itemUrl.prefix = getFullAppUrl(value.substring(0, index + 1));
             itemUrl.slug = value.substring(index + 1);
         }
     },

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

@@ -774,7 +774,9 @@ export default {
             this.report.markdown = markdown;
         },
         onRun() {
-            const runUrl = `/workflows/run?id=${this.id}`;
+            const runUrl = `/workflows/run?id=${this.id}${
+                this.version !== undefined ? `&version=${this.version}` : ""
+            }`;
             this.onNavigate(runUrl);
         },
         async onNavigate(url, forceSave = false, ignoreChanges = false) {

client/src/components/Workflow/Published/WorkflowInformation.vue

@@ -5,8 +5,8 @@ import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { computed } from "vue";
 import { RouterLink } from "vue-router";
 
-import { getAppRoot } from "@/onload/loadConfig";
 import { useUserStore } from "@/stores/userStore";
+import { getFullAppUrl } from "@/utils/utils";
 
 import Heading from "@/components/Common/Heading.vue";
 import CopyToClipboard from "@/components/CopyToClipboard.vue";
@@ -42,17 +42,12 @@ const gravatarSource = computed(
 
 const publishedByUser = computed(() => `/workflows/list_published?owner=${props.workflowInfo?.owner}`);
 
-const root = computed(() => {
-    const port = window.location.port ? `:${window.location.port}` : "";
-    return `${window.location.protocol}//${window.location.hostname}${port}${getAppRoot()}`;
-});
-
 const relativeLink = computed(() => {
     return `/published/workflow?id=${props.workflowInfo.id}`;
 });
 
 const fullLink = computed(() => {
-    return `${root.value}${relativeLink.value.substring(1)}`;
+    return getFullAppUrl(relativeLink.value.substring(1));
 });
 
 const userOwned = computed(() => {

client/src/components/Workflow/Run/WorkflowRun.vue

@@ -27,12 +27,14 @@ const router = useRouter();
 
 interface Props {
     workflowId: string;
+    version?: string;
     preferSimpleForm?: boolean;
     simpleFormTargetHistory?: string;
     simpleFormUseJobCache?: boolean;
 }
 
 const props = withDefaults(defineProps<Props>(), {
+    version: undefined,
     preferSimpleForm: false,
     simpleFormTargetHistory: "current",
     simpleFormUseJobCache: false,
@@ -49,7 +51,9 @@ const workflowName = ref("");
 const workflowModel: any = ref(null);
 
 const currentHistoryId = computed(() => historyStore.currentHistoryId);
-const editorLink = computed(() => `/workflows/edit?id=${props.workflowId}`);
+const editorLink = computed(
+    () => `/workflows/edit?id=${props.workflowId}${props.version ? `&version=${props.version}` : ""}`
+);
 const historyStatusKey = computed(() => `${currentHistoryId.value}_${lastUpdateTime.value}`);
 const isOwner = computed(() => currentUser.value?.username === workflowModel.value.runData.owner);
 const lastUpdateTime = computed(() => historyItemsStore.lastUpdateTime);
@@ -74,7 +78,7 @@ function handleSubmissionError(error: string) {
 }
 
 function loadRun() {
-    getRunData(props.workflowId)
+    getRunData(props.workflowId, props.version || undefined)
         .then((runData) => {
             const incomingModel = new WorkflowRunModel(runData);
             simpleForm.value = props.preferSimpleForm;
@@ -116,7 +120,7 @@ function loadRun() {
 }
 
 async function onImport() {
-    const response = await copyWorkflow(props.workflowId, workflowModel.value.runData.owner);
+    const response = await copyWorkflow(props.workflowId, workflowModel.value.runData.owner, props.version);
     router.push(`/workflows/edit?id=${response.id}`);
 }
 

client/src/components/Workflow/Run/WorkflowRunForm.vue

@@ -7,7 +7,7 @@
             </span>
         </BAlert>
         <div class="h4 clearfix mb-3">
-            <b>Workflow: {{ model.name }}</b>
+            <b>Workflow: {{ model.name }}</b> <i>(version: {{ model.runData.version + 1 }})</i>
             <ButtonSpinner
                 id="run-workflow"
                 class="float-right"
@@ -231,6 +231,7 @@ export default {
                 // the user is already warned if tool versions are wrong,
                 // they can still choose to invoke the workflow anyway.
                 require_exact_tool_versions: false,
+                version: this.model.runData.version,
             };
 
             console.debug("WorkflowRunForm::onExecute()", "Ready for submission.", jobDef);

client/src/components/Workflow/Run/WorkflowRunFormSimple.vue

@@ -7,7 +7,7 @@
                     or send the results to a new one using the run settings ⚙️
                 </span>
             </BAlert>
-            <b>Workflow: {{ model.name }}</b>
+            <b>Workflow: {{ model.name }}</b> <i>(version: {{ model.runData.version + 1 }})</i>
             <ButtonSpinner
                 id="run-workflow"
                 :wait="waitingForRequest"
@@ -200,6 +200,7 @@ export default {
                 batch: true,
                 use_cached_job: this.useCachedJobs,
                 require_exact_tool_versions: false,
+                version: this.model.runData.version,
             };
             if (this.sendToNewHistory) {
                 data.new_history_name = this.model.name;

client/src/components/Workflow/Run/services.js

@@ -10,9 +10,13 @@ import { rethrowSimple } from "utils/simple-error";
  * for implementation). This contains the data needed to render the UI for workflows.
  *
  * @param {String} workflowId - (Stored?) Workflow ID to fetch data for.
+ * @param {String} version - Version of the workflow to fetch.
  */
-export async function getRunData(workflowId) {
-    const url = `${getAppRoot()}api/workflows/${workflowId}/download?style=run`;
+export async function getRunData(workflowId, version = null) {
+    let url = `${getAppRoot()}api/workflows/${workflowId}/download?style=run`;
+    if (version) {
+        url += `&version=${version}`;
+    }
     try {
         const response = await axios.get(url);
         return response.data;

client/src/components/Workflow/WorkflowActionsExtend.vue

@@ -1,15 +1,6 @@
 <script setup lang="ts">
 import { library } from "@fortawesome/fontawesome-svg-core";
-import { faStar as farStar } from "@fortawesome/free-regular-svg-icons";
-import {
-    faCaretDown,
-    faCopy,
-    faDownload,
-    faFileExport,
-    faShareAlt,
-    faStar,
-    faTrashRestore,
-} from "@fortawesome/free-solid-svg-icons";
+import { faCopy, faDownload, faLink, faShareAlt, faTrashRestore } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BButton } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
@@ -19,9 +10,11 @@ import { copyWorkflow, undeleteWorkflow } from "@/components/Workflow/workflows.
 import { useConfirmDialog } from "@/composables/confirmDialog";
 import { Toast } from "@/composables/toast";
 import { useUserStore } from "@/stores/userStore";
+import { copy } from "@/utils/clipboard";
 import { withPrefix } from "@/utils/redirect";
+import { getFullAppUrl } from "@/utils/utils";
 
-library.add(faCaretDown, faCopy, faDownload, faFileExport, faShareAlt, farStar, faStar, faTrashRestore);
+library.add(faCopy, faDownload, faLink, faShareAlt, faTrashRestore);
 
 interface Props {
     workflow: any;
@@ -72,11 +65,36 @@ async function onRestore() {
         Toast.info("Workflow restored");
     }
 }
+
+const relativeLink = computed(() => {
+    return `/published/workflow?id=${props.workflow.id}`;
+});
+
+const fullLink = computed(() => {
+    return getFullAppUrl(relativeLink.value.substring(1));
+});
+
+function onCopyPublicLink() {
+    copy(fullLink.value);
+    Toast.success("Link to workflow copied");
+}
 </script>
 
 <template>
     <div class="workflow-actions-extend flex-gapx-1">
         <BButtonGroup>
+            <BButton
+                v-if="workflow.published && !workflow.deleted"
+                id="workflow-copy-public-button"
+                v-b-tooltip.hover.noninteractive
+                :size="buttonSize"
+                title="Copy link to workflow"
+                variant="outline-primary"
+                @click="onCopyPublicLink">
+                <FontAwesomeIcon :icon="faLink" fixed-width />
+                <span class="compact-view">Link to Workflow</span>
+            </BButton>
+
             <BButton
                 v-if="!isAnonymous && !shared && !workflow.deleted"
                 id="workflow-copy-button"

client/src/components/Workflow/WorkflowIndicators.vue

@@ -1,6 +1,6 @@
 <script setup lang="ts">
 import { library } from "@fortawesome/fontawesome-svg-core";
-import { faGlobe, faLink, faShieldAlt, faUser, faUsers } from "@fortawesome/free-solid-svg-icons";
+import { faFileImport, faGlobe, faShieldAlt, faUser, faUsers } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BBadge, BButton } from "bootstrap-vue";
 import { computed } from "vue";
@@ -12,7 +12,7 @@ import { copy } from "@/utils/clipboard";
 
 import UtcDate from "@/components/UtcDate.vue";
 
-library.add(faShieldAlt, faLink, faGlobe, faUsers, faUser);
+library.add(faFileImport, faGlobe, faShieldAlt, faUsers, faUser);
 
 interface Props {
     workflow: any;
@@ -116,7 +116,7 @@ function onViewUserPublished() {
             size="sm"
             class="workflow-external-link inline-icon-button"
             :title="sourceTitle">
-            <FontAwesomeIcon :icon="faLink" fixed-width @click="onCopyLink" />
+            <FontAwesomeIcon :icon="faFileImport" fixed-width @click="onCopyLink" />
         </BButton>
 
         <span class="mr-1">

client/src/components/Workflow/WorkflowRunButton.vue

@@ -3,6 +3,7 @@ import { library } from "@fortawesome/fontawesome-svg-core";
 import { faPlay } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BButton } from "bootstrap-vue";
+import { computed } from "vue";
 
 library.add(faPlay);
 
@@ -11,9 +12,14 @@ interface Props {
     full?: boolean;
     title?: string;
     disabled?: boolean;
+    version?: number;
 }
 
-defineProps<Props>();
+const props = defineProps<Props>();
+
+const runPath = computed(
+    () => `/workflows/run?id=${props.id}${props.version !== undefined ? `&version=${props.version}` : ""}`
+);
 </script>
 
 <template>
@@ -25,7 +31,7 @@ defineProps<Props>();
         variant="primary"
         size="sm"
         :disabled="disabled"
-        :to="`/workflows/run?id=${id}`">
+        :to="runPath">
         <FontAwesomeIcon :icon="faPlay" fixed-width />
 
         <span v-if="full" v-localize>Run</span>

client/src/components/Workflow/workflows.services.ts

@@ -45,8 +45,12 @@ export async function updateWorkflow(id: string, changes: object): Promise<Workf
     return data;
 }
 
-export async function copyWorkflow(id: string, currentOwner: string): Promise<Workflow> {
-    const { data: workflowData } = await axios.get(withPrefix(`/api/workflows/${id}/download`));
+export async function copyWorkflow(id: string, currentOwner: string, version?: string): Promise<Workflow> {
+    let path = `/api/workflows/${id}/download`;
+    if (version) {
+        path += `?version=${version}`;
+    }
+    const { data: workflowData } = await axios.get(withPrefix(path));
 
     workflowData.name = `Copy of ${workflowData.name}`;
     const currentUsername = useUserStore().currentUser?.username;

client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue

@@ -206,7 +206,7 @@ function getWorkflowName() {
                         size="sm"
                         variant="secondary"
                         :disabled="isDeletedWorkflow"
-                        :to="`/workflows/edit?id=${getWorkflowId()}`">
+                        :to="`/workflows/edit?id=${getWorkflowId()}&version=${workflowVersion}`">
                         <FontAwesomeIcon :icon="faEdit" />
                         <span v-localize>Edit</span>
                     </BButton>
@@ -218,7 +218,8 @@ function getWorkflowName() {
                                 : 'This workflow has been deleted.'
                         "
                         :disabled="isDeletedWorkflow"
-                        full />
+                        full
+                        :version="workflowVersion" />
                 </BButtonGroup>
             </div>
         </div>

client/src/entry/analysis/modules/Home.vue

@@ -59,6 +59,7 @@ export default {
         },
         workflowParams() {
             const workflowId = this.query.workflow_id;
+            const version = this.query.version;
             let preferSimpleForm = this.config.simplified_workflow_run_ui == "prefer";
             const preferSimpleFormOverride = this.query.simplified_workflow_run_ui;
             if (preferSimpleFormOverride == "prefer") {
@@ -68,6 +69,7 @@ export default {
             const simpleFormUseJobCache = this.config.simplified_workflow_run_ui_job_cache == "on";
             return {
                 workflowId,
+                version,
                 preferSimpleForm,
                 simpleFormTargetHistory,
                 simpleFormUseJobCache,