Merge pull request galaxyproject#18386 from jdavcs/dev_merge_241

Merge 24.1

client/src/api/schema/schema.ts

@@ -8394,6 +8394,11 @@ 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/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/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/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,

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

@@ -23,6 +23,7 @@ export default {
         return {
             storedWorkflowId: null,
             workflowId: null,
+            version: null,
             editorConfig: null,
             editorReloadKey: 0,
         };
@@ -46,6 +47,7 @@ export default {
 
             this.storedWorkflowId = Query.get("id");
             this.workflowId = Query.get("workflow_id");
+            this.version = Query.get("version");
 
             const params = {};
 
@@ -54,6 +56,9 @@ export default {
             } else if (this.storedWorkflowId) {
                 params.id = this.storedWorkflowId;
             }
+            if (this.version) {
+                params.version = this.version;
+            }
 
             this.editorConfig = await urlData({ url: "/workflow/editor", params });
 

client/src/entry/analysis/router.js

@@ -653,7 +653,10 @@ export function getRouter(Galaxy) {
                         redirect: redirectAnon(),
                         props: (route) => ({
                             config: Galaxy.config,
-                            query: { workflow_id: route.query.id },
+                            query: {
+                                workflow_id: route.query.id,
+                                version: route.query.version,
+                            },
                         }),
                     },
                     {

lib/galaxy/jobs/runners/pulsar.py

@@ -322,7 +322,12 @@ def check_watched_item_state(self, job_state):
 
     def _update_job_state_for_status(self, job_state, pulsar_status, full_status=None):
         log.debug("(%s) Received status update: %s", job_state.job_id, pulsar_status)
-        if pulsar_status in ["complete", "cancelled"] or job_state.job_wrapper.get_state() == model.Job.states.STOPPED:
+        if pulsar_status in ["complete", "cancelled"]:
+            self.mark_as_finished(job_state)
+            return None
+        if job_state.job_wrapper.get_state() == model.Job.states.STOPPED:
+            client = self.get_client_from_state(job_state)
+            client.kill()
             self.mark_as_finished(job_state)
             return None
         if pulsar_status in ["failed", "lost"]:

lib/galaxy/managers/users.py

@@ -200,7 +200,7 @@ def purge(self, user, flush=True):
         private_role = self.app.security_agent.get_private_user_role(user)
         if private_role is None:
             raise exceptions.InconsistentDatabase(
-                "User '%s' private role is missing while attempting to purge deleted user." % user.email
+                f"User {user.email} private role is missing while attempting to purge deleted user."
             )
         # Delete History
         for active_history in user.active_histories:
@@ -667,23 +667,11 @@ def get_or_create_remote_user(self, remote_user_email):
                     self.app.security_agent.user_set_default_permissions(user)
                     self.app.security_agent.user_set_default_permissions(user, history=True, dataset=True)
         elif user is None:
-            username = remote_user_email.split("@", 1)[0].lower()
             random.seed()
             user = self.app.model.User(email=remote_user_email)
             user.set_random_password(length=12)
             user.external = True
-            # Replace invalid characters in the username
-            for char in [x for x in username if x not in f"{string.ascii_lowercase + string.digits}-."]:
-                username = username.replace(char, "-")
-            # Find a unique username - user can change it later
-            stmt = select(self.app.model.User).filter_by(username=username).limit(1)
-            if self.session().scalars(stmt).first():
-                i = 1
-                stmt = select(self.app.model.User).filter_by(username=f"{username}-{str(i)}").limit(1)
-                while self.session().scalars(stmt).first():
-                    i += 1
-                username += f"-{str(i)}"
-            user.username = username
+            user.username = username_from_email(self.session(), remote_user_email, self.app.model.User)
             self.session().add(user)
             with transaction(self.session()):
                 self.session().commit()
@@ -877,3 +865,31 @@ def _add_parsers(self):
         )
 
         self.fn_filter_parsers.update({})
+
+
+def username_from_email(session, email, model_class=User):
+    """Get next available username generated based on email"""
+    username = email.split("@", 1)[0].lower()
+    username = filter_out_invalid_username_characters(username)
+    if username_exists(session, username, model_class):
+        username = generate_next_available_username(session, username, model_class)
+    return username
+
+
+def filter_out_invalid_username_characters(username):
+    """Replace invalid characters in username"""
+    for char in [x for x in username if x not in f"{string.ascii_lowercase + string.digits}-."]:
+        username = username.replace(char, "-")
+    return username
+
+
+def username_exists(session, username: str, model_class=User):
+    return bool(get_user_by_username(session, username, model_class))
+
+
+def generate_next_available_username(session, username, model_class=User):
+    """Generate unique username; user can change it later"""
+    i = 1
+    while session.execute(select(model_class).where(model_class.username == f"{username}-{i}")).first():
+        i += 1
+    return f"{username}-{i}"

lib/galaxy/managers/workflows.py

@@ -919,6 +919,9 @@ def to_format_2(wf_dict, **kwds):
             raise exceptions.RequestParameterInvalidException(f"Unknown workflow style {style}")
         if version is not None:
             wf_dict["version"] = version
+            # If returning a run-form workflow for a specific version, use that version's name
+            if style == "run":
+                wf_dict["name"] = workflow.name
         else:
             wf_dict["version"] = len(stored.workflows) - 1
         return wf_dict