Merge branch 'release_24.1' into dev

client/src/components/User/APIKey/APIKeyItem.vue

@@ -1,11 +1,16 @@
 <script setup>
+import { library } from "@fortawesome/fontawesome-svg-core";
+import { faEye, faEyeSlash, faKey, faTrash } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { getGalaxyInstance } from "app";
 import CopyToClipboard from "components/CopyToClipboard";
 import UtcDate from "components/UtcDate";
 import { ref } from "vue";
 
 import svc from "./model/service";
 
+library.add(faEye, faEyeSlash, faKey, faTrash);
+
 defineProps({
     item: {
         type: Object,
@@ -35,12 +40,7 @@ const deleteKey = () => {
     <b-card title="Current API key">
         <div class="d-flex justify-content-between w-100">
             <div class="w-100">
-                <b-input-group
-                    class="w-100"
-                    @blur="hover = false"
-                    @focus="hover = true"
-                    @mouseover="hover = true"
-                    @mouseleave="hover = false">
+                <b-input-group class="w-100">
                     <b-input-group-prepend>
                         <b-input-group-text>
                             <icon icon="key" />
@@ -57,6 +57,11 @@ const deleteKey = () => {
                         <b-input-group-text>
                             <CopyToClipboard message="Key was copied to clipboard" :text="item.key" title="Copy key" />
                         </b-input-group-text>
+
+                        <b-button v-b-tooltip.hover title="Show/hide key" @click="hover = !hover">
+                            <FontAwesomeIcon :icon="hover ? faEyeSlash : faEye" />
+                        </b-button>
+
                         <b-button title="Delete api key" @click="toggleDeleteModal">
                             <icon icon="trash" />
                         </b-button>

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

@@ -77,55 +77,66 @@ function handleSubmissionError(error: string) {
     submissionError.value = errorMessageAsString(error);
 }
 
-function loadRun() {
-    getRunData(props.workflowId, props.version || undefined)
-        .then((runData) => {
-            const incomingModel = new WorkflowRunModel(runData);
-            simpleForm.value = props.preferSimpleForm;
-            if (simpleForm.value) {
-                // These only work with PJA - the API doesn't evaluate them at
-                // all outside that context currently. The main workflow form renders
-                // these dynamically and takes care of all the validation and setup details
-                // on the frontend. If these are implemented on the backend at some
-                // point this restriction can be lifted.
-                if (incomingModel.hasReplacementParametersInToolForm) {
-                    console.log("cannot render simple workflow form - has ${} values in tool steps");
-                    simpleForm.value = false;
-                }
-                // If there are required parameters in a tool form (a disconnected runtime
-                // input), we have to render the tool form steps and cannot use the
-                // simplified tool form.
-                if (incomingModel.hasOpenToolSteps) {
-                    console.log(
-                        "cannot render simple workflow form - one or more tools have disconnected runtime inputs"
-                    );
-                    simpleForm.value = false;
-                }
-                // Just render the whole form for resource request parameters (kind of
-                // niche - I'm not sure anyone is using these currently anyway).
-                if (incomingModel.hasWorkflowResourceParameters) {
-                    console.log(`Cannot render simple workflow form - workflow resource parameters are configured`);
-                    simpleForm.value = false;
-                }
+async function loadRun() {
+    try {
+        const runData = await getRunData(props.workflowId, props.version || undefined);
+        const incomingModel = new WorkflowRunModel(runData);
+
+        simpleForm.value = props.preferSimpleForm;
+
+        if (simpleForm.value) {
+            // These only work with PJA - the API doesn't evaluate them at
+            // all outside that context currently. The main workflow form renders
+            // these dynamically and takes care of all the validation and setup details
+            // on the frontend. If these are implemented on the backend at some
+            // point this restriction can be lifted.
+            if (incomingModel.hasReplacementParametersInToolForm) {
+                console.log("cannot render simple workflow form - has ${} values in tool steps");
+                simpleForm.value = false;
             }
-            hasUpgradeMessages.value = incomingModel.hasUpgradeMessages;
-            hasStepVersionChanges.value = incomingModel.hasStepVersionChanges;
-            workflowName.value = incomingModel.name;
-            workflowModel.value = incomingModel;
-            loading.value = false;
-        })
-        .catch((response) => {
-            workflowError.value = errorMessageAsString(response);
-        });
+            // If there are required parameters in a tool form (a disconnected runtime
+            // input), we have to render the tool form steps and cannot use the
+            // simplified tool form.
+            if (incomingModel.hasOpenToolSteps) {
+                console.log("cannot render simple workflow form - one or more tools have disconnected runtime inputs");
+                simpleForm.value = false;
+            }
+            // Just render the whole form for resource request parameters (kind of
+            // niche - I'm not sure anyone is using these currently anyway).
+            if (incomingModel.hasWorkflowResourceParameters) {
+                console.log(`Cannot render simple workflow form - workflow resource parameters are configured`);
+                simpleForm.value = false;
+            }
+        }
+
+        hasUpgradeMessages.value = incomingModel.hasUpgradeMessages;
+        hasStepVersionChanges.value = incomingModel.hasStepVersionChanges;
+        workflowName.value = incomingModel.name;
+        workflowModel.value = incomingModel;
+        loading.value = false;
+    } catch (e) {
+        workflowError.value = errorMessageAsString(e);
+    }
 }
 
 async function onImport() {
     const response = await copyWorkflow(props.workflowId, workflowModel.value.runData.owner, props.version);
     router.push(`/workflows/edit?id=${response.id}`);
 }
 
+const advancedForm = ref(false);
+const fromVariant = computed<"simple" | "advanced">(() => {
+    if (advancedForm.value) {
+        return "advanced";
+    } else if (simpleForm.value) {
+        return "simple";
+    } else {
+        return "advanced";
+    }
+});
+
 function showAdvanced() {
-    simpleForm.value = false;
+    advancedForm.value = true;
 }
 
 onMounted(() => {
@@ -185,7 +196,7 @@ defineExpose({
                         Workflow submission failed: {{ submissionError }}
                     </BAlert>
                     <WorkflowRunFormSimple
-                        v-else-if="simpleForm"
+                        v-else-if="fromVariant === 'simple'"
                         :model="workflowModel"
                         :target-history="simpleFormTargetHistory"
                         :use-job-cache="simpleFormUseJobCache"

lib/galaxy/datatypes/tabular.py

@@ -1815,15 +1815,14 @@ def set_meta(
             with open(dataset.get_file_name()) as dataset_fh:
                 comment_lines = 0
                 column_headers = None
-                cleaned_column_types = None
+                cleaned_column_types = []
                 number_of_columns = 0
                 for i, line in enumerate(dataset_fh):
                     line = line.strip("\n")
                     if line.startswith("#"):
                         if line.startswith("#h"):
                             column_headers = line.split("\t")[1:]
                         elif line.startswith("#f"):
-                            cleaned_column_types = []
                             for column_type in line.split("\t")[1:]:
                                 if column_type == "Hex":
                                     cleaned_column_types.append("str")

lib/galaxy/tools/parameters/basic.py

@@ -1511,7 +1511,7 @@ def get_options(self, trans, other_values):
                 except Exception:
                     column_list = self.get_column_list(trans, other_values)
             if self.numerical:  # If numerical was requested, filter columns based on metadata
-                if hasattr(dataset, "metadata") and hasattr(dataset.metadata, "column_types"):
+                if hasattr(dataset, "metadata") and getattr(dataset.metadata, "column_types", None) is not None:
                     if len(dataset.metadata.column_types) >= len(column_list):
                         numerics = [i for i, x in enumerate(dataset.metadata.column_types) if x in ["int", "float"]]
                         column_list = [column_list[i] for i in numerics]

lib/galaxy/util/zipstream.py

@@ -41,7 +41,8 @@ def response(self) -> Iterator[bytes]:
     def get_headers(self) -> Dict[str, str]:
         headers = {}
         if self.archive_name:
-            headers["Content-Disposition"] = f'attachment; filename="{self.archive_name}.zip"'
+            archive_name = self.archive_name.encode("latin-1", "replace").decode("latin-1")
+            headers["Content-Disposition"] = f'attachment; filename="{archive_name}.zip"'
         if self.upstream_mod_zip:
             headers["X-Archive-Files"] = "zip"
         else:

lib/galaxy/web/framework/base.py

@@ -251,8 +251,13 @@ def handle_request(self, request_id, path_info, environ, start_response, body_re
                 raise
         trans.controller = controller_name
         trans.action = action
+
+        # Action can still refer to invalid and/or inaccurate paths here, so we use the actual
+        # controller and method names to set the timing key.
+
+        action_tag = getattr(method, "__name__", "default")
         environ["controller_action_key"] = (
-            f"{'api' if environ['is_api_request'] else 'web'}.{controller_name}.{action or 'default'}"
+            f"{'api' if environ['is_api_request'] else 'web'}.{controller_name}.{action_tag}"
         )
         # Combine mapper args and query string / form args and call
         kwargs = trans.request.params.mixed()

lib/galaxy/webapps/galaxy/services/tools.py

@@ -281,7 +281,8 @@ def _patch_library_inputs(self, trans: ProvidesHistoryContext, inputs, target_hi
     def _patch_library_dataset(self, trans: ProvidesHistoryContext, v, target_history):
         if isinstance(v, dict) and "id" in v and v.get("src") == "ldda":
             ldda = trans.sa_session.get(LibraryDatasetDatasetAssociation, self.decode_id(v["id"]))
-            assert ldda
+            if not ldda:
+                raise exceptions.ObjectNotFound("Could not find library dataset dataset association.")
             if trans.user_is_admin or trans.app.security_agent.can_access_dataset(
                 trans.get_current_user_roles(), ldda.dataset
             ):

lib/galaxy_test/api/test_dataset_collections.py

@@ -182,6 +182,14 @@ def test_list_list_list_download(self):
             namelist = archive.namelist()
             assert len(namelist) == 3, f"Expected 3 elements in [{namelist}]"
 
+    def test_download_non_english_characters(self):
+        with self.dataset_populator.test_history() as history_id:
+            name = "دیتاست"
+            payload = self.dataset_collection_populator.create_list_payload(history_id, name=name)
+            hdca_id = self.dataset_populator.fetch(payload, wait=True).json()["outputs"][0]["id"]
+            create_response = self._download_dataset_collection(history_id=history_id, hdca_id=hdca_id)
+            self._assert_status_code_is(create_response, 200)
+
     @requires_new_user
     def test_hda_security(self):
         with self.dataset_populator.test_history(require_new=False) as history_id: