Merge branch 'release_24.1' into dev

client/src/api/schema/schema.ts

@@ -33135,9 +33135,18 @@ export interface operations {
                  *     `is:published`
                  *     : Include only published workflows in the final result. Be sure the query parameter `show_published` is set to `true` if to include all published workflows and not just the requesting user's.
                  *
-                 *     `is:share_with_me`
+                 *     `is:importable`
+                 *     : Include only importable workflows in the final result.
+                 *
+                 *     `is:deleted`
+                 *     : Include only deleted workflows in the final result.
+                 *
+                 *     `is:shared_with_me`
                  *     : Include only workflows shared with the requesting user.  Be sure the query parameter `show_shared` is set to `true` if to include shared workflows.
                  *
+                 *     `is:bookmarked`
+                 *     : Include only workflows bookmarked by the requesting user.
+                 *
                  *     ## Free Text
                  *
                  *     Free text search terms will be searched against the following attributes of the

client/src/components/Workflow/List/WorkflowFilters.js

@@ -116,6 +116,13 @@ export function WorkflowFilters(activeList = "my") {
                     handler: equals("deleted", "deleted", toBool),
                     menuItem: true,
                 },
+                bookmarked: {
+                    placeholder: "Bookmarked",
+                    type: Boolean,
+                    boolType: "is",
+                    handler: equals("bookmarked", "bookmarked", toBool),
+                    menuItem: true,
+                },
             },
             undefined,
             false,

client/src/components/Workflow/List/WorkflowList.vue

@@ -44,7 +44,6 @@ const overlay = ref(false);
 const filterText = ref("");
 const totalWorkflows = ref(0);
 const showAdvanced = ref(false);
-const showBookmarked = ref(false);
 const listHeader = ref<any>(null);
 const workflowsLoaded = ref<WorkflowsList>([]);
 
@@ -65,6 +64,7 @@ const searchPlaceHolder = computed(() => {
 const published = computed(() => props.activeList === "published");
 const sharedWithMe = computed(() => props.activeList === "shared_with_me");
 const showDeleted = computed(() => filterText.value.includes("is:deleted"));
+const showBookmarked = computed(() => filterText.value.includes("is:bookmarked"));
 const currentPage = computed(() => Math.floor(offset.value / limit.value) + 1);
 const view = computed(() => (userStore.preferredListViewMode as ListView) || "grid");
 const sortDesc = computed(() => (listHeader.value && listHeader.value.sortDesc) ?? true);
@@ -91,17 +91,12 @@ function updateFilterValue(filterKey: string, newValue: any) {
     filterText.value = workflowFilters.value.setFilterValue(currentFilterText, filterKey, newValue);
 }
 
-function toggleBookmarked(bookmarked?: boolean) {
-    showBookmarked.value = bookmarked ?? !showBookmarked.value;
-}
-
 function onToggleBookmarked() {
-    toggleBookmarked();
+    updateFilterValue("bookmarked", true);
 }
 
 function onToggleDeleted() {
     updateFilterValue("deleted", true);
-    toggleBookmarked(false);
 }
 
 async function load(overlayLoading = false, silent = false) {
@@ -149,21 +144,15 @@ async function load(overlayLoading = false, silent = false) {
             rethrowSimple(error);
         }
 
-        let filteredWorkflows = showBookmarked.value
-            ? filter(data, (workflow: any) => workflow.show_in_tool_panel)
-            : data;
+        let filteredWorkflows = data;
 
         if (props.activeList === "my") {
             filteredWorkflows = filter(filteredWorkflows, (w: any) => userStore.matchesCurrentUsername(w.owner));
         }
 
         workflowsLoaded.value = filteredWorkflows;
 
-        if (showBookmarked.value) {
-            totalWorkflows.value = filteredWorkflows.length;
-        } else {
-            totalWorkflows.value = parseInt(response.headers.get("Total_matches") || "0", 10) || 0;
-        }
+        totalWorkflows.value = parseInt(response.headers.get("Total_matches") || "0", 10) || 0;
     } catch (e) {
         Toast.error(`Failed to load workflows: ${e}`);
     } finally {
@@ -189,7 +178,7 @@ function validatedFilterText() {
     return workflowFilters.value.getFilterText(validFilters.value, true);
 }
 
-watch([filterText, sortBy, sortDesc, showBookmarked], async () => {
+watch([filterText, sortBy, sortDesc], async () => {
     offset.value = 0;
     await load(true);
 });
@@ -269,7 +258,6 @@ onMounted(() => {
                             size="sm"
                             :title="bookmarkButtonTitle"
                             :pressed="showBookmarked"
-                            :disabled="showDeleted"
                             variant="outline-primary"
                             @click="onToggleBookmarked">
                             <FontAwesomeIcon :icon="faStar" fixed-width />

config/plugins/visualizations/editor/templates/editor.mako

@@ -62,11 +62,11 @@
 
     const ajax_url = "${h.url_for( controller='/datasets', action='index')}/" + hda_id + "/display";
     const data = httpGet(ajax_url);
-    document.getElementById("editor").innerHTML = data;
     var editor = ace.edit("editor", {
         mode: "ace/mode/powershell",
         theme: "ace/theme/textmate"
     });
+    editor.setValue(data, -1);
 </script>
 </body>
 </html>

lib/galaxy/config/__init__.py

@@ -597,7 +597,7 @@ def admin_users(self):
     @admin_users.setter
     def admin_users(self, value):
         self._admin_users = value
-        self.admin_users_list = listify(value)
+        self.admin_users_list = listify(value, do_strip=True)
 
     def is_admin_user(self, user: Optional["User"]) -> bool:
         """Determine if the provided user is listed in `admin_users`."""

lib/galaxy/managers/workflows.py

@@ -242,6 +242,12 @@ def name_filter(term):
                                 message = "Can only use tag is:shared_with_me if show_shared parameter also true."
                                 raise exceptions.RequestParameterInvalidException(message)
                             stmt = stmt.where(StoredWorkflowUserShareAssociation.user == user)
+                        elif q == "bookmarked":
+                            stmt = (
+                                stmt.join(model.StoredWorkflowMenuEntry)
+                                .where(model.StoredWorkflowMenuEntry.stored_workflow_id == StoredWorkflow.id)
+                                .where(model.StoredWorkflowMenuEntry.user_id == user.id)
+                            )
                 elif isinstance(term, RawTextTerm):
                     tf = w_tag_filter(term.text, False)
                     alias = aliased(User)

lib/galaxy/model/store/__init__.py

@@ -578,10 +578,11 @@ def handle_dataset_object_edit(dataset_instance, dataset_attrs):
                 self._attach_raw_id_if_editing(dataset_instance, dataset_attrs)
 
                 # Older style...
-                if "uuid" in dataset_attrs:
-                    dataset_instance.dataset.uuid = dataset_attrs["uuid"]
-                if "dataset_uuid" in dataset_attrs:
-                    dataset_instance.dataset.uuid = dataset_attrs["dataset_uuid"]
+                if self.import_options.allow_edit:
+                    if "uuid" in dataset_attrs:
+                        dataset_instance.dataset.uuid = dataset_attrs["uuid"]
+                    if "dataset_uuid" in dataset_attrs:
+                        dataset_instance.dataset.uuid = dataset_attrs["dataset_uuid"]
 
                 self._session_add(dataset_instance)
 

lib/galaxy/model/store/discover.py

@@ -132,11 +132,6 @@ def create_dataset(
                 )
                 self.persist_object(primary_data)
 
-                if init_from:
-                    self.permission_provider.copy_dataset_permissions(init_from, primary_data)
-                    primary_data.state = init_from.state
-                else:
-                    self.permission_provider.set_default_hda_permissions(primary_data)
             else:
                 ld = galaxy.model.LibraryDataset(folder=library_folder, name=name)
                 ldda = galaxy.model.LibraryDatasetDatasetAssociation(
@@ -208,6 +203,7 @@ def create_dataset(
                     filename=filename,
                     link_data=link_data,
                     output_name=output_name,
+                    init_from=init_from,
                 )
             else:
                 storage_callbacks.append(
@@ -218,11 +214,14 @@ def create_dataset(
                         filename=filename,
                         link_data=link_data,
                         output_name=output_name,
+                        init_from=init_from,
                     )
                 )
         return primary_data
 
-    def finalize_storage(self, primary_data, dataset_attributes, extra_files, filename, link_data, output_name):
+    def finalize_storage(
+        self, primary_data, dataset_attributes, extra_files, filename, link_data, output_name, init_from
+    ):
         if primary_data.dataset.purged:
             # metadata won't be set, maybe we should do that, then purge ?
             primary_data.dataset.file_size = 0
@@ -243,6 +242,13 @@ def finalize_storage(self, primary_data, dataset_attributes, extra_files, filena
         else:
             # We are sure there are no extra files, so optimize things that follow by settting total size also.
             primary_data.set_size(no_extra_files=True)
+
+        if init_from:
+            self.permission_provider.copy_dataset_permissions(init_from, primary_data)
+            primary_data.state = init_from.state
+        else:
+            self.permission_provider.set_default_hda_permissions(primary_data)
+
         # TODO: this might run set_meta after copying the file to the object store, which could be inefficient if job working directory is closer to the node.
         self.set_datasets_metadata(datasets=[primary_data], datasets_attributes=[dataset_attributes])
 

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -858,9 +858,21 @@ def __get_stored_workflow(self, trans, workflow_id, **kwd):
         "Include only published workflows in the final result. Be sure the query parameter `show_published` is set to `true` if to include all published workflows and not just the requesting user's.",
     ),
     IndexQueryTag(
-        "is:share_with_me",
+        "is:importable",
+        "Include only importable workflows in the final result.",
+    ),
+    IndexQueryTag(
+        "is:deleted",
+        "Include only deleted workflows in the final result.",
+    ),
+    IndexQueryTag(
+        "is:shared_with_me",
         "Include only workflows shared with the requesting user.  Be sure the query parameter `show_shared` is set to `true` if to include shared workflows.",
     ),
+    IndexQueryTag(
+        "is:bookmarked",
+        "Include only workflows bookmarked by the requesting user.",
+    ),
 ]
 
 SearchQueryParam: Optional[str] = search_query_param(

lib/galaxy/webapps/galaxy/controllers/dataset.py

@@ -21,6 +21,7 @@
 from galaxy.datatypes.sniff import guess_ext
 from galaxy.exceptions import (
     MessageException,
+    InsufficientPermissionsException,
     RequestParameterInvalidException,
 )
 from galaxy.managers.hdas import (
@@ -106,7 +107,7 @@ def _check_dataset(self, trans, hda_id):
         if not data:
             raise web.httpexceptions.HTTPNotFound(f"Invalid reference dataset id: {str(hda_id)}.")
         if not self._can_access_dataset(trans, data):
-            return trans.show_error_message("You are not allowed to access this dataset")
+            raise InsufficientPermissionsException("You are not allowed to access this dataset")
         self.app.hda_manager.ensure_dataset_on_disk(trans, data)
         return data
 

test/integration/objectstore/test_jobs.py

@@ -3,12 +3,17 @@
 import os
 import string
 
+from galaxy_test.driver.integration_util import (
+    integration_module_instance,
+    integration_tool_runner,
+)
 from ._base import (
     BaseObjectStoreIntegrationTestCase,
     files_count,
 )
+from .test_selection_with_resource_parameters import DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE
 
-DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template(
+HIERARCHICAL_OBJECT_STORE_CONFIG_TEMPLATE = string.Template(
     """<?xml version="1.0"?>
 <object_store type="hierarchical">
     <backends>
@@ -39,7 +44,20 @@
 TEST_INPUT_FILES_CONTENT = "1 2 3"
 
 
-class TestObjectStoreJobsIntegration(BaseObjectStoreIntegrationTestCase):
+class TestDistributedObjectStore(BaseObjectStoreIntegrationTestCase):
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        super().handle_galaxy_config_kwds(config)
+        config["metadata_strategy"] = "directory"
+        config["object_store_store_by"] = "uuid"
+        cls._configure_object_store(DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE, config)
+
+
+instance = integration_module_instance(TestDistributedObjectStore)
+test_tools = integration_tool_runner(["all_output_types"])
+
+
+class TestObjectStoreJobsIntegration(TestDistributedObjectStore):
     # setup by _configure_object_store
     files1_path: str
     files2_path: str
@@ -48,7 +66,7 @@ class TestObjectStoreJobsIntegration(BaseObjectStoreIntegrationTestCase):
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         super().handle_galaxy_config_kwds(config)
-        cls._configure_object_store(DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE, config)
+        cls._configure_object_store(HIERARCHICAL_OBJECT_STORE_CONFIG_TEMPLATE, config)
 
     def setUp(self):
         super().setUp()
@@ -68,7 +86,7 @@ def setUp(self):
     def test_files_count_and_content_in_each_objectstore_backend(self):
         """
         According to the ObjectStore configuration given in the
-        `DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE` variable, datasets
+        `HIERARCHICAL_OBJECT_STORE_CONFIG_TEMPLATE` variable, datasets
         can be stored on three backends, named:
             -   primary/files1;
             -   primary/files2;

test/integration/test_extended_metadata.py

@@ -43,6 +43,7 @@
     "collection_creates_dynamic_nested_from_json_elements",
     "implicit_conversion",
     "environment_variables",
+    "all_output_types",
 ]