Merge branch 'release_24.1' into dev

client/src/api/schema/schema.ts

@@ -12918,7 +12918,10 @@ export interface components {
              * @enum {string}
              */
             type: "aws_s3" | "azure_blob" | "boto3" | "disk" | "generic_s3";
-            /** Uuid */
+            /**
+             * Uuid
+             * Format: uuid4
+             */
             uuid: string;
             /** Variables */
             variables: {
@@ -12992,7 +12995,10 @@ export interface components {
             type: "ftp" | "posix" | "s3fs" | "azure";
             /** Uri Root */
             uri_root: string;
-            /** Uuid */
+            /**
+             * Uuid
+             * Format: uuid4
+             */
             uuid: string;
             /** Variables */
             variables: {

client/src/components/Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue

@@ -89,6 +89,9 @@ const canDelete = computed(() => {
 const datasetManipulation = computed(() => {
     return !!(containsFileOrFolder.value && Galaxy.user);
 });
+const totalRows = computed(() => {
+    return props.metadata?.total_rows ?? 0;
+});
 
 function updateSearch(value: string) {
     emit("updateSearch", value);
@@ -106,7 +109,8 @@ async function getSelected() {
             const selected = await services.getFilteredFolderContents(
                 props.folderId,
                 props.unselected,
-                props.searchText
+                props.searchText,
+                totalRows.value
             );
 
             emit("setBusy", false);

client/src/components/Libraries/LibraryFolder/services.js

@@ -30,12 +30,13 @@ export class Services {
         }
     }
 
-    async getFilteredFolderContents(id, excluded, searchText) {
+    async getFilteredFolderContents(id, excluded, searchText, limit) {
         // The intent of this method is to get folder contents applying
-        // seachText filters only; we explicitly set limit to 0
+        // seachText filters only; limit should match the total number of
+        // items in the folder, so that all items are returned.
         const config = {
             params: {
-                limit: 0,
+                limit,
             },
         };
         searchText = searchText?.trim();

lib/galaxy/exceptions/__init__.py

@@ -209,6 +209,11 @@ class UserCannotRunAsException(MessageException):
     err_code = error_codes_by_name["USER_CANNOT_RUN_AS"]
 
 
+class UserRequiredException(MessageException):
+    status_code = 403
+    err_code = error_codes_by_name["USER_REQUIRED"]
+
+
 class AdminRequiredException(MessageException):
     status_code = 403
     err_code = error_codes_by_name["ADMIN_REQUIRED"]

lib/galaxy/exceptions/error_codes.json

@@ -144,6 +144,11 @@
         "code": 403007,
         "message": "Action requires account activation."
     },
+    {
+        "name": "USER_REQUIRED",
+        "code": 403008,
+        "message": "Action requires user authentication."
+    },
     {
         "name": "USER_OBJECT_NOT_FOUND",
         "code": 404001,

lib/galaxy/jobs/__init__.py

@@ -2005,13 +2005,13 @@ def fail(message=job.info, exception=None):
         # Once datasets are collected, set the total dataset size (includes extra files)
         for dataset_assoc in job.output_datasets:
             dataset = dataset_assoc.dataset.dataset
-            if not dataset.purged:
-                # assume all datasets in a job get written to the same objectstore
-                quota_source_info = dataset.quota_source_info
-                collected_bytes += dataset.set_total_size()
-            else:
+            # assume all datasets in a job get written to the same objectstore
+            quota_source_info = dataset.quota_source_info
+            collected_bytes += dataset.set_total_size()
+            if dataset.purged:
                 # Purge, in case job wrote directly to object store
                 dataset.full_delete()
+                collected_bytes = 0
 
         user = job.user
         if user and collected_bytes > 0 and quota_source_info is not None and quota_source_info.use:

lib/galaxy/managers/file_source_instances.py

@@ -13,6 +13,7 @@
 
 from pydantic import (
     BaseModel,
+    UUID4,
     ValidationError,
 )
 
@@ -87,7 +88,7 @@
 
 
 class UserFileSourceModel(BaseModel):
-    uuid: str
+    uuid: UUID4
     uri_root: str
     name: str
     description: Optional[str]
@@ -142,16 +143,16 @@ def index(self, trans: ProvidesUserContext) -> List[UserFileSourceModel]:
         stores = self._sa_session.query(UserFileSource).filter(UserFileSource.user_id == trans.user.id).all()
         return [self._to_model(trans, s) for s in stores]
 
-    def show(self, trans: ProvidesUserContext, uuid: str) -> UserFileSourceModel:
+    def show(self, trans: ProvidesUserContext, uuid: UUID4) -> UserFileSourceModel:
         user_file_source = self._get(trans, uuid)
         return self._to_model(trans, user_file_source)
 
-    def purge_instance(self, trans: ProvidesUserContext, uuid: str) -> None:
+    def purge_instance(self, trans: ProvidesUserContext, uuid: UUID4) -> None:
         persisted_file_source = self._get(trans, uuid)
         purge_template_instance(trans, persisted_file_source, self._app_config)
 
     def modify_instance(
-        self, trans: ProvidesUserContext, id: str, payload: ModifyInstancePayload
+        self, trans: ProvidesUserContext, id: UUID4, payload: ModifyInstancePayload
     ) -> UserFileSourceModel:
         if isinstance(payload, UpgradeInstancePayload):
             return self._upgrade_instance(trans, id, payload)
@@ -162,7 +163,7 @@ def modify_instance(
             return self._update_instance(trans, id, payload)
 
     def _upgrade_instance(
-        self, trans: ProvidesUserContext, id: str, payload: UpgradeInstancePayload
+        self, trans: ProvidesUserContext, id: UUID4, payload: UpgradeInstancePayload
     ) -> UserFileSourceModel:
         persisted_file_source = self._get(trans, id)
         template = self._get_template(persisted_file_source, payload.template_version)
@@ -181,15 +182,15 @@ def _upgrade_instance(
         return self._to_model(trans, persisted_file_source)
 
     def _update_instance(
-        self, trans: ProvidesUserContext, id: str, payload: UpdateInstancePayload
+        self, trans: ProvidesUserContext, id: UUID4, payload: UpdateInstancePayload
     ) -> UserFileSourceModel:
         persisted_file_source = self._get(trans, id)
         template = self._get_template(persisted_file_source)
         update_template_instance(self._sa_session, persisted_file_source, payload, template)
         return self._to_model(trans, persisted_file_source)
 
     def _update_instance_secret(
-        self, trans: ProvidesUserContext, id: str, payload: UpdateInstanceSecretPayload
+        self, trans: ProvidesUserContext, id: UUID4, payload: UpdateInstanceSecretPayload
     ) -> UserFileSourceModel:
         persisted_file_source = self._get(trans, id)
         template = self._get_template(persisted_file_source)
@@ -300,10 +301,10 @@ def _connection_status(
             exception = e
         return file_source, connection_exception_to_status("file source", exception)
 
-    def _index_filter(self, uuid: str):
+    def _index_filter(self, uuid: UUID4):
         return UserFileSource.__table__.c.uuid == uuid
 
-    def _get(self, trans: ProvidesUserContext, uuid: str) -> UserFileSource:
+    def _get(self, trans: ProvidesUserContext, uuid: UUID4) -> UserFileSource:
         filter = self._index_filter(uuid)
         user_file_source = self._sa_session.query(UserFileSource).filter(filter).one_or_none()
         if user_file_source is None:

lib/galaxy/managers/object_store_instances.py

@@ -16,6 +16,8 @@
 )
 from uuid import uuid4
 
+from pydantic import UUID4
+
 from galaxy.exceptions import (
     ItemOwnershipException,
     RequestParameterInvalidException,
@@ -73,7 +75,7 @@
 
 
 class UserConcreteObjectStoreModel(ConcreteObjectStoreModel):
-    uuid: str
+    uuid: UUID4
     type: ObjectStoreTemplateType
     template_id: str
     template_version: int
@@ -106,7 +108,7 @@ def summaries(self) -> ObjectStoreTemplateSummaries:
         return self._catalog.summaries
 
     def modify_instance(
-        self, trans: ProvidesUserContext, id: str, payload: ModifyInstancePayload
+        self, trans: ProvidesUserContext, id: UUID4, payload: ModifyInstancePayload
     ) -> UserConcreteObjectStoreModel:
         if isinstance(payload, UpgradeInstancePayload):
             return self._upgrade_instance(trans, id, payload)
@@ -116,12 +118,12 @@ def modify_instance(
             assert isinstance(payload, UpdateInstancePayload)
             return self._update_instance(trans, id, payload)
 
-    def purge_instance(self, trans: ProvidesUserContext, id: str) -> None:
+    def purge_instance(self, trans: ProvidesUserContext, id: UUID4) -> None:
         persisted_object_store = self._get(trans, id)
         purge_template_instance(trans, persisted_object_store, self._app_config)
 
     def _upgrade_instance(
-        self, trans: ProvidesUserContext, id: str, payload: UpgradeInstancePayload
+        self, trans: ProvidesUserContext, id: UUID4, payload: UpgradeInstancePayload
     ) -> UserConcreteObjectStoreModel:
         persisted_object_store = self._get(trans, id)
         template = self._get_template(persisted_object_store, payload.template_version)
@@ -140,15 +142,15 @@ def _upgrade_instance(
         return self._to_model(trans, persisted_object_store)
 
     def _update_instance(
-        self, trans: ProvidesUserContext, id: str, payload: UpdateInstancePayload
+        self, trans: ProvidesUserContext, id: UUID4, payload: UpdateInstancePayload
     ) -> UserConcreteObjectStoreModel:
         persisted_object_store = self._get(trans, id)
         template = self._get_template(persisted_object_store)
         update_template_instance(self._sa_session, persisted_object_store, payload, template)
         return self._to_model(trans, persisted_object_store)
 
     def _update_instance_secret(
-        self, trans: ProvidesUserContext, id: str, payload: UpdateInstanceSecretPayload
+        self, trans: ProvidesUserContext, id: UUID4, payload: UpdateInstanceSecretPayload
     ) -> UserConcreteObjectStoreModel:
         persisted_object_store = self._get(trans, id)
         template = self._get_template(persisted_object_store)
@@ -200,14 +202,14 @@ def index(self, trans: ProvidesUserContext) -> List[UserConcreteObjectStoreModel
         stores = self._sa_session.query(UserObjectStore).filter(UserObjectStore.user_id == trans.user.id).all()
         return [self._to_model(trans, s) for s in stores]
 
-    def show(self, trans: ProvidesUserContext, id: str) -> UserConcreteObjectStoreModel:
+    def show(self, trans: ProvidesUserContext, id: UUID4) -> UserConcreteObjectStoreModel:
         user_object_store = self._get(trans, id)
         return self._to_model(trans, user_object_store)
 
     def _save(self, persisted_object_store: UserObjectStore) -> None:
         save_template_instance(self._sa_session, persisted_object_store)
 
-    def _get(self, trans: ProvidesUserContext, id: str) -> UserObjectStore:
+    def _get(self, trans: ProvidesUserContext, id: UUID4) -> UserObjectStore:
         filter = self._index_filter(id)
         user_object_store = self._sa_session.query(UserObjectStore).filter(filter).one_or_none()
         if user_object_store is None:
@@ -274,7 +276,7 @@ def _connection_status(
             exception = e
         return object_store, connection_exception_to_status("storage location", exception)
 
-    def _index_filter(self, uuid: str):
+    def _index_filter(self, uuid: UUID4):
         return UserObjectStore.__table__.c.uuid == uuid
 
     def _get_template(

lib/galaxy/model/store/__init__.py

@@ -668,9 +668,9 @@ def handle_dataset_object_edit(dataset_instance, dataset_attrs):
                                 assert file_source_root
                                 dataset_extra_files_path = os.path.join(file_source_root, dataset_extra_files_path)
                                 persist_extra_files(self.object_store, dataset_extra_files_path, dataset_instance)
-                            # Don't trust serialized file size
-                        dataset_instance.dataset.file_size = None
-                        dataset_instance.dataset.set_total_size()  # update the filesize record in the database
+                            # Only trust file size if the dataset is purged. If we keep the data we should check the file size.
+                            dataset_instance.dataset.file_size = None
+                            dataset_instance.dataset.set_total_size()  # update the filesize record in the database
 
                     if dataset_instance.deleted:
                         dataset_instance.dataset.deleted = True

lib/galaxy/webapps/galaxy/api/__init__.py

@@ -68,6 +68,7 @@
 from galaxy.exceptions import (
     AdminRequiredException,
     UserCannotRunAsException,
+    UserRequiredException,
 )
 from galaxy.managers.session import GalaxySessionManager
 from galaxy.managers.users import UserManager
@@ -183,6 +184,17 @@ def get_user(
     return api_user
 
 
+def get_required_user(
+    galaxy_session=cast(Optional[model.GalaxySession], Depends(get_session)),
+    api_user=cast(Optional[User], Depends(get_api_user)),
+) -> User:
+    if galaxy_session and (user := galaxy_session.user):
+        return user
+    if api_user:
+        return api_user
+    raise UserRequiredException
+
+
 class UrlBuilder:
     def __init__(self, request: Request):
         self.request = request
@@ -310,7 +322,7 @@ def set_cookie(
         )
 
 
-DependsOnUser = cast(Optional[User], Depends(get_user))
+DependsOnUser = cast(User, Depends(get_required_user))
 
 
 def get_current_history_from_session(galaxy_session: Optional[model.GalaxySession]) -> Optional[model.History]:
@@ -485,6 +497,7 @@ def cbv(self):
 
 class Router(FrameworkRouter):
     admin_user_dependency = AdminUserRequired
+    user_dependency = DependsOnUser
 
 
 class APIContentTypeRoute(APIRoute):

lib/galaxy/webapps/galaxy/api/file_sources.py

@@ -7,6 +7,7 @@
     Response,
     status,
 )
+from pydantic import UUID4
 
 from galaxy.files.templates import FileSourceTemplateSummaries
 from galaxy.managers.context import ProvidesUserContext
@@ -16,10 +17,12 @@
     ModifyInstancePayload,
     UserFileSourceModel,
 )
+from galaxy.model import User
 from galaxy.util.config_templates import PluginStatus
 from . import (
     depends,
     DependsOnTrans,
+    DependsOnUser,
     Router,
 )
 
@@ -28,14 +31,15 @@
 router = Router(tags=["file_sources"])
 
 
-UserFileSourceIdPathParam: str = Path(
+UserFileSourceIdPathParam: UUID4 = Path(
     ..., title="User File Source UUID", description="The UUID index for a persisted UserFileSourceStore object."
 )
 
 
 @router.cbv
 class FastAPIFileSources:
     file_source_instances_manager: FileSourceInstancesManager = depends(FileSourceInstancesManager)
+    user: User = DependsOnUser
 
     @router.get(
         "/api/file_source_templates",
@@ -92,7 +96,7 @@ def instance_index(
     def instances_show(
         self,
         trans: ProvidesUserContext = DependsOnTrans,
-        user_file_source_id: str = UserFileSourceIdPathParam,
+        user_file_source_id: UUID4 = UserFileSourceIdPathParam,
     ) -> UserFileSourceModel:
         return self.file_source_instances_manager.show(trans, user_file_source_id)
 
@@ -104,7 +108,7 @@ def instances_show(
     def update_instance(
         self,
         trans: ProvidesUserContext = DependsOnTrans,
-        user_file_source_id: str = UserFileSourceIdPathParam,
+        user_file_source_id: UUID4 = UserFileSourceIdPathParam,
         payload: ModifyInstancePayload = Body(...),
     ) -> UserFileSourceModel:
         return self.file_source_instances_manager.modify_instance(trans, user_file_source_id, payload)
@@ -118,7 +122,7 @@ def update_instance(
     def purge_instance(
         self,
         trans: ProvidesUserContext = DependsOnTrans,
-        user_file_source_id: str = UserFileSourceIdPathParam,
+        user_file_source_id: UUID4 = UserFileSourceIdPathParam,
     ):
         self.file_source_instances_manager.purge_instance(trans, user_file_source_id)
         return Response(status_code=status.HTTP_204_NO_CONTENT)