Commit a703be5b authored by Yakubov, Sergey's avatar Yakubov, Sergey
Browse files

call pass user to delete dataset functions

parent 6fdc2efa

lib/galaxy/celery/tasks.py

+2 −2
Original line number Diff line number Diff line
@@ -91,8 +91,8 @@ def purge_hda(hda_manager: HDAManager, hda_id: int): 




@galaxy_task(ignore_result=True, action="completely removes a set of datasets from the object_store")

def purge_datasets(dataset_manager: DatasetManager, request: PurgeDatasetsTaskRequest):

    dataset_manager.purge_datasets(request)

def purge_datasets(dataset_manager: DatasetManager, request: PurgeDatasetsTaskRequest, user: model.User):

    dataset_manager.purge_datasets(request, user)





@galaxy_task(ignore_result=True, action="materializing dataset instance")

lib/galaxy/jobs/__init__.py

+1 −1
Original line number Diff line number Diff line
@@ -2428,7 +2428,7 @@ class MinimalJobWrapper(HasResourceParameters): 
                # is a bit of hack - our object store abstractions would be stronger

                # and more consistent if tools weren't writing there directly.

                try:

                    dataset.full_delete()

                    dataset.full_delete(user=hda.user)

                except ObjectNotFound:

                    pass

lib/galaxy/managers/datasets.py

+2 −2
Original line number Diff line number Diff line
@@ -93,7 +93,7 @@ class DatasetManager(base.ModelManager[model.Dataset], secured.AccessibleManager 
                session.commit()

        return dataset



    def purge_datasets(self, request: PurgeDatasetsTaskRequest):

    def purge_datasets(self, request: PurgeDatasetsTaskRequest, user: model.User):

        """

        Caution: any additional security checks must be done before executing this action.
@@ -106,7 +106,7 @@ class DatasetManager(base.ModelManager[model.Dataset], secured.AccessibleManager 
                dataset: model.Dataset = self.session().query(model.Dataset).get(dataset_id)

                if dataset.user_can_purge:

                    try:

                        dataset.full_delete()

                        dataset.full_delete(user)

                    except Exception:

                        log.exception(f"Unable to purge dataset ({dataset.id})")

lib/galaxy/managers/hdas.py

+4 −4
Original line number Diff line number Diff line
@@ -439,7 +439,7 @@ class HDAStorageCleanerManager(base.StorageCleanerManager): 
            with transaction(session):

                session.commit()



        self._request_full_delete_all(dataset_ids_to_remove)

        self._request_full_delete_all(dataset_ids_to_remove, user=user)



        return StorageItemsCleanupResult(

            total_item_count=len(item_ids),
@@ -448,15 +448,15 @@ class HDAStorageCleanerManager(base.StorageCleanerManager): 
            errors=errors,

        )



    def _request_full_delete_all(self, dataset_ids_to_remove: Set[int]):

    def _request_full_delete_all(self, dataset_ids_to_remove: Set[int], user: model.User):

        use_tasks = self.dataset_manager.app.config.enable_celery_tasks

        request = PurgeDatasetsTaskRequest(dataset_ids=list(dataset_ids_to_remove))

        if use_tasks:

            from galaxy.celery.tasks import purge_datasets



            purge_datasets.delay(request=request)

            purge_datasets.delay(request=request, user=user)

        else:

            self.dataset_manager.purge_datasets(request)

            self.dataset_manager.purge_datasets(request, user=user)





class HDASerializer(  # datasets._UnflattenedMetadataDatasetAssociationSerializer,

lib/galaxy/model/__init__.py

+2 −2
Original line number Diff line number Diff line
@@ -4145,7 +4145,7 @@ class Dataset(Base, StorableObject, Serializable): 
            and len(self.history_associations) == len(self.purged_history_associations)

        )



    def full_delete(self, user):

    def full_delete(self, user=None):

        """Remove the file and extra files, marks deleted and purged"""

        # os.unlink( self.file_name )

        try:
@@ -5000,7 +5000,7 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot 
            self.copy_tags_from(self.user, other_hda)

        self.dataset = new_dataset or other_hda.dataset

        if old_dataset:

            old_dataset.full_delete()

            old_dataset.full_delete(user=self.user)



    def copy(self, parent_id=None, copy_tags=None, flush=True, copy_hid=True, new_name=None):

        """