Unverified Commit f8721ccb authored by mvdbeek's avatar mvdbeek
Browse files

Create MetadataTempFile for transient dataset 

by passing `metadata_tmp_files_dir` to `set_meta`. This ensures that
we're creating a MetadataTempFile instead of a MetadataFile, and that
we're creating it in the appropriate directory.
parent d4e2dae1

lib/galaxy/model/deferred.py

+10 −6
Original line number Diff line number Diff line
@@ -40,6 +40,7 @@ log = logging.getLogger(__name__) 
class TransientDatasetPaths(NamedTuple):

    external_filename: str

    external_extra_files_path: str

    metadata_files_dir: str





class TransientPathMapper:
@@ -61,7 +62,7 @@ class SimpleTransientPathMapper(TransientPathMapper): 
        external_filename = os.path.join(self._staging_directory, external_filename_basename)

        external_extras_basename = "dataset_%s_files" % str(old_dataset.uuid)

        external_extras = os.path.join(self._staging_directory, external_extras_basename)

        return TransientDatasetPaths(external_filename, external_extras)

        return TransientDatasetPaths(external_filename, external_extras, self._staging_directory)





class DatasetInstanceMaterializer:
@@ -110,6 +111,7 @@ class DatasetInstanceMaterializer: 
        materialized_dataset.hashes = [h.copy() for h in dataset.hashes]



        target_source = self._find_closest_dataset_source(dataset)

        transient_paths = None

        if attached:

            object_store_populator = self._object_store_populator

            assert object_store_populator
@@ -157,12 +159,14 @@ class DatasetInstanceMaterializer: 
            materialized_dataset_instance.has_metadata_files or materialized_dataset_instance.metadata_deferred

        )

        if require_metadata_regeneration:

            if attached and self._sa_session:

                # as of mid April 2022, we now get JSON encoding errors if this

                # isn't bound to the session before metadata generation.

                self._sa_session.add(materialized_dataset_instance)

            materialized_dataset_instance.init_meta()

            materialized_dataset_instance.set_meta()

            if transient_paths:

                metadata_tmp_files_dir = transient_paths.metadata_files_dir

            else:

                # If metadata_tmp_files_dir is set we generate a MetdataTempFile,

                # which we don't want when we're generating an attached materialized dataset instance

                metadata_tmp_files_dir = None

            materialized_dataset_instance.set_meta(metadata_tmp_files_dir=metadata_tmp_files_dir)

            materialized_dataset_instance.metadata_deferred = False

        return materialized_dataset_instance