Unverified Commit 33f9edf3 authored by mvdbeek's avatar mvdbeek
Browse files

Fix extra files path if metadata job runs in celery 

The job runner may have moved files to the object store already before
calling `_handle_metadata_externally`, so the
celery task needs to process files from the object store, not the job
working directory.
parent f487d804

lib/galaxy/metadata/set_metadata.py

+9 −3
Original line number Diff line number Diff line
@@ -407,13 +407,19 @@ def set_metadata_portable( 
                    files_path = os.path.abspath(

                        os.path.join(tool_job_working_directory, "working", extra_files_dir_name)

                    )

                    if not os.path.exists(files_path):

                    if os.path.exists(files_path):

                        dataset.dataset.external_extra_files_path = files_path

                    else:

                        # could be pulsar, stores extra files in outputs directory

                        pulsar_extra_files_path = os.path.join(

                            tool_job_working_directory, "outputs", extra_files_dir_name

                        )

                        if os.path.exists(pulsar_extra_files_path):

                            files_path = pulsar_extra_files_path

                    dataset.dataset.external_extra_files_path = files_path

                            dataset.dataset.external_extra_files_path = pulsar_extra_files_path

                        elif dataset_filename_override and not object_store:

                            # pulsar, no remote metadata and no extended metadata

                            dataset.dataset.external_extra_files_path = os.path.join(os.path.dirname(dataset_filename_override), extra_files_dir_name)



            file_dict = tool_provided_metadata.get_dataset_meta(output_name, dataset.dataset.id, dataset.dataset.uuid)

            if "ext" in file_dict:

                dataset.extension = file_dict["ext"]