Loading lib/galaxy/job_execution/output_collect.py +4 −3 Original line number Diff line number Diff line Loading @@ -727,18 +727,19 @@ def collect_extra_files(object_store, dataset, job_working_directory): # Fall back to working dir, remove in 23.2 output_location = "working" temp_file_path = os.path.join(job_working_directory, output_location, file_name) extra_dir = None if not os.path.exists(temp_file_path): # no outputs to working directory, but may still need to push form cache to backend temp_file_path = dataset.extra_files_path try: # This skips creation of directories - object store # automatically creates them. However, empty directories will # not be created in the object store at all, which might be a # problem. for root, _dirs, files in os.walk(temp_file_path): extra_dir = root.replace(os.path.join(job_working_directory, output_location), "", 1).lstrip(os.path.sep) for f in files: object_store.update_from_file( dataset.dataset, extra_dir=extra_dir, extra_dir=os.path.normpath(os.path.join(file_name, os.path.relpath(root, temp_file_path))), alt_name=f, file_name=os.path.join(root, f), create=True, Loading test/integration/test_tool_data_bundles.py +1 −0 Original line number Diff line number Diff line Loading @@ -33,6 +33,7 @@ class TestDataBundlesIntegration(BaseSwiftObjectStoreIntegrationTestCase, DataMa history_id, to_ext="data_manager_json", type="bytes" ) temp_directory = decompress_bytes_to_directory(content) assert os.path.exists(os.path.join(temp_directory, "newvalue.txt")) uri = f"file://{os.path.normpath(temp_directory)}" data = { "source": { Loading Loading
lib/galaxy/job_execution/output_collect.py +4 −3 Original line number Diff line number Diff line Loading @@ -727,18 +727,19 @@ def collect_extra_files(object_store, dataset, job_working_directory): # Fall back to working dir, remove in 23.2 output_location = "working" temp_file_path = os.path.join(job_working_directory, output_location, file_name) extra_dir = None if not os.path.exists(temp_file_path): # no outputs to working directory, but may still need to push form cache to backend temp_file_path = dataset.extra_files_path try: # This skips creation of directories - object store # automatically creates them. However, empty directories will # not be created in the object store at all, which might be a # problem. for root, _dirs, files in os.walk(temp_file_path): extra_dir = root.replace(os.path.join(job_working_directory, output_location), "", 1).lstrip(os.path.sep) for f in files: object_store.update_from_file( dataset.dataset, extra_dir=extra_dir, extra_dir=os.path.normpath(os.path.join(file_name, os.path.relpath(root, temp_file_path))), alt_name=f, file_name=os.path.join(root, f), create=True, Loading
test/integration/test_tool_data_bundles.py +1 −0 Original line number Diff line number Diff line Loading @@ -33,6 +33,7 @@ class TestDataBundlesIntegration(BaseSwiftObjectStoreIntegrationTestCase, DataMa history_id, to_ext="data_manager_json", type="bytes" ) temp_directory = decompress_bytes_to_directory(content) assert os.path.exists(os.path.join(temp_directory, "newvalue.txt")) uri = f"file://{os.path.normpath(temp_directory)}" data = { "source": { Loading