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Fix link_data_only in extended metadata mode

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The problem was that we'd override external_filename and then set it to
None.
This commit is contained in:
mvdbeek
2021-10-26 17:59:04 +02:00
parent f9e4aea1c1
commit 46dc1ded77
1 changed files with 15 additions and 10 deletions
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lib/galaxy/metadata/set_metadata.py
+15 -10
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@@ -255,11 +255,15 @@ def set_metadata_portable():
set_meta_kwds = stringify_dictionary_keys(json.load(open(filename_kwds))) # load kwds; need to ensure our keywords are not unicode
try:
external_filename = unnamed_id_to_path.get(dataset_instance_id, dataset_filename_override)
dataset.dataset.external_filename = external_filename
store_by = output_dict.get("object_store_store_by", legacy_object_store_store_by)
extra_files_dir_name = f"dataset_{getattr(dataset.dataset, store_by)}_files"
files_path = os.path.abspath(os.path.join(tool_job_working_directory, "working", extra_files_dir_name))
dataset.dataset.external_extra_files_path = files_path
override_filenames = external_filename.startswith(tool_job_working_directory) and os.path.getsize(external_filename)
if override_filenames:
# Only set external filename if we're dealing with files in job working directory.
# Fixes link_data_only uploads
dataset.dataset.external_filename = external_filename
store_by = output_dict.get("object_store_store_by", legacy_object_store_store_by)
extra_files_dir_name = f"dataset_{getattr(dataset.dataset, store_by)}_files"
files_path = os.path.abspath(os.path.join(tool_job_working_directory, "working", extra_files_dir_name))
dataset.dataset.external_extra_files_path = files_path
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']
@@ -277,10 +281,10 @@ def set_metadata_portable():
set_meta(dataset, file_dict)
if extended_metadata_collection:
collect_extra_files(object_store, dataset, ".")
dataset.dataset.state = final_job_state
dataset.state = dataset.dataset.state = final_job_state
if extended_metadata_collection:
if external_filename.startswith(tool_job_working_directory) and os.path.getsize(external_filename):
if override_filenames:
# outputs to working directory, and not already pushed by pulsar + extended metadata,
# move output to final destination.
object_store.update_from_file(dataset.dataset, file_name=external_filename, create=True)
@@ -314,9 +318,10 @@ def set_metadata_portable():
if context_key in context:
context_value = context[context_key]
setattr(dataset, context_key, context_value)
# We never want to persist the external_filename.
dataset.dataset.external_filename = None
dataset.dataset.extra_files_path = None
# We only want to persist the external_filename if the dataset has been linked in.
if override_filenames:
dataset.dataset.external_filename = None
dataset.dataset.extra_files_path = None
export_store.add_dataset(dataset)
else:
dataset.metadata.to_JSON_dict(filename_out) # write out results of set_meta