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Improve various error conditions around downloading metadata files #16706

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Improve various error conditions around downloading metadata files #16706

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d699486
List extra files only for terminal datasets
mvdbeek Sep 16, 2023
516a430
Improve various error conditions around downloading metadata files
mvdbeek Sep 16, 2023
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30 changes: 20 additions & 10 deletions lib/galaxy/webapps/galaxy/services/datasets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -545,15 +545,16 @@ def extra_files(
Generate list of extra files.
"""
hda = self.hda_manager.get_accessible(history_content_id, trans.user)
extra_files_path = hda.extra_files_path
rval = []
for root, directories, files in safe_walk(extra_files_path):
for directory in directories:
rval.append(
{"class": "Directory", "path": os.path.relpath(os.path.join(root, directory), extra_files_path)}
)
for file in files:
rval.append({"class": "File", "path": os.path.relpath(os.path.join(root, file), extra_files_path)})
if not hda.is_pending and hda.extra_files_path_exists():
extra_files_path = hda.extra_files_path
for root, directories, files in safe_walk(extra_files_path):
for directory in directories:
rval.append(
{"class": "Directory", "path": os.path.relpath(os.path.join(root, directory), extra_files_path)}
)
for file in files:
rval.append({"class": "File", "path": os.path.relpath(os.path.join(root, file), extra_files_path)})

return rval

Expand Down Expand Up @@ -642,12 +643,21 @@ def get_metadata_file(
TODO: Remove the `open_file` parameter when removing the associated legacy endpoint.
"""
hda = self.hda_manager.get_accessible(history_content_id, trans.user)
file_ext = hda.metadata.spec.get(metadata_file).get("file_ext", metadata_file)
if hda.is_pending:
raise galaxy_exceptions.AcceptedRetryLater("dataset not in terminal state, retry later.", retry_after=60)
file_ext = hda.metadata.spec.get(metadata_file, {}).get("file_ext", metadata_file)
fname = "".join(c in util.FILENAME_VALID_CHARS and c or "_" for c in hda.name)[0:150]
headers = {}
headers["Content-Type"] = "application/octet-stream"
headers["Content-Disposition"] = f'attachment; filename="Galaxy{hda.hid}-[{fname}].{file_ext}"'
file_path = hda.metadata.get(metadata_file).file_name
metadata_file_instance = hda.metadata.get(metadata_file)
if not metadata_file_instance:
return galaxy_exceptions.RequestParameterInvalidException(
f"metadata file '{metadata_file}' not valid for dataset."
)
file_path = metadata_file_instance.file_name
if not os.path.exists(file_path):
return galaxy_exceptions.ObjectNotFound(f"metadata file '{metadata_file}' not found.")
if open_file:
return open(file_path, "rb"), headers
return file_path, headers
Expand Down