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REALLY do not update metadata.tsv files when publishing a Component D… #840

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Merged
merged 1 commit into from
Nov 3, 2025
Merged

REALLY do not update metadata.tsv files when publishing a Component D… #840

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33 changes: 17 additions & 16 deletions src/app.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1365,22 +1365,23 @@ def publish_datastage(identifier):

#find all of the files that match *metadata.tsv under the dataset's directory
#strip the columns that can hold lab identifiers of any data
tsv_files = glob.glob(os.path.join(ds_path,"*metadata.tsv"))
for tsv_file in tsv_files:
tsv_data = pandas.read_csv(tsv_file, sep='\t')
columns = tsv_data.columns.tolist()
changes = False
for col_name in tsv_columns_to_blank:
if col_name in columns:
changes = True
tsv_data[col_name] = None
if changes:
meta_filename = os.path.basename(os.path.normpath(tsv_file))
dtnow = datetime.datetime.now().strftime('%Y-%m-%d-%H:%M:%S')
backup_filename = f"({dataset_uuid}.{dtnow}) {meta_filename}"
backup_file_path = os.path.join(tsv_backup_dir,backup_filename)
shutil.copy(tsv_file, f"{backup_file_path}")
tsv_data.to_csv(tsv_file, sep='\t', index=False)
if not is_component:
tsv_files = glob.glob(os.path.join(ds_path,"*metadata.tsv"))
for tsv_file in tsv_files:
tsv_data = pandas.read_csv(tsv_file, sep='\t')
columns = tsv_data.columns.tolist()
changes = False
for col_name in tsv_columns_to_blank:
if col_name in columns:
changes = True
tsv_data[col_name] = None
if changes:
meta_filename = os.path.basename(os.path.normpath(tsv_file))
dtnow = datetime.datetime.now().strftime('%Y-%m-%d-%H:%M:%S')
backup_filename = f"({dataset_uuid}.{dtnow}) {meta_filename}"
backup_file_path = os.path.join(tsv_backup_dir,backup_filename)
shutil.copy(tsv_file, f"{backup_file_path}")
tsv_data.to_csv(tsv_file, sep='\t', index=False)

if no_indexing_and_acls:
r_val = {'acl_cmd': acls_cmd, 'donors_for_indexing': donors_to_reindex, 'relink_cmd': relink_cmd}
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