Mercurial > repos > greg > data_manager_plant_tribes_scaffolds_downloader
changeset 5:83834587ba93 draft
Uploaded
| author | greg |
|---|---|
| date | Wed, 23 Nov 2016 10:11:54 -0500 |
| parents | e87b66359c13 |
| children | e7c4d4c7c1dd |
| files | data_manager/data_manager_plant_tribes_scaffolds_download.py |
| diffstat | 1 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/data_manager/data_manager_plant_tribes_scaffolds_download.py Wed Nov 23 10:06:02 2016 -0500 +++ b/data_manager/data_manager_plant_tribes_scaffolds_download.py Wed Nov 23 10:11:54 2016 -0500 @@ -41,7 +41,7 @@ return files -def import_from_server(data_manager_dict, target_directory, file_system_paths, description, link_to_data=False, data_table_names=DEFAULT_DATA_TABLE_NAMES): +def import_from_server(data_manager_dict, target_directory, file_system_paths, description, create_symlink, data_table_names=DEFAULT_DATA_TABLE_NAMES): """ Creates references to the specified file(s) on the Galaxy server in the data table. @@ -53,7 +53,7 @@ source_file = os.path.basename(f) target_file = os.path.join(target_directory, source_file) entry_name = source_file - if link_to_data: + if create_symlink == 'create_symlink': os.symlink(f, target_file) else: shutil.copyfile(f, target_file) @@ -150,7 +150,7 @@ if args.data_source == 'web_url': data_manager_dict = url_download(data_manager_dict, target_directory, args.web_url, description, data_table_names=DEFAULT_DATA_TABLE_NAMES) else: - data_manager_dict = import_from_server(data_manager_dict, target_directory, args.file_system_paths, description, create_symlink=args.create_symlink, data_table_names=DEFAULT_DATA_TABLE_NAMES) + data_manager_dict = import_from_server(data_manager_dict, target_directory, args.file_system_paths, description, args.create_symlink, data_table_names=DEFAULT_DATA_TABLE_NAMES) # Write the JSON output dataset. file(args.out_file, 'w').write(json.dumps(data_manager_dict))