Mercurial > repos > iuc > data_manager_ncbi_taxonomy_sqlite
changeset 2:37560eebb5ce draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
| author | iuc |
|---|---|
| date | Sun, 22 Nov 2020 12:52:03 +0000 |
| parents | 54a0869d0051 |
| children | f9650b178bfd |
| files | data_manager/data_manager_ncbi_taxonomy_sqlite.py |
| diffstat | 1 files changed, 5 insertions(+), 7 deletions(-) [+] |
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--- a/data_manager/data_manager_ncbi_taxonomy_sqlite.py Wed Jul 22 11:54:58 2020 -0400 +++ b/data_manager/data_manager_ncbi_taxonomy_sqlite.py Sun Nov 22 12:52:03 2020 +0000 @@ -55,7 +55,8 @@ ) args = parser.parse_args() - config = json.load(open(args.galaxy_datamanager_filename)) + with open(args.galaxy_datamanager_filename) as fh: + config = json.load(fh) output_directory = config.get("output_data", [{}])[0].get("extra_files_path", None) if output_directory is None: output_directory = args.output_directory @@ -64,10 +65,7 @@ os.makedirs(output_directory) data_manager_dict = {} - data_manager_dict["data_tables"] = json.load( - open(args.galaxy_datamanager_filename) - ).get("data_tables", {}) - data_manager_dict["data_tables"] = data_manager_dict.get("data_tables", {}) + data_manager_dict["data_tables"] = config.get("data_tables", {}) data_manager_dict["data_tables"][DATA_TABLE_NAME] = data_manager_dict[ "data_tables" ].get(DATA_TABLE_NAME, []) @@ -75,5 +73,5 @@ data = build_sqlite(args.taxonomy_dir, output_directory, args.name, args.description) data_manager_dict["data_tables"][DATA_TABLE_NAME].extend(data) - print(json.dumps(data_manager_dict)) - json.dump(data_manager_dict, open(args.galaxy_datamanager_filename, "w")) + with open(args.galaxy_datamanager_filename, "w") as fh: + json.dump(data_manager_dict, fh, sort_keys=True)