Mercurial > repos > iuc > data_manager_ncbi_taxonomy_sqlite
changeset 2:20bb7de2c067 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
| author | iuc |
|---|---|
| date | Sun, 16 Apr 2023 08:28:04 +0000 |
| parents | 8667bfab227a |
| children | |
| files | data_manager/data_manager_ncbi_taxonomy_sqlite.py data_manager_conf.xml |
| diffstat | 2 files changed, 6 insertions(+), 8 deletions(-) [+] |
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--- a/data_manager/data_manager_ncbi_taxonomy_sqlite.py Wed Jul 22 15:54:04 2020 +0000 +++ b/data_manager/data_manager_ncbi_taxonomy_sqlite.py Sun Apr 16 08:28:04 2023 +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)
--- a/data_manager_conf.xml Wed Jul 22 15:54:04 2020 +0000 +++ b/data_manager_conf.xml Sun Apr 16 08:28:04 2023 +0000 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <data_managers> - <data_manager tool_file="data_manager/data_manager_ncbi_taxonomy_sqlite.xml" id="data_manager_ncbi_taxonomy_sqlite" version="0.0.1"> + <data_manager tool_file="data_manager/data_manager_ncbi_taxonomy_sqlite.xml" id="data_manager_ncbi_taxonomy_sqlite"> <data_table name="ncbi_taxonomy_sqlite"> <output> <column name="value" />