Mercurial > repos > iuc > data_manager_ncbi_taxonomy_sqlite
comparison data_manager/data_manager_ncbi_taxonomy_sqlite.py @ 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 |
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| 1:54a0869d0051 | 2:37560eebb5ce |
|---|---|
| 53 "galaxy_datamanager_filename", | 53 "galaxy_datamanager_filename", |
| 54 help="Galaxy JSON format file describing data manager inputs", | 54 help="Galaxy JSON format file describing data manager inputs", |
| 55 ) | 55 ) |
| 56 args = parser.parse_args() | 56 args = parser.parse_args() |
| 57 | 57 |
| 58 config = json.load(open(args.galaxy_datamanager_filename)) | 58 with open(args.galaxy_datamanager_filename) as fh: |
| 59 config = json.load(fh) | |
| 59 output_directory = config.get("output_data", [{}])[0].get("extra_files_path", None) | 60 output_directory = config.get("output_data", [{}])[0].get("extra_files_path", None) |
| 60 if output_directory is None: | 61 if output_directory is None: |
| 61 output_directory = args.output_directory | 62 output_directory = args.output_directory |
| 62 | 63 |
| 63 if not os.path.isdir(output_directory): | 64 if not os.path.isdir(output_directory): |
| 64 os.makedirs(output_directory) | 65 os.makedirs(output_directory) |
| 65 | 66 |
| 66 data_manager_dict = {} | 67 data_manager_dict = {} |
| 67 data_manager_dict["data_tables"] = json.load( | 68 data_manager_dict["data_tables"] = config.get("data_tables", {}) |
| 68 open(args.galaxy_datamanager_filename) | |
| 69 ).get("data_tables", {}) | |
| 70 data_manager_dict["data_tables"] = data_manager_dict.get("data_tables", {}) | |
| 71 data_manager_dict["data_tables"][DATA_TABLE_NAME] = data_manager_dict[ | 69 data_manager_dict["data_tables"][DATA_TABLE_NAME] = data_manager_dict[ |
| 72 "data_tables" | 70 "data_tables" |
| 73 ].get(DATA_TABLE_NAME, []) | 71 ].get(DATA_TABLE_NAME, []) |
| 74 | 72 |
| 75 data = build_sqlite(args.taxonomy_dir, output_directory, args.name, args.description) | 73 data = build_sqlite(args.taxonomy_dir, output_directory, args.name, args.description) |
| 76 | 74 |
| 77 data_manager_dict["data_tables"][DATA_TABLE_NAME].extend(data) | 75 data_manager_dict["data_tables"][DATA_TABLE_NAME].extend(data) |
| 78 print(json.dumps(data_manager_dict)) | 76 with open(args.galaxy_datamanager_filename, "w") as fh: |
| 79 json.dump(data_manager_dict, open(args.galaxy_datamanager_filename, "w")) | 77 json.dump(data_manager_dict, fh, sort_keys=True) |