diff options
| -rwxr-xr-x | covid19_tool.py | 42 |
1 files changed, 18 insertions, 24 deletions
diff --git a/covid19_tool.py b/covid19_tool.py index e984c28..1cd0e48 100755 --- a/covid19_tool.py +++ b/covid19_tool.py @@ -38,25 +38,29 @@ def main(): default=9119, help="listen on this port") - sub_enrich = subparsers.add_parser('enrich', - help="enrich CORD-19 dataset (JSON) with fatcat metadata") - sub_enrich.set_defaults( - action='enrich', - ) - sub_enrich.add_argument('json_file', - help="CORD-19 parsed JSON file", + sub_enrich_fatcat = subparsers.add_parser('enrich-fatcat', + help="lookup fatcat releases from JSON metadata") + sub_enrich_fatcat.add_argument('json_file', + help="input JSON rows file (eg, CORD-19 parsed JSON)", type=argparse.FileType('r')) + sub_enrich_fatcat.add_argument('--json-output', + help="file to write to", + type=argparse.FileType('r'), + default=sys.stdout) - sub_derivatives = subparsers.add_parser('derivatives', + sub_enrich_derivatives = subparsers.add_parser('enrich-derivatives', help="enrich JSON rows with existing derivative files") - sub_derivatives.add_argument('json_file', + sub_enrich_derivatives.set_defaults( + action='enrich-derivatives', + ) + sub_enrich_derivatives.add_argument('json_file', help="enriched (with fatcat_release) metadata file", type=argparse.FileType('r')) - sub_derivatives.add_argument('--json-output', + sub_enrich_derivatives.add_argument('--json-output', help="file to write ", type=argparse.FileType('r'), default=sys.stdout) - sub_derivatives.add_argument('--base-dir', + sub_enrich_derivatives.add_argument('--base-dir', help="directory to look for files (in 'pdf' subdirectory)", default="fulltext_web") @@ -70,27 +74,17 @@ def main(): type=argparse.FileType('r'), default=sys.stdout) - sub_enrich_fatcat = subparsers.add_parser('enrich-fatcat', - help="lookup fatcat releases from JSON metadata") - sub_enrich_fatcat.add_argument('json_file', - help="input JSON rows file (eg, CORD-19 parsed JSON)", - type=argparse.FileType('r')) - sub_enrich_fatcat.add_argument('--json-output', - help="file to write to", - type=argparse.FileType('r'), - default=sys.stdout) - args = parser.parse_args() if args.action == 'webface': app.run(debug=args.debug, host=args.host, port=args.port) - elif args.action == 'derivatives': + elif args.action == 'enrich-fatcat': + transform_es_file(args.json_file, args.json_output) + elif args.action == 'enrich-derivatives': enrich_derivatives_file(args.json_file, args.json_output, args.base_dir) elif args.action == 'transform-es': transform_es_file(args.json_file, args.json_output) - elif args.action == 'enrich-fatcat': - transform_es_file(args.json_file, args.json_output) else: print("tell me what to do!") sys.exit(-1) |