diff options
| author | Bryan Newbold <bnewbold@robocracy.org> | 2019-05-22 15:59:14 -0700 |
|---|---|---|
| committer | Bryan Newbold <bnewbold@robocracy.org> | 2019-05-22 15:59:14 -0700 |
| commit | a9752a685be5a0ff7794ba652ca7954cb7508124 (patch) | |
| tree | 45a996b19d4216fe5b5b173448861acf77073358 /python | |
| parent | be86ebbdcee910f3187305470440189331a16911 (diff) | |
| download | fatcat-a9752a685be5a0ff7794ba652ca7954cb7508124.tar.gz fatcat-a9752a685be5a0ff7794ba652ca7954cb7508124.zip | |
make pubmed ref lookups configurable
Diffstat (limited to 'python')
| -rwxr-xr-x | python/fatcat_import.py | 9 |
1 files changed, 8 insertions, 1 deletions
diff --git a/python/fatcat_import.py b/python/fatcat_import.py index 02a3441f..21e40750 100755 --- a/python/fatcat_import.py +++ b/python/fatcat_import.py @@ -34,7 +34,8 @@ def run_arxiv(args): def run_pubmed(args): pi = PubmedImporter(args.api, args.issn_map_file, - edit_batch_size=args.batch_size) + edit_batch_size=args.batch_size, + lookup_refs=(not args.no_lookup_refs)) if args.kafka_mode: raise NotImplementedError #KafkaBs4XmlPusher(pi, args.kafka_hosts, args.kafka_env, "api-pubmed", "fatcat-import").run() @@ -167,6 +168,9 @@ def main(): sub_crossref.add_argument('--extid-map-file', help="DOI-to-other-identifiers sqlite3 database", default=None, type=str) + sub_crossref.add_argument('--no-lookup-refs', + action='store_true', + help="skip lookup of references (PMID or DOI)") sub_crossref.add_argument('--kafka-mode', action='store_true', help="consume from kafka topic (not stdin)") @@ -212,6 +216,9 @@ def main(): sub_pubmed.add_argument('issn_map_file', help="ISSN to ISSN-L mapping file", default=None, type=argparse.FileType('r')) + sub_pubmed.add_argument('--no-lookup-refs', + action='store_true', + help="skip lookup of references (PMID or DOI)") sub_pubmed.add_argument('--kafka-mode', action='store_true', help="consume from kafka topic (not stdin)") |