def pubmed_importer(api): with open('tests/files/ISSN-to-ISSN-L.snip.txt', 'r') as issn_file: yield PubmedImporter(api, issn_file, extid_map_file='tests/files/example_map.sqlite3', bezerk_mode=True, lookup_refs=True)
def pubmed_importer(api): with open("tests/files/ISSN-to-ISSN-L.snip.txt", "r") as issn_file: yield PubmedImporter( api, issn_file, bezerk_mode=True, lookup_refs=True, )
def run_pubmed(args: argparse.Namespace) -> None: pi = PubmedImporter( args.api, args.issn_map_file, edit_batch_size=args.batch_size, do_updates=args.do_updates, lookup_refs=(not args.no_lookup_refs), ) if args.kafka_mode: KafkaBs4XmlPusher( pi, args.kafka_hosts, args.kafka_env, "ftp-pubmed", "fatcat-{}-import-pubmed".format(args.kafka_env), ).run() else: Bs4XmlLargeFilePusher( pi, args.xml_file, ["PubmedArticle"], ).run()