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()