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#!/usr/bin/env python3
import os, sys, argparse
from fatcat_tools import authenticated_api
from fatcat_tools.importers import *
def run_crossref(args):
fci = CrossrefImporter(args.api,
args.issn_map_file,
extid_map_file=args.extid_map_file,
edit_batch_size=args.batch_size,
bezerk_mode=args.bezerk_mode)
if args.kafka_mode:
KafkaJsonPusher(fci, args.kafka_hosts, args.kafka_env, "api-crossref", "fatcat-import").run()
else:
JsonLinePusher(fci).run()
def run_orcid(args):
foi = OrcidImporter(args.api,
edit_batch_size=args.batch_size)
JsonLinePusher(foi, args.json_file).run()
def run_journal_metadata(args):
fii = JournalMetadataImporter(args.api,
edit_batch_size=args.batch_size)
CsvLinePusher(fii, args.csv_file).run()
def run_matched(args):
fmi = MatchedImporter(args.api,
bezerk_mode=args.bezerk_mode,
edit_batch_size=args.batch_size)
JsonLinePusher(fmi, args.json_file).run()
def run_grobid_metadata(args):
fmi = GrobidMetadataImporter(args.api, edit_batch_size=args.batch_size)
LinePusher(fmi, args.tsv_file).run()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--debug',
action='store_true',
help="enable debugging interface")
parser.add_argument('--host-url',
default="http://localhost:9411/v0",
help="connect to this host/port")
parser.add_argument('--kafka-hosts',
default="localhost:9092",
help="list of Kafka brokers (host/port) to use")
parser.add_argument('--kafka-env',
default="qa",
help="Kafka topic namespace to use (eg, prod, qa)")
subparsers = parser.add_subparsers()
sub_crossref = subparsers.add_parser('crossref')
sub_crossref.set_defaults(
func=run_crossref,
auth_var="FATCAT_AUTH_WORKER_CROSSREF",
)
sub_crossref.add_argument('json_file',
help="crossref JSON file to import from",
default=sys.stdin, type=argparse.FileType('r'))
sub_crossref.add_argument('issn_map_file',
help="ISSN to ISSN-L mapping file",
default=None, type=argparse.FileType('r'))
sub_crossref.add_argument('--extid-map-file',
help="DOI-to-other-identifiers sqlite3 database",
default=None, type=str)
sub_crossref.add_argument('--batch-size',
help="size of batch to send",
default=50, type=int)
sub_crossref.add_argument('--kafka-mode',
action='store_true',
help="consume from kafka topic (not stdin)")
sub_crossref.add_argument('--bezerk-mode',
action='store_true',
help="don't lookup existing DOIs, just insert (clobbers; only for fast bootstrap)")
sub_orcid = subparsers.add_parser('orcid')
sub_orcid.set_defaults(
func=run_orcid,
auth_var="FATCAT_AUTH_WORKER_ORCID"
)
sub_orcid.add_argument('json_file',
help="orcid JSON file to import from (or stdin)",
default=sys.stdin, type=argparse.FileType('r'))
sub_orcid.add_argument('--batch-size',
help="size of batch to send",
default=50, type=int)
sub_journal_metadata = subparsers.add_parser('journal-metadata')
sub_journal_metadata.set_defaults(
func=run_journal_metadata,
auth_var="FATCAT_AUTH_WORKER_JOURNAL_METADATA",
)
sub_journal_metadata.add_argument('csv_file',
help="Journal ISSN CSV metadata file to import from (or stdin)",
default=sys.stdin, type=argparse.FileType('r'))
sub_journal_metadata.add_argument('--batch-size',
help="size of batch to send",
default=50, type=int)
sub_matched = subparsers.add_parser('matched')
sub_matched.set_defaults(
func=run_matched,
auth_var="FATCAT_API_AUTH_TOKEN",
)
sub_matched.add_argument('json_file',
help="JSON file to import from (or stdin)",
default=sys.stdin, type=argparse.FileType('r'))
sub_matched.add_argument('--batch-size',
help="size of batch to send",
default=50, type=int)
sub_matched.add_argument('--bezerk-mode',
action='store_true',
help="don't lookup existing files, just insert (clobbers; only for fast bootstrap)")
sub_grobid_metadata = subparsers.add_parser('grobid-metadata')
sub_grobid_metadata.set_defaults(
func=run_grobid_metadata,
auth_var="FATCAT_API_AUTH_TOKEN",
)
sub_grobid_metadata.add_argument('tsv_file',
help="TSV file to import from (or stdin)",
default=sys.stdin, type=argparse.FileType('r'))
sub_grobid_metadata.add_argument('--group-size',
help="editgroup group size to use",
default=75, type=int)
args = parser.parse_args()
if not args.__dict__.get("func"):
print("tell me what to do!")
sys.exit(-1)
args.api = authenticated_api(
args.host_url,
# token is an optional kwarg (can be empty string, None, etc)
token=os.environ.get(args.auth_var))
args.func(args)
if __name__ == '__main__':
main()
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