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#!/usr/bin/env python3
"""
"""
import os, sys, argparse
from fatcat_tools import authenticated_api
from fatcat_tools.importers import CrossrefImporter, OrcidImporter, \
JournalMetadataImporter, MatchedImporter, GrobidMetadataImporter, make_kafka_consumer
def run_crossref(args):
fci = CrossrefImporter(args.api, args.issn_map_file,
extid_map_file=args.extid_map_file,
create_containers=(not args.no_create_containers),
check_existing=(not args.no_release_updates))
if args.kafka_mode:
consumer = make_kafka_consumer(
args.kafka_hosts, args.kafka_env, "api-crossref", "fatcat-import")
fci.process_batch(consumer, size=args.batch_size, decode_kafka=True)
else:
fci.process_batch(args.json_file, size=args.batch_size)
fci.describe_run()
def run_orcid(args):
foi = OrcidImporter(args.api)
foi.process_batch(args.json_file, size=args.batch_size)
foi.describe_run()
def run_journal_metadata(args):
fii = JournalMetadataImporter(args.api)
fii.process_csv_batch(args.csv_file, size=args.batch_size)
fii.describe_run()
def run_matched(args):
fmi = MatchedImporter(args.api,
skip_file_updates=args.no_file_updates)
fmi.process_batch(args.json_file, size=args.batch_size)
fmi.describe_run()
def run_grobid_metadata(args):
fmi = GrobidMetadataImporter(args.api)
fmi.process_source(args.tsv_file, group_size=args.group_size)
fmi.describe_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('--no-create-containers',
action='store_true',
help="skip creation of new container entities based on ISSN")
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('--no-release-updates',
action='store_true',
help="don't lookup existing DOIs, just insert (only for 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_AUTH_WORKER_MATCHED",
)
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('--no-file-updates',
action='store_true',
help="don't lookup existing files, just insert (only for bootstrap)")
sub_matched.add_argument('--batch-size',
help="size of batch to send",
default=50, type=int)
sub_grobid_metadata = subparsers.add_parser('grobid-metadata')
sub_grobid_metadata.set_defaults(
func=run_grobid_metadata,
auth_var="FATCAT_AUTH_WORKER_GROBID_METADATA",
)
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=os.environ.get(args.auth_var))
args.func(args)
if __name__ == '__main__':
main()
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