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#!/usr/bin/env python3
import sys
import argparse
import datetime
import raven
from fatcat_tools.harvest import HarvestCrossrefWorker, HarvestDataciteWorker,\
HarvestArxivWorker, HarvestPubmedWorker, HarvestDoajArticleWorker,\
HarvestDoajJournalWorker, PubmedFTPWorker
# Yep, a global. Gets DSN from `SENTRY_DSN` environment variable
sentry_client = raven.Client()
def run_crossref(args):
worker = HarvestCrossrefWorker(
kafka_hosts=args.kafka_hosts,
produce_topic="fatcat-{}.api-crossref".format(args.env),
state_topic="fatcat-{}.api-crossref-state".format(args.env),
contact_email=args.contact_email,
start_date=args.start_date,
end_date=args.end_date)
worker.run(continuous=args.continuous)
def run_datacite(args):
worker = HarvestDataciteWorker(
kafka_hosts=args.kafka_hosts,
produce_topic="fatcat-{}.api-datacite".format(args.env),
state_topic="fatcat-{}.api-datacite-state".format(args.env),
contact_email=args.contact_email,
start_date=args.start_date,
end_date=args.end_date)
worker.run(continuous=args.continuous)
def run_arxiv(args):
worker = HarvestArxivWorker(
kafka_hosts=args.kafka_hosts,
produce_topic="fatcat-{}.oaipmh-arxiv".format(args.env),
state_topic="fatcat-{}.oaipmh-arxiv-state".format(args.env),
start_date=args.start_date,
end_date=args.end_date)
worker.run(continuous=args.continuous)
def run_pubmed(args):
# worker = HarvestPubmedWorker(
# kafka_hosts=args.kafka_hosts,
# produce_topic="fatcat-{}.oaipmh-pubmed".format(args.env),
# state_topic="fatcat-{}.oaipmh-pubmed-state".format(args.env),
# start_date=args.start_date,
# end_date=args.end_date)
# worker.run(continuous=args.continuous)
worker = PubmedFTPWorker(
kafka_hosts=args.kafka_hosts,
produce_topic="fatcat-{}.ftp-pubmed".format(args.env),
state_topic="fatcat-{}.ftp-pubmed-state".format(args.env),
start_date=args.start_date,
end_date=args.end_date)
worker.run(continuous=args.continuous)
def run_doaj_article(args):
worker = HarvestDoajArticleWorker(
kafka_hosts=args.kafka_hosts,
produce_topic="fatcat-{}.oaipmh-doaj-article".format(args.env),
state_topic="fatcat-{}.oaipmh-doaj-article-state".format(args.env),
start_date=args.start_date,
end_date=args.end_date)
worker.run(continuous=args.continuous)
def run_doaj_journal(args):
worker = HarvestDoajJournalWorker(
kafka_hosts=args.kafka_hosts,
produce_topic="fatcat-{}.oaipmh-doaj-journal".format(args.env),
state_topic="fatcat-{}.oaipmh-doaj-journal-state".format(args.env),
start_date=args.start_date,
end_date=args.end_date)
worker.run(continuous=args.continuous)
def mkdate(raw):
return datetime.datetime.strptime(raw, "%Y-%m-%d").date()
def main():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--kafka-hosts',
default="localhost:9092",
help="list of Kafka brokers (host/port) to use")
parser.add_argument('--env',
default="dev",
help="Kafka topic namespace to use (eg, prod, qa, dev)")
parser.add_argument('--start-date',
default=None, type=mkdate,
help="begining of harvest period")
parser.add_argument('--end-date',
default=None, type=mkdate,
help="end of harvest period")
parser.add_argument('--contact-email',
default="undefined", # better?
help="contact email to use in API header")
parser.add_argument('--continuous',
action='store_true',
help="continue harvesting indefinitely in a loop?")
subparsers = parser.add_subparsers()
sub_crossref = subparsers.add_parser('crossref',
help="harvest DOI metadata from Crossref API (JSON)")
sub_crossref.set_defaults(func=run_crossref)
sub_datacite = subparsers.add_parser('datacite',
help="harvest DOI metadata from Datacite API (JSON)")
sub_datacite.set_defaults(func=run_datacite)
sub_arxiv = subparsers.add_parser('arxiv',
help="harvest metadata from arxiv.org OAI-PMH endpoint (XML)")
sub_arxiv.set_defaults(func=run_arxiv)
sub_pubmed = subparsers.add_parser('pubmed',
help="harvest MEDLINE/PubMed metadata from daily FTP updates (XML)")
sub_pubmed.set_defaults(func=run_pubmed)
# DOAJ stuff disabled because API range-requests are broken
#sub_doaj_article = subparsers.add_parser('doaj-article')
#sub_doaj_article.set_defaults(func=run_doaj_article)
#sub_doaj_journal = subparsers.add_parser('doaj-journal')
#sub_doaj_journal.set_defaults(func=run_doaj_journal)
args = parser.parse_args()
if not args.__dict__.get("func"):
print("tell me what to do!")
sys.exit(-1)
args.func(args)
if __name__ == '__main__':
main()
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