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#!/usr/bin/env python3
import argparse
import datetime
import sys
import raven
from fatcat_tools.harvest import (
HarvestArxivWorker,
HarvestCrossrefWorker,
HarvestDataciteWorker,
HarvestDoajArticleWorker,
HarvestDoajJournalWorker,
PubmedFTPWorker,
)
# Yep, a global. Gets DSN from `SENTRY_DSN` environment variable
sentry_client = raven.Client()
def run_crossref(args: argparse.Namespace) -> None:
worker = HarvestCrossrefWorker(
kafka_hosts=args.kafka_hosts,
produce_topic=f"fatcat-{args.env}.api-crossref",
state_topic=f"fatcat-{args.env}.api-crossref-state",
contact_email=args.contact_email,
start_date=args.start_date,
end_date=args.end_date,
)
worker.run(continuous=args.continuous)
def run_datacite(args: argparse.Namespace) -> None:
worker = HarvestDataciteWorker(
kafka_hosts=args.kafka_hosts,
produce_topic=f"fatcat-{args.env}.api-datacite",
state_topic=f"fatcat-{args.env}.api-datacite-state",
contact_email=args.contact_email,
start_date=args.start_date,
end_date=args.end_date,
)
worker.run(continuous=args.continuous)
def run_arxiv(args: argparse.Namespace) -> None:
worker = HarvestArxivWorker(
kafka_hosts=args.kafka_hosts,
produce_topic=f"fatcat-{args.env}.oaipmh-arxiv",
state_topic=f"fatcat-{args.env}.oaipmh-arxiv-state",
start_date=args.start_date,
end_date=args.end_date,
)
worker.run(continuous=args.continuous)
def run_pubmed(args: argparse.Namespace) -> None:
worker = PubmedFTPWorker(
kafka_hosts=args.kafka_hosts,
produce_topic=f"fatcat-{args.env}.ftp-pubmed",
state_topic=f"fatcat-{args.env}.ftp-pubmed-state",
start_date=args.start_date,
end_date=args.end_date,
)
worker.run(continuous=args.continuous)
def run_doaj_article(args: argparse.Namespace) -> None:
worker = HarvestDoajArticleWorker(
kafka_hosts=args.kafka_hosts,
produce_topic=f"fatcat-{args.env}.oaipmh-doaj-article",
state_topic="fatcat-{args.env}.oaipmh-doaj-article-state",
start_date=args.start_date,
end_date=args.end_date,
)
worker.run(continuous=args.continuous)
def run_doaj_journal(args: argparse.Namespace) -> None:
worker = HarvestDoajJournalWorker(
kafka_hosts=args.kafka_hosts,
produce_topic=f"fatcat-{args.env}.oaipmh-doaj-journal",
state_topic=f"fatcat-{args.env}.oaipmh-doaj-journal-state",
start_date=args.start_date,
end_date=args.end_date,
)
worker.run(continuous=args.continuous)
def mkdate(raw: str) -> datetime.date:
return datetime.datetime.strptime(raw, "%Y-%m-%d").date()
def main() -> None:
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="beginning 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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