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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, args.json_file).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)
JsonLinePusher(fii, args.json_file).run()
def run_matched(args):
fmi = MatchedImporter(args.api,
edit_batch_size=args.batch_size)
JsonLinePusher(fmi, args.json_file).run()
def run_arabesque_matched(args):
ami = ArabesqueMatchImporter(args.api,
do_updates=args.do_updates,
extid_type=args.extid_type,
crawl_id=args.crawl_id,
default_link_rel=args.default_link_rel,
edit_batch_size=args.batch_size)
SqlitePusher(ami, args.db_file, "crawl_result",
ARABESQUE_MATCH_WHERE_CLAUSE).run()
def run_grobid_metadata(args):
fmi = GrobidMetadataImporter(args.api,
edit_batch_size=args.batch_size,
longtail_oa=args.longtail_oa,
bezerk_mode=args.bezerk_mode)
LinePusher(fmi, args.tsv_file).run()
def run_wayback_static(args):
api = args.api
# find the release
if args.release_id:
release_id = args.release_id
elif args.extid:
idtype = args.extid.split(':')[0]
extid = ':'.join(args.extid.split(':')[1:])
if idtype == "doi":
release_id = api.lookup_release(doi=extid).ident
elif idtype == "pmid":
release_id = api.lookup_release(pmid=extid).ident
elif idtype == "wikidata":
release_id = api.lookup_release(wikidata_qid=extid).ident
else:
raise NotImplementedError("extid type: {}".format(idtype))
else:
raise Exception("need either release_id or extid argument")
# create it
(editgroup_id, wc) = auto_wayback_static(api, release_id, args.wayback_url,
editgroup_id=args.editgroup_id)
if not wc:
return
print("release_id: {}".format(release_id))
print("editgroup_id: {}".format(editgroup_id))
print("webcapture id: {}".format(wc.ident))
print("link: https://fatcat.wiki/webcapture/{}".format(wc.ident))
def run_cdl_dash_dat(args):
api = args.api
# create it
(editgroup_id, release, fs) = auto_cdl_dash_dat(api, args.dat_path,
release_id=args.release_id, editgroup_id=args.editgroup_id)
if not fs:
return
print("release_id: {}".format(release.ident))
print("editgroup_id: {}".format(editgroup_id))
print("fileset id: {}".format(fs.ident))
print("link: https://fatcat.wiki/fileset/{}".format(fs.ident))
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)")
parser.add_argument('--batch-size',
help="size of batch to send",
default=50, type=int)
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('--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_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('json_file',
help="Journal JSON metadata file to import from (or stdin)",
default=sys.stdin, type=argparse.FileType('r'))
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('--bezerk-mode',
action='store_true',
help="don't lookup existing files, just insert (clobbers; only for fast bootstrap)")
sub_arabesque_matched = subparsers.add_parser('arabesque_matched')
sub_arabesque_matched.set_defaults(
func=run_arabesque_matched,
auth_var="FATCAT_API_AUTH_TOKEN",
)
sub_arabesque_matched.add_argument('db_file',
help="sqlite database file to import from")
sub_arabesque_matched.add_argument('--do-updates',
action='store_true',
help="update pre-existing file entities if new match (instead of skipping)")
sub_arabesque_matched.add_argument('--extid-type',
default="doi",
help="identifer type in the database (eg, 'doi', 'pmcid'")
sub_arabesque_matched.add_argument('--crawl-id',
help="crawl ID (optionally included in editgroup metadata)")
sub_arabesque_matched.add_argument('--default-link-rel',
help="default URL rel for matches (eg, 'publisher', 'web')")
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)
sub_grobid_metadata.add_argument('--longtail-oa',
action='store_true',
help="if this is an import of longtail OA content (sets an 'extra' flag)")
sub_grobid_metadata.add_argument('--bezerk-mode',
action='store_true',
help="don't lookup existing files, just insert (clobbers; only for fast bootstrap)")
sub_wayback_static = subparsers.add_parser('wayback-static')
sub_wayback_static.set_defaults(
func=run_wayback_static,
auth_var="FATCAT_API_AUTH_TOKEN",
)
sub_wayback_static.add_argument('wayback_url',
type=str,
help="URL of wayback capture to extract from")
sub_wayback_static.add_argument('--extid',
type=str,
help="external identifier for release lookup")
sub_wayback_static.add_argument('--release-id',
type=str,
help="release entity identifier")
sub_wayback_static.add_argument('--editgroup-id',
type=str,
help="use existing editgroup (instead of creating a new one)")
sub_cdl_dash_dat = subparsers.add_parser('cdl-dash-dat')
sub_cdl_dash_dat.set_defaults(
func=run_cdl_dash_dat,
auth_var="FATCAT_API_AUTH_TOKEN",
)
sub_cdl_dash_dat.add_argument('dat_path',
type=str,
help="local path dat to import (must be the dat discovery key)")
sub_cdl_dash_dat.add_argument('--release-id',
type=str,
help="release entity identifier")
sub_cdl_dash_dat.add_argument('--editgroup-id',
type=str,
help="use existing editgroup (instead of creating a new one)")
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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