#!/usr/bin/env python3 import argparse import os import sys import sentry_sdk from fatcat_tools import authenticated_api from fatcat_tools.importers import ( ARABESQUE_MATCH_WHERE_CLAUSE, ArabesqueMatchImporter, ArxivRawImporter, Bs4XmlFileListPusher, Bs4XmlFilePusher, Bs4XmlLargeFilePusher, Bs4XmlLinesPusher, ChoculaImporter, CrossrefImporter, DataciteImporter, DblpContainerImporter, DblpReleaseImporter, DoajArticleImporter, FileMetaImporter, FilesetImporter, GrobidMetadataImporter, IngestFileResultImporter, IngestFilesetResultImporter, IngestWebResultImporter, JalcImporter, JournalMetadataImporter, JsonLinePusher, JstorImporter, KafkaBs4XmlPusher, KafkaJsonPusher, LinePusher, MatchedImporter, OrcidImporter, PubmedImporter, SavePaperNowFileImporter, SavePaperNowFilesetImporter, SavePaperNowWebImporter, ShadowLibraryImporter, SqlitePusher, ) def run_crossref(args: argparse.Namespace) -> None: fci = CrossrefImporter( args.api, args.issn_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-crossref".format(args.kafka_env), consume_batch_size=args.batch_size, ).run() else: JsonLinePusher(fci, args.json_file).run() def run_jalc(args: argparse.Namespace) -> None: ji = JalcImporter(args.api, args.issn_map_file) Bs4XmlLinesPusher(ji, args.xml_file, " None: ari = ArxivRawImporter(args.api, edit_batch_size=args.batch_size) if args.kafka_mode: KafkaBs4XmlPusher( ari, args.kafka_hosts, args.kafka_env, "oaipmh-arxiv", "fatcat-{}-import-arxiv".format(args.kafka_env), ).run() else: if args.xml_file == sys.stdin: print("note: reading from stdin", file=sys.stderr) Bs4XmlFilePusher(ari, args.xml_file, "record").run() def run_pubmed(args: argparse.Namespace) -> None: pi = PubmedImporter( args.api, args.issn_map_file, edit_batch_size=args.batch_size, do_updates=args.do_updates, lookup_refs=(not args.no_lookup_refs), ) if args.kafka_mode: KafkaBs4XmlPusher( pi, args.kafka_hosts, args.kafka_env, "ftp-pubmed", "fatcat-{}-import-pubmed".format(args.kafka_env), ).run() else: Bs4XmlLargeFilePusher( pi, args.xml_file, ["PubmedArticle"], ).run() def run_jstor(args: argparse.Namespace) -> None: ji = JstorImporter(args.api, args.issn_map_file, edit_batch_size=args.batch_size) Bs4XmlFileListPusher(ji, args.list_file, "article").run() def run_orcid(args: argparse.Namespace) -> None: foi = OrcidImporter(args.api, edit_batch_size=args.batch_size) JsonLinePusher(foi, args.json_file).run() def run_journal_metadata(args: argparse.Namespace) -> None: fii = JournalMetadataImporter(args.api, edit_batch_size=args.batch_size) JsonLinePusher(fii, args.json_file).run() def run_chocula(args: argparse.Namespace) -> None: fii = ChoculaImporter(args.api, edit_batch_size=args.batch_size, do_updates=args.do_updates) JsonLinePusher(fii, args.json_file).run() def run_matched(args: argparse.Namespace) -> None: fmi = MatchedImporter( args.api, edit_batch_size=args.batch_size, editgroup_description=args.editgroup_description_override, default_link_rel=args.default_link_rel, default_mimetype=args.default_mimetype, ) JsonLinePusher(fmi, args.json_file).run() def run_arabesque_match(args: argparse.Namespace) -> None: if (args.sqlite_file and args.json_file) or not (args.sqlite_file or args.json_file): print("Supply one of --sqlite-file or --json-file") ami = ArabesqueMatchImporter( args.api, editgroup_description=args.editgroup_description_override, do_updates=args.do_updates, require_grobid=(not args.no_require_grobid), extid_type=args.extid_type, crawl_id=args.crawl_id, default_link_rel=args.default_link_rel, edit_batch_size=args.batch_size, ) if args.sqlite_file: SqlitePusher(ami, args.sqlite_file, "crawl_result", ARABESQUE_MATCH_WHERE_CLAUSE).run() elif args.json_file: JsonLinePusher(ami, args.json_file).run() def run_ingest_file(args: argparse.Namespace) -> None: ifri = IngestFileResultImporter( args.api, editgroup_description=args.editgroup_description_override, skip_source_allowlist=args.skip_source_allowlist, do_updates=args.do_updates, default_link_rel=args.default_link_rel, require_grobid=(not args.no_require_grobid), edit_batch_size=args.batch_size, ) if args.kafka_mode: KafkaJsonPusher( ifri, args.kafka_hosts, args.kafka_env, "ingest-file-results", "fatcat-{}-ingest-file-result".format(args.kafka_env), kafka_namespace="sandcrawler", consume_batch_size=args.batch_size, ).run() else: JsonLinePusher(ifri, args.json_file).run() def run_ingest_web(args: argparse.Namespace) -> None: iwri = IngestWebResultImporter( args.api, editgroup_description=args.editgroup_description_override, skip_source_allowlist=args.skip_source_allowlist, do_updates=args.do_updates, default_link_rel=args.default_link_rel, edit_batch_size=args.batch_size, ) if args.kafka_mode: KafkaJsonPusher( iwri, args.kafka_hosts, args.kafka_env, "ingest-file-results", "fatcat-{}-ingest-web-result".format(args.kafka_env), kafka_namespace="sandcrawler", consume_batch_size=args.batch_size, force_flush=True, ).run() else: JsonLinePusher(iwri, args.json_file).run() def run_ingest_fileset(args: argparse.Namespace) -> None: ifri = IngestFilesetResultImporter( args.api, editgroup_description=args.editgroup_description_override, skip_source_allowlist=args.skip_source_allowlist, do_updates=args.do_updates, default_link_rel=args.default_link_rel, edit_batch_size=args.batch_size, ) if args.kafka_mode: KafkaJsonPusher( ifri, args.kafka_hosts, args.kafka_env, "ingest-fileset-results", "fatcat-{}-ingest-fileset-result".format(args.kafka_env), kafka_namespace="sandcrawler", consume_batch_size=args.batch_size, force_flush=True, ).run() else: JsonLinePusher(ifri, args.json_file).run() def run_savepapernow_file(args: argparse.Namespace) -> None: ifri = SavePaperNowFileImporter( args.api, editgroup_description=args.editgroup_description_override, edit_batch_size=args.batch_size, ) if args.kafka_mode: KafkaJsonPusher( ifri, args.kafka_hosts, args.kafka_env, "ingest-file-results", "fatcat-{}-savepapernow-file-result".format(args.kafka_env), kafka_namespace="sandcrawler", consume_batch_size=args.batch_size, force_flush=True, ).run() else: JsonLinePusher(ifri, args.json_file).run() def run_savepapernow_web(args: argparse.Namespace) -> None: ifri = SavePaperNowWebImporter( args.api, editgroup_description=args.editgroup_description_override, edit_batch_size=args.batch_size, ) if args.kafka_mode: KafkaJsonPusher( ifri, args.kafka_hosts, args.kafka_env, "ingest-file-results", "fatcat-{}-savepapernow-web-result".format(args.kafka_env), kafka_namespace="sandcrawler", consume_batch_size=args.batch_size, force_flush=True, ).run() else: JsonLinePusher(ifri, args.json_file).run() def run_savepapernow_fileset(args: argparse.Namespace) -> None: ifri = SavePaperNowFilesetImporter( args.api, editgroup_description=args.editgroup_description_override, edit_batch_size=args.batch_size, ) if args.kafka_mode: KafkaJsonPusher( ifri, args.kafka_hosts, args.kafka_env, "ingest-file-results", "fatcat-{}-savepapernow-fileset-result".format(args.kafka_env), kafka_namespace="sandcrawler", consume_batch_size=args.batch_size, force_flush=True, ).run() else: JsonLinePusher(ifri, args.json_file).run() def run_grobid_metadata(args: argparse.Namespace) -> None: 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_shadow_lib(args: argparse.Namespace) -> None: fmi = ShadowLibraryImporter(args.api, edit_batch_size=100) JsonLinePusher(fmi, args.json_file).run() def run_datacite(args: argparse.Namespace) -> None: dci = DataciteImporter( args.api, args.issn_map_file, edit_batch_size=args.batch_size, bezerk_mode=args.bezerk_mode, debug=args.debug, insert_log_file=args.insert_log_file, ) if args.kafka_mode: KafkaJsonPusher( dci, args.kafka_hosts, args.kafka_env, "api-datacite", "fatcat-{}-import-datacite".format(args.kafka_env), consume_batch_size=args.batch_size, ).run() else: JsonLinePusher(dci, args.json_file).run() def run_doaj_article(args: argparse.Namespace) -> None: dai = DoajArticleImporter( args.api, args.issn_map_file, edit_batch_size=args.batch_size, do_updates=args.do_updates, ) if args.kafka_mode: KafkaJsonPusher( dai, args.kafka_hosts, args.kafka_env, "api-doaj", "fatcat-{}-import-doaj".format(args.kafka_env), consume_batch_size=args.batch_size, ).run() else: JsonLinePusher(dai, args.json_file).run() def run_dblp_release(args: argparse.Namespace) -> None: dri = DblpReleaseImporter( args.api, dblp_container_map_file=args.dblp_container_map_file, edit_batch_size=args.batch_size, do_updates=args.do_updates, dump_json_mode=args.dump_json_mode, ) Bs4XmlLargeFilePusher( dri, args.xml_file, DblpReleaseImporter.ELEMENT_TYPES, use_lxml=True, ).run() def run_dblp_container(args: argparse.Namespace) -> None: dci = DblpContainerImporter( args.api, args.issn_map_file, dblp_container_map_file=args.dblp_container_map_file, dblp_container_map_output=args.dblp_container_map_output, edit_batch_size=args.batch_size, do_updates=args.do_updates, ) JsonLinePusher(dci, args.json_file).run() def run_file_meta(args: argparse.Namespace) -> None: # do_updates defaults to true for this importer fmi = FileMetaImporter( args.api, edit_batch_size=100, editgroup_description=args.editgroup_description_override, ) JsonLinePusher(fmi, args.json_file).run() def run_fileset(args: argparse.Namespace) -> None: fmi = FilesetImporter( args.api, edit_batch_size=100, skip_release_fileset_check=args.skip_release_fileset_check, ) JsonLinePusher(fmi, args.json_file).run() def main() -> None: parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter) 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="dev", help="Kafka topic namespace to use (eg, prod, qa)" ) parser.add_argument("--batch-size", help="size of batch to send", default=50, type=int) parser.add_argument( "--editgroup-description-override", help="editgroup description override", default=None, type=str, ) subparsers = parser.add_subparsers() sub_crossref = subparsers.add_parser( "crossref", help="import Crossref API metadata format (JSON)" ) 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( "--no-lookup-refs", action="store_true", help="skip lookup of references (PMID or DOI)" ) 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_jalc = subparsers.add_parser("jalc", help="import JALC DOI metadata from XML dump") sub_jalc.set_defaults( func=run_jalc, auth_var="FATCAT_AUTH_WORKER_JALC", ) sub_jalc.add_argument( "xml_file", help="Jalc RDF XML file (record-per-line) to import from", default=sys.stdin, type=argparse.FileType("r"), ) sub_jalc.add_argument( "issn_map_file", help="ISSN to ISSN-L mapping file", default=None, type=argparse.FileType("r"), ) sub_arxiv = subparsers.add_parser("arxiv", help="import arxiv.org metadata from XML files") sub_arxiv.set_defaults( func=run_arxiv, auth_var="FATCAT_AUTH_WORKER_ARXIV", ) sub_arxiv.add_argument( "xml_file", nargs="?", help="arXivRaw XML file to import from", default=sys.stdin, type=argparse.FileType("r"), ) sub_arxiv.add_argument( "--kafka-mode", action="store_true", help="consume from kafka topic (not stdin)" ) sub_pubmed = subparsers.add_parser( "pubmed", help="import MEDLINE/PubMed work-level metadata (XML)" ) sub_pubmed.set_defaults( func=run_pubmed, auth_var="FATCAT_AUTH_WORKER_PUBMED", ) sub_pubmed.add_argument( "xml_file", nargs="?", help="Pubmed XML file to import from", default=sys.stdin, type=argparse.FileType("r"), ) sub_pubmed.add_argument( "issn_map_file", help="ISSN to ISSN-L mapping file", default=None, type=argparse.FileType("r"), ) sub_pubmed.add_argument( "--no-lookup-refs", action="store_true", help="skip lookup of references (PMID or DOI)" ) sub_pubmed.add_argument( "--do-updates", action="store_true", help="update pre-existing release entities" ) sub_pubmed.add_argument( "--kafka-mode", action="store_true", help="consume from kafka topic (not stdin)" ) sub_jstor = subparsers.add_parser( "jstor", help="import JSTOR work-level metadata from XML dump" ) sub_jstor.set_defaults( func=run_jstor, auth_var="FATCAT_AUTH_WORKER_JSTOR", ) sub_jstor.add_argument( "list_file", help="List of JSTOR XML file paths to import from", default=sys.stdin, type=argparse.FileType("r"), ) sub_jstor.add_argument( "issn_map_file", help="ISSN to ISSN-L mapping file", default=None, type=argparse.FileType("r"), ) sub_orcid = subparsers.add_parser( "orcid", help="import creator entities from ORCID XML dump" ) 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", help="import/update container metadata from old manual munging format", ) 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_chocula = subparsers.add_parser( "chocula", help="import/update container metadata from chocula JSON export" ) sub_chocula.set_defaults( func=run_chocula, auth_var="FATCAT_AUTH_WORKER_JOURNAL_METADATA", ) sub_chocula.add_argument( "json_file", help="chocula JSON entities file (or stdin)", default=sys.stdin, type=argparse.FileType("r"), ) sub_chocula.add_argument( "--do-updates", action="store_true", help="update pre-existing container entities" ) sub_matched = subparsers.add_parser( "matched", help="add file entities matched against existing releases; custom JSON format", ) 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( "--default-mimetype", default=None, help="default mimetype for imported files (if not specified per-file)", ) sub_matched.add_argument( "--bezerk-mode", action="store_true", help="don't lookup existing files, just insert (clobbers; only for fast bootstrap)", ) sub_matched.add_argument( "--default-link-rel", default="web", help="default URL rel for matches (eg, 'publisher', 'web')", ) sub_arabesque_match = subparsers.add_parser( "arabesque", help="add file entities matched to releases from crawl log analysis" ) sub_arabesque_match.set_defaults( func=run_arabesque_match, auth_var="FATCAT_AUTH_WORKER_CRAWL", ) sub_arabesque_match.add_argument( "--sqlite-file", help="sqlite database file to import from" ) sub_arabesque_match.add_argument( "--json-file", help="JSON file to import from (or stdin)", type=argparse.FileType("r") ) sub_arabesque_match.add_argument( "--do-updates", action="store_true", help="update pre-existing file entities if new match (instead of skipping)", ) sub_arabesque_match.add_argument( "--no-require-grobid", action="store_true", help="whether postproc_status column must be '200'", ) sub_arabesque_match.add_argument( "--extid-type", default="doi", help="identifier type in the database (eg, 'doi', 'pmcid'", ) sub_arabesque_match.add_argument( "--crawl-id", help="crawl ID (optionally included in editgroup metadata)" ) sub_arabesque_match.add_argument( "--default-link-rel", default="web", help="default URL rel for matches (eg, 'publisher', 'web')", ) sub_ingest_file = subparsers.add_parser( "ingest-file-results", help="add/update file entities linked to releases based on sandcrawler ingest results", ) sub_ingest_file.set_defaults( func=run_ingest_file, auth_var="FATCAT_AUTH_WORKER_CRAWL", ) sub_ingest_file.add_argument( "json_file", help="ingest_file JSON file to import from", default=sys.stdin, type=argparse.FileType("r"), ) sub_ingest_file.add_argument( "--skip-source-allowlist", action="store_true", help="don't filter import based on request source allowlist", ) sub_ingest_file.add_argument( "--kafka-mode", action="store_true", help="consume from kafka topic (not stdin)" ) sub_ingest_file.add_argument( "--do-updates", action="store_true", help="update pre-existing file entities if new match (instead of skipping)", ) sub_ingest_file.add_argument( "--no-require-grobid", action="store_true", help="whether postproc_status column must be '200'", ) sub_ingest_file.add_argument( "--default-link-rel", default="web", help="default URL rel for matches (eg, 'publisher', 'web')", ) sub_ingest_web = subparsers.add_parser( "ingest-web-results", help="add/update web entities linked to releases based on sandcrawler ingest results", ) sub_ingest_web.set_defaults( func=run_ingest_web, auth_var="FATCAT_AUTH_WORKER_CRAWL", ) sub_ingest_web.add_argument( "json_file", help="ingest_web JSON file to import from", default=sys.stdin, type=argparse.FileType("r"), ) sub_ingest_web.add_argument( "--skip-source-allowlist", action="store_true", help="don't filter import based on request source allowlist", ) sub_ingest_web.add_argument( "--kafka-mode", action="store_true", help="consume from kafka topic (not stdin)" ) sub_ingest_web.add_argument( "--do-updates", action="store_true", help="update pre-existing web entities if new match (instead of skipping)", ) sub_ingest_web.add_argument( "--default-link-rel", default="web", help="default URL rel for matches (eg, 'publisher', 'web')", ) sub_ingest_fileset = subparsers.add_parser( "ingest-fileset-results", help="add/update fileset entities linked to releases based on sandcrawler ingest results", ) sub_ingest_fileset.set_defaults( func=run_ingest_fileset, auth_var="FATCAT_AUTH_WORKER_CRAWL", ) sub_ingest_fileset.add_argument( "json_file", help="ingest_fileset JSON file to import from", default=sys.stdin, type=argparse.FileType("r"), ) sub_ingest_fileset.add_argument( "--skip-source-allowlist", action="store_true", help="don't filter import based on request source allowlist", ) sub_ingest_fileset.add_argument( "--kafka-mode", action="store_true", help="consume from kafka topic (not stdin)" ) sub_ingest_fileset.add_argument( "--do-updates", action="store_true", help="update pre-existing fileset entities if new match (instead of skipping)", ) sub_ingest_fileset.add_argument( "--default-link-rel", default="fileset", help="default URL rel for matches (eg, 'publisher', 'web')", ) sub_savepapernow_file = subparsers.add_parser( "savepapernow-file-results", help="add file entities crawled due to async Save Paper Now request", ) sub_savepapernow_file.set_defaults( func=run_savepapernow_file, auth_var="FATCAT_AUTH_WORKER_SAVEPAPERNOW", ) sub_savepapernow_file.add_argument( "json_file", help="ingest-file JSON file to import from", default=sys.stdin, type=argparse.FileType("r"), ) sub_savepapernow_file.add_argument( "--kafka-mode", action="store_true", help="consume from kafka topic (not stdin)" ) sub_savepapernow_web = subparsers.add_parser( "savepapernow-web-results", help="add webcapture entities crawled due to async Save Paper Now request", ) sub_savepapernow_web.set_defaults( func=run_savepapernow_web, auth_var="FATCAT_AUTH_WORKER_SAVEPAPERNOW", ) sub_savepapernow_web.add_argument( "json_file", help="ingest-file JSON file to import from", default=sys.stdin, type=argparse.FileType("r"), ) sub_savepapernow_web.add_argument( "--kafka-mode", action="store_true", help="consume from kafka topic (not stdin)" ) sub_savepapernow_fileset = subparsers.add_parser( "savepapernow-fileset-results", help="add fileset entities crawled due to async Save Paper Now request", ) sub_savepapernow_fileset.set_defaults( func=run_savepapernow_fileset, auth_var="FATCAT_AUTH_WORKER_SAVEPAPERNOW", ) sub_savepapernow_fileset.add_argument( "json_file", help="ingest-file JSON file to import from", default=sys.stdin, type=argparse.FileType("r"), ) sub_savepapernow_fileset.add_argument( "--kafka-mode", action="store_true", help="consume from kafka topic (not stdin)" ) sub_grobid_metadata = subparsers.add_parser( "grobid-metadata", help="create release and file entities based on GROBID PDF metadata extraction", ) 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_shadow_lib = subparsers.add_parser( "shadow-lib", help="create release and file entities based on GROBID PDF metadata extraction", ) sub_shadow_lib.set_defaults( func=run_shadow_lib, auth_var="FATCAT_AUTH_WORKER_SHADOW", ) sub_shadow_lib.add_argument( "json_file", help="JSON file to import from (or stdin)", default=sys.stdin, type=argparse.FileType("r"), ) sub_datacite = subparsers.add_parser("datacite", help="import datacite.org metadata") sub_datacite.add_argument( "json_file", help="File with jsonlines from datacite.org v2 API to import from", default=sys.stdin, type=argparse.FileType("r"), ) sub_datacite.add_argument( "issn_map_file", help="ISSN to ISSN-L mapping file", default=None, type=argparse.FileType("r"), ) sub_datacite.add_argument( "--kafka-mode", action="store_true", help="consume from kafka topic (not stdin)" ) sub_datacite.add_argument( "--bezerk-mode", action="store_true", help="don't lookup existing DOIs, just insert (clobbers; only for fast bootstrap)", ) sub_datacite.add_argument( "--debug", action="store_true", help="write converted JSON to stdout" ) sub_datacite.add_argument( "--insert-log-file", default="", type=str, help="write inserted documents into file (for debugging)", ) sub_datacite.set_defaults( func=run_datacite, auth_var="FATCAT_AUTH_WORKER_DATACITE", ) sub_doaj_article = subparsers.add_parser( "doaj-article", help="import doaj.org article metadata" ) sub_doaj_article.add_argument( "json_file", help="File with JSON lines from DOAJ API (or bulk dump) to import from", default=sys.stdin, type=argparse.FileType("r"), ) sub_doaj_article.add_argument( "--issn-map-file", help="ISSN to ISSN-L mapping file", default=None, type=argparse.FileType("r"), ) sub_doaj_article.add_argument( "--kafka-mode", action="store_true", help="consume from kafka topic (not stdin)" ) sub_doaj_article.add_argument( "--do-updates", action="store_true", help="update any pre-existing release entities" ) sub_doaj_article.set_defaults( func=run_doaj_article, auth_var="FATCAT_AUTH_WORKER_DOAJ", ) sub_dblp_release = subparsers.add_parser( "dblp-release", help="import dblp release metadata" ) sub_dblp_release.add_argument( "xml_file", help="File with DBLP XML to import from", default=sys.stdin, type=argparse.FileType("rb"), ) sub_dblp_release.add_argument( "--dblp-container-map-file", help="file path to dblp prefix to container_id TSV file", default=None, type=argparse.FileType("r"), ) sub_dblp_release.add_argument( "--do-updates", action="store_true", help="update any pre-existing release entities" ) sub_dblp_release.add_argument( "--dump-json-mode", action="store_true", help="print release entities to stdout instead of importing", ) sub_dblp_release.set_defaults( func=run_dblp_release, auth_var="FATCAT_AUTH_WORKER_DBLP", ) sub_dblp_container = subparsers.add_parser( "dblp-container", help="import dblp container metadata" ) sub_dblp_container.add_argument( "json_file", help="File with DBLP container JSON to import from (see extra/dblp/)", default=sys.stdin, type=argparse.FileType("rb"), ) sub_dblp_container.add_argument( "--dblp-container-map-file", help="file path to dblp pre-existing prefix to container_id TSV file", default=None, type=argparse.FileType("r"), ) sub_dblp_container.add_argument( "--dblp-container-map-output", help="file path to output new dblp container map TSV to", default=None, type=argparse.FileType("w"), ) sub_dblp_container.add_argument( "--issn-map-file", help="ISSN to ISSN-L mapping file", default=None, type=argparse.FileType("r"), ) sub_dblp_container.add_argument( "--do-updates", action="store_true", help="update any pre-existing container entities" ) sub_dblp_container.set_defaults( func=run_dblp_container, auth_var="FATCAT_AUTH_WORKER_DBLP", ) sub_file_meta = subparsers.add_parser( "file-meta", help="simple update-only importer for file metadata" ) sub_file_meta.set_defaults( func=run_file_meta, auth_var="FATCAT_API_AUTH_TOKEN", ) sub_file_meta.add_argument( "json_file", help="File with jsonlines from file_meta schema to import from", default=sys.stdin, type=argparse.FileType("r"), ) sub_fileset = subparsers.add_parser("fileset", help="generic fileset importer") sub_fileset.set_defaults( func=run_fileset, auth_var="FATCAT_API_AUTH_TOKEN", ) sub_fileset.add_argument( "json_file", help="File with jsonlines of fileset entities to import", default=sys.stdin, type=argparse.FileType("r"), ) sub_fileset.add_argument( "--skip-release-fileset-check", action="store_true", help="create without checking if releases already have related filesets", ) args = parser.parse_args() if not args.__dict__.get("func"): print("tell me what to do!") sys.exit(-1) # allow editgroup description override via env variable (but CLI arg takes # precedence) if not args.editgroup_description_override and os.environ.get( "FATCAT_EDITGROUP_DESCRIPTION" ): args.editgroup_description_override = os.environ.get("FATCAT_EDITGROUP_DESCRIPTION") 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), ) sentry_sdk.init(environment=args.env) args.func(args) if __name__ == "__main__": main()