diff options
Diffstat (limited to 'python/grobid_tool.py')
| -rwxr-xr-x | python/grobid_tool.py | 149 |
1 files changed, 99 insertions, 50 deletions
diff --git a/python/grobid_tool.py b/python/grobid_tool.py index 2a1d8b5..3ffac98 100755 --- a/python/grobid_tool.py +++ b/python/grobid_tool.py @@ -1,21 +1,28 @@ #!/usr/bin/env python3 - """ These are generally for running one-off tasks from the command line. Output might go to stdout, or might go to Kafka topic. Example of large parallel run, locally: - cat /srv/sandcrawler/tasks/ungrobided.2019-09-23.json | pv -l | parallel -j30 --pipe ./grobid_tool.py --kafka-env prod --kafka-hosts wbgrp-svc263.us.archive.org:9092,wbgrp-svc284.us.archive.org:9092,wbgrp-svc285.us.archive.org:9092 --kafka-mode --grobid-host http://localhost:8070 -j0 extract-json - + cat /srv/sandcrawler/tasks/ungrobided.2019-09-23.json | pv -l | parallel -j30 --pipe ./grobid_tool.py --kafka-env prod --kafka-hosts wbgrp-svc350.us.archive.org:9092,wbgrp-svc284.us.archive.org:9092,wbgrp-svc285.us.archive.org:9092 --kafka-mode --grobid-host http://localhost:8070 -j0 extract-json - """ -import sys -import json import argparse -import datetime +import json +import sys + +from grobid_tei_xml import parse_document_xml -from grobid2json import teixml2json from sandcrawler import * +from sandcrawler.grobid import CrossrefRefsWorker + + +def run_single(args): + grobid_client = GrobidClient(host_url=args.grobid_host) + resp = grobid_client.process_fulltext(blob=args.pdf_file.read()) + resp["_metadata"] = grobid_client.metadata(resp) + print(json.dumps(resp, sort_keys=True)) def run_extract_json(args): @@ -30,6 +37,7 @@ def run_extract_json(args): pusher = JsonLinePusher(worker, args.json_file) pusher.run() + def run_extract_cdx(args): grobid_client = GrobidClient(host_url=args.grobid_host) wayback_client = WaybackClient() @@ -40,7 +48,7 @@ def run_extract_cdx(args): multi_worker, args.cdx_file, filter_http_statuses=[200, 226], - filter_mimetypes=['application/pdf'], + filter_mimetypes=["application/pdf"], batch_size=args.jobs, ) else: @@ -49,10 +57,11 @@ def run_extract_cdx(args): worker, args.cdx_file, filter_http_statuses=[200, 226], - filter_mimetypes=['application/pdf'], + filter_mimetypes=["application/pdf"], ) pusher.run() + def run_extract_zipfile(args): grobid_client = GrobidClient(host_url=args.grobid_host) if args.jobs > 1: @@ -65,6 +74,7 @@ def run_extract_zipfile(args): pusher = ZipfilePusher(worker, args.zip_file) pusher.run() + def run_transform(args): grobid_client = GrobidClient() for line in args.json_file: @@ -74,62 +84,101 @@ def run_transform(args): if args.metadata_only: out = grobid_client.metadata(line) else: - out = teixml2json(line['tei_xml']) + tei_doc = parse_document_xml(line["tei_xml"]) + out = tei_doc.to_legacy_dict() if out: - if 'source' in line: - out['source'] = line['source'] + if "source" in line: + out["source"] = line["source"] print(json.dumps(out)) +def run_parse_crossref_refs(args): + grobid_client = GrobidClient(host_url=args.grobid_host) + worker = CrossrefRefsWorker(grobid_client, sink=args.sink) + pusher = JsonLinePusher(worker, args.json_file) + pusher.run() + + def main(): - parser = argparse.ArgumentParser( - formatter_class=argparse.ArgumentDefaultsHelpFormatter) - parser.add_argument('--kafka-mode', - action='store_true', - help="send output to Kafka (not stdout)") - parser.add_argument('--kafka-hosts', + parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter) + parser.add_argument( + "--kafka-mode", action="store_true", help="send output to Kafka (not stdout)" + ) + 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, dev)") - parser.add_argument('-j', '--jobs', - default=8, type=int, - help="parallelism for batch CPU jobs") - parser.add_argument('--grobid-host', - default="http://grobid.qa.fatcat.wiki", - help="GROBID API host/port") + 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, dev)" + ) + parser.add_argument( + "-j", "--jobs", default=8, type=int, help="parallelism for batch CPU jobs" + ) + parser.add_argument( + "--grobid-host", default="https://grobid.qa.fatcat.wiki", help="GROBID API host/port" + ) subparsers = parser.add_subparsers() - sub_extract_json = subparsers.add_parser('extract-json', - help="for each JSON line with CDX info, fetches PDF and does GROBID extraction") + sub_single = subparsers.add_parser("single") + sub_single.set_defaults(func=run_single) + sub_single.add_argument( + "pdf_file", + help="path to PDF file to process", + type=argparse.FileType("rb"), + ) + + sub_extract_json = subparsers.add_parser( + "extract-json", + help="for each JSON line with CDX info, fetches PDF and does GROBID extraction", + ) sub_extract_json.set_defaults(func=run_extract_json) - sub_extract_json.add_argument('json_file', + sub_extract_json.add_argument( + "json_file", help="JSON file to import from (or '-' for stdin)", - type=argparse.FileType('r')) + type=argparse.FileType("r"), + ) - sub_extract_cdx = subparsers.add_parser('extract-cdx', - help="for each CDX line, fetches PDF and does GROBID extraction") + sub_extract_cdx = subparsers.add_parser( + "extract-cdx", help="for each CDX line, fetches PDF and does GROBID extraction" + ) sub_extract_cdx.set_defaults(func=run_extract_cdx) - sub_extract_cdx.add_argument('cdx_file', + sub_extract_cdx.add_argument( + "cdx_file", help="CDX file to import from (or '-' for stdin)", - type=argparse.FileType('r')) + type=argparse.FileType("r"), + ) - sub_extract_zipfile = subparsers.add_parser('extract-zipfile', - help="opens zipfile, iterates over PDF files inside and does GROBID extract for each") + sub_extract_zipfile = subparsers.add_parser( + "extract-zipfile", + help="opens zipfile, iterates over PDF files inside and does GROBID extract for each", + ) sub_extract_zipfile.set_defaults(func=run_extract_zipfile) - sub_extract_zipfile.add_argument('zip_file', - help="zipfile with PDFs to extract", - type=str) - - sub_transform = subparsers.add_parser('transform') + sub_extract_zipfile.add_argument("zip_file", help="zipfile with PDFs to extract", type=str) + + sub_parse_crossref_refs = subparsers.add_parser( + "parse-crossref-refs", + help="reads Crossref metadata records, parses any unstructured refs with GROBID", + ) + sub_parse_crossref_refs.set_defaults(func=run_parse_crossref_refs) + sub_parse_crossref_refs.add_argument( + "json_file", + help="JSON-L file to process (or '-' for stdin)", + type=argparse.FileType("r"), + ) + + sub_transform = subparsers.add_parser("transform") sub_transform.set_defaults(func=run_transform) - sub_transform.add_argument('--metadata-only', - action='store_true', - help="Only pass through bibliographic metadata, not fulltext") - sub_transform.add_argument('json_file', + sub_transform.add_argument( + "--metadata-only", + action="store_true", + help="Only pass through bibliographic metadata, not fulltext", + ) + sub_transform.add_argument( + "json_file", help="convert TEI-XML to JSON. Input is JSON lines with tei_xml field", - type=argparse.FileType('r')) + type=argparse.FileType("r"), + ) args = parser.parse_args() if not args.__dict__.get("func"): @@ -140,10 +189,10 @@ def main(): if args.kafka_mode: produce_topic = "sandcrawler-{}.grobid-output-pg".format(args.kafka_env) print("Running in kafka output mode, publishing to {}\n".format(produce_topic)) - args.sink = KafkaCompressSink(kafka_hosts=args.kafka_hosts, - produce_topic=produce_topic) + args.sink = KafkaCompressSink(kafka_hosts=args.kafka_hosts, produce_topic=produce_topic) args.func(args) -if __name__ == '__main__': + +if __name__ == "__main__": main() |