#!/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 - """ import sys import json import argparse import datetime from grobid2json import teixml2json from sandcrawler import * def run_extract_json(args): grobid_client = GrobidClient(host_url=args.grobid_host) wayback_client = WaybackClient() if args.jobs > 1: worker = GrobidWorker(grobid_client, wayback_client, sink=None) multi_worker = MultiprocessWrapper(worker, args.sink) pusher = JsonLinePusher(multi_worker, args.json_file, batch_size=args.jobs) else: worker = GrobidWorker(grobid_client, wayback_client, sink=args.sink) pusher = JsonLinePusher(worker, args.json_file) pusher.run() def run_extract_cdx(args): grobid_client = GrobidClient(host_url=args.grobid_host) wayback_client = WaybackClient() if args.jobs > 1: worker = GrobidWorker(grobid_client, wayback_client, sink=None) multi_worker = MultiprocessWrapper(worker, args.sink) pusher = CdxLinePusher( multi_worker, args.cdx_file, filter_http_statuses=[200, 226], filter_mimetypes=['application/pdf'], batch_size=args.jobs, ) else: worker = GrobidWorker(grobid_client, wayback_client, sink=args.sink) pusher = CdxLinePusher( worker, args.cdx_file, filter_http_statuses=[200, 226], filter_mimetypes=['application/pdf'], ) pusher.run() def run_extract_zipfile(args): grobid_client = GrobidClient(host_url=args.grobid_host) if args.jobs > 1: print("multi-processing: {}".format(args.jobs), file=sys.stderr) worker = GrobidBlobWorker(grobid_client, sink=None) multi_worker = MultiprocessWrapper(worker, args.sink, jobs=args.jobs) pusher = ZipfilePusher(multi_worker, args.zip_file, batch_size=args.jobs) else: worker = GrobidBlobWorker(grobid_client, sink=args.sink) pusher = ZipfilePusher(worker, args.zip_file) pusher.run() def run_transform(args): grobid_client = GrobidClient() for line in args.json_file: if not line.strip(): continue line = json.loads(line) if args.metadata_only: out = grobid_client.metadata(line) else: out = teixml2json(line['tei_xml']) if out: if 'source' in line: out['source'] = line['source'] print(json.dumps(out)) 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', 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") 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_extract_json.set_defaults(func=run_extract_json) sub_extract_json.add_argument('json_file', help="JSON file to import from (or '-' for stdin)", 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.set_defaults(func=run_extract_cdx) sub_extract_cdx.add_argument('cdx_file', help="CDX file to import from (or '-' for stdin)", 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.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_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', help="convert TEI-XML to JSON. Input is JSON lines with tei_xml field", type=argparse.FileType('r')) args = parser.parse_args() if not args.__dict__.get("func"): parser.print_help(file=sys.stderr) sys.exit(-1) args.sink = None 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.func(args) if __name__ == '__main__': main()