1 files changed, 149 insertions, 0 deletions
diff --git a/python/grobid_tool.py b/python/grobid_tool.py
new file mode 100755
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+++ b/python/grobid_tool.py
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+#!/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()