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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-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 argparse
import json
import sys
from grobid_tei_xml import parse_document_xml
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):
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:
tei_doc = parse_document_xml(line["tei_xml"])
out = tei_doc.to_legacy_dict()
if out:
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",
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="https://grobid.qa.fatcat.wiki", help="GROBID API host/port"
)
subparsers = parser.add_subparsers()
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",
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_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",
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()
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