diff options
Diffstat (limited to 'python/sandcrawler_worker.py')
| -rwxr-xr-x | python/sandcrawler_worker.py | 495 |
1 files changed, 495 insertions, 0 deletions
diff --git a/python/sandcrawler_worker.py b/python/sandcrawler_worker.py new file mode 100755 index 0000000..aebcbe1 --- /dev/null +++ b/python/sandcrawler_worker.py @@ -0,0 +1,495 @@ +#!/usr/bin/env python3 +""" +These are generally for continuously running workers that consume from Kafka. +Outputs might either be pushed back into Kafka, or directly into sandcrawler-db +or S3 (SeaweedFS). +""" + +import argparse +import os +import subprocess +import sys + +import sentry_sdk + +from sandcrawler import * +from sandcrawler.persist import ( + PersistCrossrefWorker, + PersistHtmlTeiXmlWorker, + PersistXmlDocWorker, +) + + +def run_grobid_extract(args): + consume_topic = "sandcrawler-{}.ungrobided-pg".format(args.env) + produce_topic = "sandcrawler-{}.grobid-output-pg".format(args.env) + sink = KafkaSink( + kafka_hosts=args.kafka_hosts, + produce_topic=produce_topic, + ) + grobid_client = GrobidClient( + host_url=args.grobid_host, + ) + wayback_client = WaybackClient( + host_url=args.grobid_host, + ) + worker = GrobidWorker( + grobid_client=grobid_client, + wayback_client=wayback_client, + sink=sink, + ) + pusher = KafkaJsonPusher( + worker=worker, + kafka_hosts=args.kafka_hosts, + consume_topic=consume_topic, + group="grobid-extract", + batch_size=1, + ) + pusher.run() + + +def run_pdf_extract(args): + consume_topic = "sandcrawler-{}.unextracted".format(args.env) + pdftext_topic = "sandcrawler-{}.pdf-text".format(args.env) + thumbnail_topic = "sandcrawler-{}.pdf-thumbnail-180px-jpg".format(args.env) + pdftext_sink = KafkaCompressSink( + kafka_hosts=args.kafka_hosts, + produce_topic=pdftext_topic, + ) + thumbnail_sink = KafkaSink( + kafka_hosts=args.kafka_hosts, + produce_topic=thumbnail_topic, + ) + wayback_client = WaybackClient( + host_url=args.grobid_host, + ) + worker = PdfExtractWorker( + wayback_client=wayback_client, + sink=pdftext_sink, + thumbnail_sink=thumbnail_sink, + ) + pusher = KafkaJsonPusher( + worker=worker, + kafka_hosts=args.kafka_hosts, + consume_topic=consume_topic, + group="pdf-extract", + batch_size=1, + push_timeout_sec=120, + ) + pusher.run() + + +def run_persist_grobid(args): + consume_topic = "sandcrawler-{}.grobid-output-pg".format(args.env) + worker = PersistGrobidWorker( + db_url=args.db_url, + s3_url=args.s3_url, + s3_bucket=args.s3_bucket, + s3_access_key=args.s3_access_key, + s3_secret_key=args.s3_secret_key, + s3_only=args.s3_only, + db_only=args.db_only, + ) + kafka_group = "persist-grobid" + if args.s3_only: + kafka_group += "-s3" + if args.kafka_group_suffix: + kafka_group += args.kafka_group_suffix + pusher = KafkaJsonPusher( + worker=worker, + kafka_hosts=args.kafka_hosts, + consume_topic=consume_topic, + group=kafka_group, + push_batches=True, + batch_size=25, + ) + pusher.run() + + +def run_persist_pdftext(args): + consume_topic = "sandcrawler-{}.pdf-text".format(args.env) + worker = PersistPdfTextWorker( + db_url=args.db_url, + s3_url=args.s3_url, + s3_bucket=args.s3_bucket, + s3_access_key=args.s3_access_key, + s3_secret_key=args.s3_secret_key, + s3_only=args.s3_only, + db_only=args.db_only, + ) + kafka_group = "persist-pdf-text" + if args.s3_only: + kafka_group += "-s3" + if args.kafka_group_suffix: + kafka_group += args.kafka_group_suffix + pusher = KafkaJsonPusher( + worker=worker, + kafka_hosts=args.kafka_hosts, + consume_topic=consume_topic, + group=kafka_group, + push_batches=True, + batch_size=25, + ) + pusher.run() + + +def run_persist_thumbnail(args): + consume_topic = "sandcrawler-{}.pdf-thumbnail-180px-jpg".format(args.env) + worker = PersistThumbnailWorker( + s3_url=args.s3_url, + s3_bucket=args.s3_bucket, + s3_access_key=args.s3_access_key, + s3_secret_key=args.s3_secret_key, + s3_extension=".180px.jpg", + s3_folder="pdf", + ) + kafka_group = "persist-pdf-thumbnail" + if args.kafka_group_suffix: + kafka_group += args.kafka_group_suffix + pusher = KafkaJsonPusher( + worker=worker, + kafka_hosts=args.kafka_hosts, + consume_topic=consume_topic, + group=kafka_group, + push_batches=False, + raw_records=True, + batch_size=25, + ) + pusher.run() + + +def run_persist_xml_doc(args: argparse.Namespace) -> None: + consume_topic = f"sandcrawler-{args.env}.xml-doc" + worker = PersistXmlDocWorker( + s3_url=args.s3_url, + s3_bucket=args.s3_bucket, + s3_access_key=args.s3_access_key, + s3_secret_key=args.s3_secret_key, + ) + kafka_group = "persist-xml-doc" + if args.kafka_group_suffix: + kafka_group += args.kafka_group_suffix + pusher = KafkaJsonPusher( + worker=worker, + kafka_hosts=args.kafka_hosts, + consume_topic=consume_topic, + group=kafka_group, + push_batches=False, + batch_size=25, + ) + pusher.run() + + +def run_persist_html_teixml(args: argparse.Namespace) -> None: + consume_topic = f"sandcrawler-{args.env}.html-teixml" + worker = PersistHtmlTeiXmlWorker( + s3_url=args.s3_url, + s3_bucket=args.s3_bucket, + s3_access_key=args.s3_access_key, + s3_secret_key=args.s3_secret_key, + ) + kafka_group = "persist-html-teixml" + if args.kafka_group_suffix: + kafka_group += args.kafka_group_suffix + pusher = KafkaJsonPusher( + worker=worker, + kafka_hosts=args.kafka_hosts, + consume_topic=consume_topic, + group=kafka_group, + push_batches=False, + batch_size=25, + ) + pusher.run() + + +def run_persist_pdftrio(args): + consume_topic = "sandcrawler-{}.pdftrio-output".format(args.env) + worker = PersistPdfTrioWorker( + db_url=args.db_url, + ) + pusher = KafkaJsonPusher( + worker=worker, + kafka_hosts=args.kafka_hosts, + consume_topic=consume_topic, + group="persist-pdftrio", + push_batches=True, + batch_size=100, + ) + pusher.run() + + +def run_ingest_file(args): + spn_cdx_retry_sec = 9.0 + if args.bulk: + consume_group = "sandcrawler-{}-ingest-file-bulk".format(args.env) + consume_topic = "sandcrawler-{}.ingest-file-requests-bulk".format(args.env) + elif args.priority: + spn_cdx_retry_sec = 45.0 + consume_group = "sandcrawler-{}-ingest-file-priority".format(args.env) + consume_topic = "sandcrawler-{}.ingest-file-requests-priority".format(args.env) + else: + spn_cdx_retry_sec = 1.0 + consume_group = "sandcrawler-{}-ingest-file".format(args.env) + consume_topic = "sandcrawler-{}.ingest-file-requests-daily".format(args.env) + produce_topic = "sandcrawler-{}.ingest-file-results".format(args.env) + grobid_topic = "sandcrawler-{}.grobid-output-pg".format(args.env) + pdftext_topic = "sandcrawler-{}.pdf-text".format(args.env) + thumbnail_topic = "sandcrawler-{}.pdf-thumbnail-180px-jpg".format(args.env) + xmldoc_topic = "sandcrawler-{}.xml-doc".format(args.env) + htmlteixml_topic = "sandcrawler-{}.html-teixml".format(args.env) + sink = KafkaSink( + kafka_hosts=args.kafka_hosts, + produce_topic=produce_topic, + ) + grobid_sink = KafkaSink( + kafka_hosts=args.kafka_hosts, + produce_topic=grobid_topic, + ) + grobid_client = GrobidClient( + host_url=args.grobid_host, + ) + pdftext_sink = KafkaCompressSink( + kafka_hosts=args.kafka_hosts, + produce_topic=pdftext_topic, + ) + thumbnail_sink = KafkaSink( + kafka_hosts=args.kafka_hosts, + produce_topic=thumbnail_topic, + ) + xmldoc_sink = KafkaSink( + kafka_hosts=args.kafka_hosts, + produce_topic=xmldoc_topic, + ) + htmlteixml_sink = KafkaSink( + kafka_hosts=args.kafka_hosts, + produce_topic=htmlteixml_topic, + ) + worker = IngestFileWorker( + grobid_client=grobid_client, + sink=sink, + grobid_sink=grobid_sink, + thumbnail_sink=thumbnail_sink, + pdftext_sink=pdftext_sink, + xmldoc_sink=xmldoc_sink, + htmlteixml_sink=htmlteixml_sink, + # don't SPNv2 for --bulk or --skip-spn + try_spn2=not (args.bulk or args.skip_spn), + spn_cdx_retry_sec=spn_cdx_retry_sec, + ) + pusher = KafkaJsonPusher( + worker=worker, + kafka_hosts=args.kafka_hosts, + consume_topic=consume_topic, + group=consume_group, + batch_size=1, + ) + pusher.run() + + +def run_persist_ingest_file(args): + consume_topic = "sandcrawler-{}.ingest-file-results".format(args.env) + worker = PersistIngestFileResultWorker( + db_url=args.db_url, + ) + pusher = KafkaJsonPusher( + worker=worker, + kafka_hosts=args.kafka_hosts, + consume_topic=consume_topic, + group="persist-ingest", + push_batches=True, + batch_size=100, + ) + pusher.run() + + +def run_persist_crossref(args): + batch_size = 200 + if args.parse_refs: + batch_size = 10 + grobid_client = GrobidClient(host_url=args.grobid_host) + consume_topic = "fatcat-{}.api-crossref".format(args.env) + worker = PersistCrossrefWorker( + db_url=args.db_url, + grobid_client=grobid_client, + parse_refs=args.parse_refs, + ) + pusher = KafkaJsonPusher( + worker=worker, + kafka_hosts=args.kafka_hosts, + consume_topic=consume_topic, + group="persist-crossref", + push_batches=True, + # small batch size because doing GROBID processing + batch_size=batch_size, + ) + pusher.run() + + +def main(): + parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter) + parser.add_argument( + "--kafka-hosts", + default="localhost:9092", + help="list of Kafka brokers (host/port) to use", + ) + parser.add_argument( + "--env", default="dev", help="Kafka topic namespace to use (eg, prod, qa, dev)" + ) + parser.add_argument( + "--kafka-group-suffix", default="", help="Kafka consumer group suffix (optional)" + ) + parser.add_argument( + "--grobid-host", default="https://grobid.qa.fatcat.wiki", help="GROBID API host/port" + ) + parser.add_argument( + "--db-url", + help="postgresql database connection string", + default="postgres:///sandcrawler", + ) + parser.add_argument("--s3-url", help="S3 (seaweedfs) backend URL", default="localhost:9000") + parser.add_argument( + "--s3-access-key", + help="S3 (seaweedfs) credential", + default=os.environ.get("SANDCRAWLER_BLOB_ACCESS_KEY") + or os.environ.get("MINIO_ACCESS_KEY"), + ) + parser.add_argument( + "--s3-secret-key", + help="S3 (seaweedfs) credential", + default=os.environ.get("SANDCRAWLER_BLOB_SECRET_KEY") + or os.environ.get("MINIO_SECRET_KEY"), + ) + parser.add_argument( + "--s3-bucket", help="S3 (seaweedfs) bucket to persist into", default="sandcrawler-dev" + ) + subparsers = parser.add_subparsers() + + sub_grobid_extract = subparsers.add_parser( + "grobid-extract", + help="daemon that consumes CDX JSON objects from Kafka, uses GROBID to extract XML, pushes to Kafka", + ) + sub_grobid_extract.set_defaults(func=run_grobid_extract) + + sub_pdf_extract = subparsers.add_parser( + "pdf-extract", + help="daemon that consumes CDX JSON objects from Kafka, extracts text and thumbnail, pushes to Kafka", + ) + sub_pdf_extract.set_defaults(func=run_pdf_extract) + + sub_persist_grobid = subparsers.add_parser( + "persist-grobid", + help="daemon that consumes GROBID output from Kafka and pushes to S3 (seaweedfs) and postgres", + ) + sub_persist_grobid.add_argument( + "--s3-only", + action="store_true", + help="only upload TEI-XML to S3 (don't write to database)", + ) + sub_persist_grobid.add_argument( + "--db-only", + action="store_true", + help="only write status to database (don't upload TEI-XML to S3)", + ) + sub_persist_grobid.set_defaults(func=run_persist_grobid) + + sub_persist_pdftext = subparsers.add_parser( + "persist-pdftext", + help="daemon that consumes pdftext output from Kafka and pushes to S3 (seaweedfs) and postgres", + ) + sub_persist_pdftext.add_argument( + "--s3-only", + action="store_true", + help="only upload TEI-XML to S3 (don't write to database)", + ) + sub_persist_pdftext.add_argument( + "--db-only", + action="store_true", + help="only write status to database (don't upload TEI-XML to S3)", + ) + sub_persist_pdftext.set_defaults(func=run_persist_pdftext) + + sub_persist_thumbnail = subparsers.add_parser( + "persist-thumbnail", + help="daemon that consumes thumbnail output from Kafka and pushes to S3 (seaweedfs) and postgres", + ) + sub_persist_thumbnail.set_defaults(func=run_persist_thumbnail) + + sub_persist_xml_doc = subparsers.add_parser( + "persist-xml-doc", + help="daemon that consumes xml-doc output from Kafka and pushes to S3 (seaweedfs) bucket", + ) + sub_persist_xml_doc.set_defaults(func=run_persist_xml_doc) + + sub_persist_html_teixml = subparsers.add_parser( + "persist-html-teixml", + help="daemon that consumes html-teixml output from Kafka and pushes to S3 (seaweedfs) bucket", + ) + sub_persist_html_teixml.set_defaults(func=run_persist_html_teixml) + + sub_persist_pdftrio = subparsers.add_parser( + "persist-pdftrio", + help="daemon that consumes pdftrio output from Kafka and pushes to postgres", + ) + sub_persist_pdftrio.set_defaults(func=run_persist_pdftrio) + + sub_ingest_file = subparsers.add_parser( + "ingest-file", + help="daemon that consumes requests from Kafka, ingests, pushes results to Kafka", + ) + sub_ingest_file.add_argument( + "--bulk", + action="store_true", + help="consume from bulk kafka topic (eg, for ingest backfill)", + ) + sub_ingest_file.add_argument( + "--skip-spn", + action="store_true", + help="don't do SPN lookups", + ) + sub_ingest_file.add_argument( + "--priority", + action="store_true", + help="consume from priority kafka topic (eg, for SPN requests)", + ) + sub_ingest_file.set_defaults(func=run_ingest_file) + + sub_persist_ingest_file = subparsers.add_parser( + "persist-ingest-file", + help="daemon that consumes ingest-file output from Kafka and pushes to postgres", + ) + sub_persist_ingest_file.set_defaults(func=run_persist_ingest_file) + + sub_persist_crossref = subparsers.add_parser( + "persist-crossref", + help="daemon that persists crossref to postgres; also does GROBID ref transform", + ) + sub_persist_crossref.add_argument( + "--grobid-host", default="https://grobid.qa.fatcat.wiki", help="GROBID API host/port" + ) + sub_persist_crossref.add_argument( + "--parse-refs", + action="store_true", + help="use GROBID to parse any unstructured references (default is to not)", + ) + sub_persist_crossref.set_defaults(func=run_persist_crossref) + + args = parser.parse_args() + if not args.__dict__.get("func"): + parser.print_help(file=sys.stderr) + sys.exit(-1) + + # configure sentry *after* parsing args + try: + GIT_REVISION = ( + subprocess.check_output(["git", "describe", "--always"]).strip().decode("utf-8") + ) + except Exception: + print("failed to configure git revision", file=sys.stderr) + GIT_REVISION = None + sentry_sdk.init(release=GIT_REVISION, environment=args.env, max_breadcrumbs=10) + + args.func(args) + + +if __name__ == "__main__": + main() |