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#!/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()
|