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authorBryan Newbold <bnewbold@archive.org>2020-05-26 19:43:44 -0700
committerBryan Newbold <bnewbold@archive.org>2020-05-26 19:43:46 -0700
commit79c3d690c12ad46d7ac7c2bfcded536dbbf5fe20 (patch)
tree59e1cef6660ed25d7f14fad9bac46c01cc68cb5c /python
parente96972ef531818eff610327a2a4c310a12ecdb14 (diff)
downloadsandcrawler-79c3d690c12ad46d7ac7c2bfcded536dbbf5fe20.tar.gz
sandcrawler-79c3d690c12ad46d7ac7c2bfcded536dbbf5fe20.zip
remove deprecated kafka_grobid.py worker
All use of pykafka was refactored to use the confluent library some time ago. And all kafka workers have been using the newer sandcrawler style worker for some time.
Diffstat (limited to 'python')
-rwxr-xr-xpython/kafka_grobid.py331
1 files changed, 0 insertions, 331 deletions
diff --git a/python/kafka_grobid.py b/python/kafka_grobid.py
deleted file mode 100755
index b0920bc..0000000
--- a/python/kafka_grobid.py
+++ /dev/null
@@ -1,331 +0,0 @@
-#!/usr/bin/env python3
-"""
-DEPRECATED: this worker uses old kafka topics and an old schema. Use
-`sandcrawler_worker.py` instead.
-
-Kafka worker that does GROBID extraction from one queue and into another.
-
-Based on the ungrobided Hadoop job code. Does not talk to HBase at all, just
-petabox and GROBID. Will delegate tasks to random GROBID workers.
-
-Lines (tasks) are enqueued using a trivial kafkacat invocation; output is
-persisted in Kakfa (in compressed format), and also drained into HBase by a
-second worker.
-
-Schema of tasks is the 'ungrobided' TSV output. Schema of output is JSON with
-keys:
-
- "key": SHA1 in base32 with prefix, eg, "sha1:DLCCSMMVTCCIR6LRXHEQLZ4PWO6NG2YT"
- "grobid0:status_code": HTTP status code (integer)
- "grobid0:status": dict/json
- "grobid0:tei_xml": xml as a single string
- "f:c": dict/json from input
- "file:mime": string from input
- "file:cdx": dict/json from input
- # NOT grobid0:tei_json, grobid0:metadata, or grobid0:quality, which can be
- # re-derived from tei_xml
-
-Requires:
-- requests
-- pykafka
-- wayback/GWB libraries
-"""
-
-# XXX: some broken MRO thing going on in here due to python3 object wrangling
-# in `wayback` library. Means we can't run pylint.
-# pylint: skip-file
-
-import os
-import sys
-import xml
-import json
-import raven
-import struct
-import argparse
-import requests
-import pykafka
-import wayback.exception
-from http.client import IncompleteRead
-from wayback.resourcestore import ResourceStore
-from gwb.loader import CDXLoaderFactory
-
-from common import parse_ungrobided_line
-from grobid2json import teixml2json
-
-# Yep, a global. Gets DSN from `SENTRY_DSN` environment variable
-sentry_client = raven.Client()
-
-# Specific poison-pill rows we should skip
-KEY_DENYLIST = (
- 'sha1:DLCCSMMVTCCIR6LRXHEQLZ4PWO6NG2YT', # "failed to guess ARC header format"
-)
-
-class KafkaGrobidWorker:
-
- def __init__(self, kafka_hosts, consume_topic, produce_topic, **kwargs):
- self.consume_topic = consume_topic
- self.produce_topic = produce_topic
- self.consumer_group = kwargs.get('consumer_group', 'grobid-extraction')
- self.kafka_hosts = kafka_hosts or 'localhost:9092'
- self.grobid_uri = kwargs.get('grobid_uri')
- # /serve/ instead of /download/ doesn't record view count
- self.petabox_base_url = kwargs.get('petabox_base_url', 'http://archive.org/serve/')
- # gwb library will fall back to reading from /opt/.petabox/webdata.secret
- self.petabox_webdata_secret = kwargs.get('petabox_webdata_secret', os.environ.get('PETABOX_WEBDATA_SECRET'))
- self.warc_uri_prefix = kwargs.get('warc_uri_prefix')
- self.mime_filter = ['application/pdf']
- self.rstore = None
- self.produce_max_request_size = 20000000 # Kafka producer batch size tuning; also limit on size of single extracted document
-
- def grobid_process_fulltext(self, content):
- r = requests.post(self.grobid_uri + "/api/processFulltextDocument",
- files={'input': content})
- return r
-
- def parse_line(self, raw_line):
- """Line should be TSV and have non-null fields:
-
- - key (string) (separated in Kafka case)
- - f:c (string, json)
- - file:mime (string)
- - file:cdx (string, json)
- """
-
- if (raw_line.startswith(' ') or raw_line.startswith('#') or raw_line.startswith('\t')):
- return None, dict(status="invalid", reason="line prefix", input=raw_line)
-
- info = parse_ungrobided_line(raw_line)
- if info is None:
- return None, dict(status="invalid", reason="ungrobided parse")
-
- if info['file:mime'] not in self.mime_filter:
- return None, dict(status="skip", reason="mimetype", mimetype=info['file:mime'])
-
- # If warc is not item/file.(w)arc.gz form, skip it
- if len(info['file:cdx']['warc'].split('/')) != 2:
- return None, dict(status="skip", reason="WARC path not petabox item/file", path=info['file:cdx']['warc'])
-
- return info, None
-
- def fetch_warc_content(self, warc_path, offset, c_size):
- warc_uri = self.warc_uri_prefix + warc_path
- if not self.rstore:
- self.rstore = ResourceStore(loaderfactory=CDXLoaderFactory(
- webdata_secret=self.petabox_webdata_secret,
- download_base_url=self.petabox_base_url))
- try:
- gwb_record = self.rstore.load_resource(warc_uri, offset, c_size)
- except wayback.exception.ResourceUnavailable:
- return None, dict(status="error",
- reason="failed to load file contents from wayback/petabox (ResourceUnavailable)")
- except ValueError as ve:
- return None, dict(status="error",
- reason="failed to load file contents from wayback/petabox (ValueError: {})".format(ve))
- except EOFError as eofe:
- return None, dict(status="error",
- reason="failed to load file contents from wayback/petabox (EOFError: {})".format(eofe))
- except TypeError as te:
- return None, dict(status="error",
- reason="failed to load file contents from wayback/petabox (TypeError: {}; likely a bug in wayback python code)".format(te))
- # Note: could consider a generic "except Exception" here, as we get so
- # many petabox errors. Do want jobs to fail loud and clear when the
- # whole cluster is down though.
-
- if gwb_record.get_status()[0] != 200:
- return None, dict(status="error",
- reason="archived HTTP response (WARC) was not 200",
- warc_status=gwb_record.get_status()[0])
-
- try:
- raw_content = gwb_record.open_raw_content().read()
- except IncompleteRead as ire:
- return None, dict(status="error",
- reason="failed to read actual file contents from wayback/petabox (IncompleteRead: {})".format(ire))
- return raw_content, None
-
- def extract(self, info):
-
- # Fetch data from WARCs in petabox
- original_content, status = self.fetch_warc_content(
- info['file:cdx']['warc'],
- info['file:cdx']['offset'],
- info['file:cdx']['c_size'])
- if status:
- return None, status
-
- info['file:size'] = len(original_content)
-
- # Submit to GROBID
- try:
- grobid_response = self.grobid_process_fulltext(original_content)
- except requests.exceptions.ConnectionError:
- return None, dict(status="error", reason="connection to GROBID worker")
-
- info['grobid0:status_code'] = grobid_response.status_code
-
- # 4 MByte XML size limit; don't record GROBID status on this path
- if len(grobid_response.content) > 4000000:
- info['grobid0:status'] = {'status': 'oversize'}
- return info, dict(status="oversize", reason="TEI response was too large")
-
- if grobid_response.status_code != 200:
- # response.text is .content decoded as utf-8
- info['grobid0:status'] = dict(status='error', description=grobid_response.text)
- return info, dict(status="error", reason="non-200 GROBID HTTP status",
- extra=grobid_response.text)
-
- info['grobid0:status'] = {'status': 'partial'}
- info['grobid0:tei_xml'] = grobid_response.content
- info['grobid0:status'] = {'status': 'success'}
-
- return info, None
-
- def do_work(self, raw_line):
- """
- 1. parse filtered line
- 2. fetch data from wayback
- 3. submit to GROBID
- 4. convert GROBID response to JSON (and metadata)
- 6. determine "quality"
- 6. produce result to kafka
-
- Returns: (grobid_output, status) (both are None or dict)
- If grobid_output is None, error was recovered, status returned.
- Otherwise, we were successful; grobid_output should be JSON serialized
- and published to kafka.
- """
-
- #self.increment_counter('lines', 'total')
-
- # Parse line and filter down
- info, status = self.parse_line(raw_line)
- if info is None:
- #self.increment_counter('lines', status['status'])
- return None, status
- key = info['key']
- if key in KEY_DENYLIST:
- #self.increment_counter('lines', 'denylist')
- return None, dict(status='denylist', key=key)
-
- # Note: this may not get "cleared" correctly
- sentry_client.extra_context(dict(
- row_key=key,
- cdx_url=info['file:cdx']['url'],
- cdx_dt=info['file:cdx']['dt'],
- cdx_warc=info['file:cdx']['warc'],
- ))
-
- # Do the extraction
- info, status = self.extract(info)
- if info is None:
- #self.increment_counter('lines', status['status'])
- status['key'] = key
- return None, status
- extraction_status = status
-
- # Need to encode 'bytes' as 'str' for JSON serialization
- if info.get('grobid0:tei_xml'):
- info['grobid0:tei_xml'] = info['grobid0:tei_xml'].decode('utf-8')
-
- #self.increment_counter('lines', 'success')
-
- grobid_status_code = info.get('grobid0:status_code', None)
- if extraction_status is not None:
- return info, dict(status="partial", key=key,
- grobid_status_code=grobid_status_code,
- reason=extraction_status['reason'])
- else:
- return info, dict(status="success",
- grobid_status_code=grobid_status_code, key=key,
- extra=extraction_status)
-
- def run(self):
-
- # 1. start consumer (in managed/balanced fashion, with consumer group)
- # 2. for each thingie, do the work; if success publish to kafka; either
- # way... print? log?
- # 3. repeat!
-
- print("Starting Kafka GROBID extraction worker...")
- kafka = pykafka.KafkaClient(hosts=self.kafka_hosts, broker_version="2.0.0")
- produce_topic = kafka.topics[self.produce_topic]
- consume_topic = kafka.topics[self.consume_topic]
-
- sequential_failures = 0
- # Configure producer to basically *immediately* publish messages,
- # one-at-a-time, but asynchronously (don't block). Fetch and GROBID
- # process takes a while, and we want to send as soon as processing is
- # done.
- with produce_topic.get_producer(sync=False,
- compression=pykafka.common.CompressionType.GZIP,
- retry_backoff_ms=250,
- max_queued_messages=50,
- min_queued_messages=10,
- linger_ms=5000,
- max_request_size=self.produce_max_request_size) as producer:
- print("Producing to: {}".format(self.produce_topic))
- consumer = consume_topic.get_balanced_consumer(
- consumer_group=self.consumer_group,
- managed=True,
- auto_commit_enable=True,
- auto_commit_interval_ms=30000, # 30 seconds
- # LATEST because best to miss processing than waste time re-process
- auto_offset_reset=pykafka.common.OffsetType.LATEST,
- queued_max_messages=50,
- compacted_topic=True)
- print("Consuming from: {} as {}".format(self.consume_topic, self.consumer_group))
- sys.stdout.flush()
- for msg in consumer:
- grobid_output, status = self.do_work(msg.value.decode('utf-8'))
- if grobid_output:
- print("extracted {}: {}".format(
- grobid_output.get('key'),
- status))
- sys.stdout.flush()
- producer.produce(json.dumps(grobid_output, sort_keys=True).encode('utf-8'))
- sequential_failures = 0
- else:
- print("failed to extract: {}".format(status), file=sys.stderr)
- sequential_failures += 1
- if sequential_failures > 20:
- print("too many failures in a row, bailing out", file=sys.stderr)
- sys.exit(-1)
-
-
-@sentry_client.capture_exceptions
-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('--kafka-env',
- default="qa",
- help="eg, 'qa' or 'prod'")
- parser.add_argument('--consume-topic',
- default=None,
- help="Kafka topic to consume from")
- parser.add_argument('--produce-topic',
- default=None,
- help="Kafka topic to produce to")
- parser.add_argument('--grobid-uri',
- type=str,
- default='http://localhost:8070',
- help='URI of GROBID API Server')
- parser.add_argument('--warc-uri-prefix',
- type=str,
- default='https://archive.org/serve/',
- help='URI where WARCs can be found')
- args = parser.parse_args()
-
- if args.consume_topic is None:
- args.consume_topic = "sandcrawler-{}.ungrobided".format(args.kafka_env)
- if args.produce_topic is None:
- args.produce_topic = "sandcrawler-{}.grobid-output".format(args.kafka_env)
-
- worker = KafkaGrobidWorker(**args.__dict__)
- worker.run()
-
-if __name__ == '__main__': # pragma: no cover
- main()