#!/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()