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#!/usr/bin/env python3
"""
Variant of extraction_cdx_grobid which takes a partial metadata list as input
instead of CDX.
This task list is dumped by another Hadoop job which scans over the HBase table
quickly, which allows this job to skip a (relatively) expensive HBase read
per-row.
Requires:
- happybase
- mrjob
- 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 xml
import json
import raven
import struct
import mrjob
from common import parse_ungrobided_line
from extraction_cdx_grobid import MRExtractCdxGrobid, KEY_BLACKLIST, \
sentry_client
class MRExtractUnGrobided(MRExtractCdxGrobid):
# "ungrobided" TSV lines in; JSON status out
#HADOOP_INPUT_FORMAT = 'org.apache.hadoop.mapred.lib.NLineInputFormat'
#INPUT_PROTOCOL = mrjob.protocol.RawProtocol
INPUT_PROTOCOL = mrjob.protocol.RawValueProtocol
OUTPUT_PROTOCOL = mrjob.protocol.JSONValueProtocol
def parse_ungrobided_line(self, raw_line):
"""Line should be TSV and have non-null fields:
- key (string)
- f:c (string, json)
- file:mime (string)
- file:cdx (string, json)
"""
if (raw_line.startswith(' ') or raw_line.startswith('#')):
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
@sentry_client.capture_exceptions
def mapper(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. push results to hbase
"""
self.increment_counter('lines', 'total')
# Parse line and filter down
info, status = self.parse_ungrobided_line(raw_line)
if info is None:
self.increment_counter('lines', status['status'])
yield _, status
return
key = info['key']
if key in KEY_BLACKLIST:
self.increment_counter('lines', 'blacklist')
yield _, dict(status='blacklist', key=key)
return
# Note: this may not get "cleared" correctly
sentry_client.extra_context(dict(row_key=key))
# Do the extraction
info, status = self.extract(info)
if info is None:
self.increment_counter('lines', status['status'])
status['key'] = key
yield _, status
return
extraction_status = status
# Decide what to bother inserting back into HBase
# Basically, don't overwrite backfill fields.
grobid_status_code = info.get('grobid0:status_code', None)
for k in list(info.keys()):
if k.encode('utf-8') in ('f:c', 'file:mime', 'file:cdx'):
info.pop(k)
# Convert fields to binary
for k in list(info.keys()):
if info[k] is None:
info.pop(k)
# NOTE: we're not actually sending these f:*, file:* keys...
elif k in ('f:c', 'file:cdx', 'grobid0:status', 'grobid0:tei_json',
'grobid0:metadata'):
assert type(info[k]) == dict
info[k] = json.dumps(info[k], sort_keys=True, indent=None)
elif k in ('file:size', 'grobid0:status_code'):
# encode as int64 in network byte order
if info[k] != {} and info[k] != None:
info[k] = struct.pack('!q', info[k])
key = info.pop('key')
self.hb_table.put(key, info)
self.increment_counter('lines', 'success')
if extraction_status is not None:
yield _, dict(status="partial", key=key,
grobid_status_code=grobid_status_code,
reason=extraction_status['reason'])
else:
yield _, dict(status="success",
grobid_status_code=grobid_status_code, key=key,
extra=extraction_status)
if __name__ == '__main__': # pragma: no cover
MRExtractCdxGrobid.run()
|
