1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
|
#!/usr/bin/env python3
"""
Streaming Hadoop script to import extract metadata and body from fulltext (eg,
PDF) files using GROBID. Input is a CDX file; results primarly go to HBase,
with status written to configurable output stream.
Fulltext files are loaded directly from WARC files in petabox, instead of going
through the wayback replay.
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 requests
import happybase
import mrjob
from mrjob.job import MRJob
import wayback.exception
from wayback.resource import Resource
from wayback.resource import ArcResource
from wayback.resourcestore import ResourceStore
from gwb.loader import CDXLoaderFactory
from common import parse_cdx_line
from grobid2json import teixml2json
# Yep, a global. Gets DSN from `SENTRY_DSN` environment variable
sentry_client = raven.Client()
class MRExtractCdxGrobid(MRJob):
# CDX lines in; JSON status out
INPUT_PROTOCOL = mrjob.protocol.RawValueProtocol
OUTPUT_PROTOCOL = mrjob.protocol.JSONValueProtocol
def configure_args(self):
super(MRExtractCdxGrobid, self).configure_args()
self.add_passthru_arg('--hbase-table',
type=str,
default='wbgrp-journal-extract-0-qa',
help='HBase table to backfill into (must exist)')
self.add_passthru_arg('--hbase-host',
type=str,
default='localhost',
help='HBase thrift API host to connect to')
self.add_passthru_arg('--grobid-uri',
type=str,
default='http://localhost:8070',
help='URI of GROBID API Server')
self.add_passthru_arg('--warc-uri-prefix',
type=str,
default='https://archive.org/serve/',
help='URI where WARCs can be found')
def __init__(self, *args, **kwargs):
super(MRExtractCdxGrobid, self).__init__(*args, **kwargs)
self.mime_filter = ['application/pdf']
self.hb_table = None
def grobid_process_fulltext(self, content):
r = requests.post(self.options.grobid_uri + "/api/processFulltextDocument",
files={'input': content})
return r
def mapper_init(self):
if self.hb_table:
return
sentry_client.tags_context(dict(hbase_table=self.options.hbase_table))
try:
host = self.options.hbase_host
# TODO: make these configs accessible from... mrconf.cfg?
hb_conn = happybase.Connection(host=host, transport="framed",
protocol="compact")
except Exception:
raise Exception("Couldn't connect to HBase using host: {}".format(host))
self.hb_table = hb_conn.table(self.options.hbase_table)
def parse_line(self, raw_cdx):
if (raw_cdx.startswith(' ') or raw_cdx.startswith('filedesc') or
raw_cdx.startswith('#')):
return None, dict(status="invalid", reason="line prefix")
info = parse_cdx_line(raw_cdx)
if info is None:
return None, dict(status="invalid", reason="CDX parse")
if info['file:mime'] not in self.mime_filter:
return None, dict(status="skip", reason="mimetype")
# 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")
return info, None
def fetch_warc_content(self, warc_path, offset, c_size):
warc_uri = self.options.warc_uri_prefix + warc_path
try:
rstore = ResourceStore(loaderfactory=CDXLoaderFactory())
gwb_record = 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")
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])
return gwb_record.open_raw_content().read(), 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
if grobid_response.status_code != 200:
# response.text is .content decoded as utf-8
info['grobid0:status'] = dict(description=grobid_response.text)
return info, dict(status="error", reason="non-200 GROBID HTTP status",
extra=grobid_response.text)
info['grobid0:status'] = {'status': 'success'}
info['grobid0:tei_xml'] = grobid_response.content
# Convert TEI XML to JSON
try:
info['grobid0:tei_json'] = teixml2json(grobid_response.content, encumbered=True)
except xml.etree.ElementTree.ParseError:
return info, dict(status="fail", reason="GROBID 200 XML parse error")
except ValueError:
return info, dict(status="fail", reason="GROBID 200 XML non-TEI content")
tei_metadata = info['grobid0:tei_json'].copy()
for k in ('body', 'annex'):
# Remove fulltext (copywritted) content
tei_metadata.pop(k, None)
info['grobid0:metadata'] = tei_metadata
# Determine extraction "quality"
# TODO:
info['grobid0:quality'] = None
return info, None
@sentry_client.capture_exceptions
def mapper(self, _, raw_cdx):
"""
1. parse CDX line
2. check what is already in hbase
3. fetch data from wayback
4. submit to GROBID
5. convert GROBID response to JSON (and metadata)
6. determine "quality"
7. push results to hbase
"""
self.increment_counter('lines', 'total')
# Parse line and filter down
info, status = self.parse_line(raw_cdx)
if info is None:
self.increment_counter('lines', status['status'])
yield _, status
return
key = info['key']
# Note: this may not get "cleared" correctly
sentry_client.extra_context(dict(row_key=key))
# Check if we've already processed this line
oldrow = self.hb_table.row(key,
columns=[b'f:c', b'file', b'grobid0:status_code'])
if oldrow.get(b'grobid0:status_code', None) != None:
# This file has already been processed; skip it
self.increment_counter('lines', 'existing')
yield _, dict(status="existing", key=key)
return
# 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
# Particularly: ('f:c', 'file:mime', 'file:size', 'file:cdx')
grobid_status_code = info.get('grobid0:status_code', None)
for k in list(info.keys()):
if k.encode('utf-8') in oldrow:
info.pop(k)
# Convert fields to binary
for k in list(info.keys()):
if info[k] is None:
info.pop(k)
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()
|
