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
|
#!/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
"""
import io
import sys
import json
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 do_tei
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')
def __init__(self, *args, **kwargs):
# Allow passthrough for tests
if 'hb_table' in kwargs:
self.hb_table = kwargs.pop('hb_table')
else:
self.hb_table = None
super(MRExtractCdxGrobid, self).__init__(*args, **kwargs)
self.mime_filter = ['application/pdf']
def grobid_process_fulltext(self, content):
r = requests.post(self.options.grobid_uri + "/api/processFulltextDocument",
files={'input': content})
if r.status_code is not 200:
# XXX:
return None
return r
def mapper_init(self):
if self.hb_table is None:
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 as err:
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:
self.increment_counter('lines', 'skip')
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:
self.increment_counter('lines', 'skip')
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):
try:
rstore = ResourceStore(loaderfactory=CDXLoaderFactory())
gwb_record = rstore.load_resource(warc_path, offset, c_size)
except wayback.exception.ResourceUnavailable as err:
# XXX: during testing
raise err
self.increment_counter('lines', 'petabox_error')
return None, dict(status="petabox_error", reason="failed to load file contents")
if gwb_record.get_status()[0] != 200:
self.increment_counter('lines', 'error')
return None, dict(status="error", reason="non-HTTP-200 WARC content")
return gwb_record.open_raw_content()
def extract(self, info):
# Fetch data from WARCs in petabox
content, status = self.fetch_warc_content(
info['file:cdx']['warc'],
info['file:cdx']['offset'],
info['file:cdx']['c_size'])
if status:
self.increment_counter('lines', status['status'])
return None, status
info['file:size'] = len(content)
# Submit to GROBID
try:
grobid_response = self.grobid_process_fulltext(content)
except IOError as ioe:
raise ioe
# XXX: catch correct error
self.increment_counter('lines', 'fail')
return None, dict(status="fail", reason="GROBID connection")
info['grobid0:status_code'] = grobid_response.status_code
info['grobid0:tei_xml'] = grobid_response.content
info['grobid0:status'] = {} # TODO
# Convert TEI XML to JSON
# TODO:
info['grobid0:tei_json'] = do_tei(grobid_response.content, encumbered=True)
info['grobid0:metadata'] = do_tei(grobid_response.content, encumbered=False)
# Determine extraction "quality"
# TODO:
info['grobid0:quality'] = None
return info, None
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
# Check if we've already processed this line
oldrow = self.hb_table.row(info['key'], columns=['f', 'file',
'grobid:status_code'])
if oldrow.get('grobid0:status', None):
# This file has already been processed; skip it
self.increment_counter('lines', 'existing')
yield _, dict(status="existing")
return
# Do the extraction
info, status = self.extract(info)
if info is None:
self.increment_counter('lines', status['status'])
yield _, status
return
# Decide what to bother inserting back into HBase
# Particularly: ('f:c', 'file:mime', 'file:size', 'file:cdx')
grobid_status = info.get('grobid0:status_code', None)
for k in list(info.keys()):
if k in oldrow:
info.pop(k)
# Convert fields to binary
for k in list(info.keys()):
if info[k] == 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')
yield _, dict(status="success", grobid_status=grobid_status)
if __name__ == '__main__': # pragma: no cover
MRExtractCdxGrobid.run()
|
