aboutsummaryrefslogtreecommitdiffstats
path: root/python_hadoop/extraction_cdx_grobid.py
blob: 88580e12452d07ac254affab160fa1821c437bd3 (plain)
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
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
#!/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 os
import xml
import json
import raven
import struct
import requests
import happybase
import mrjob
from mrjob.job import MRJob
import wayback.exception
from http.client import IncompleteRead
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()

# Specific poison-pill rows we should skip
KEY_DENYLIST = (
    'sha1:DLCCSMMVTCCIR6LRXHEQLZ4PWO6NG2YT',    # "failed to guess ARC header format"
)

class MRExtractCdxGrobid(MRJob):

    # CDX 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 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')
        self.add_passthru_arg('--force-existing',
                              action="store_true",
                              help='Re-processes (with GROBID) existing lines')

    def __init__(self, *args, **kwargs):
        super(MRExtractCdxGrobid, self).__init__(*args, **kwargs)
        self.hb_table = None
        self.petabox_webdata_secret = kwargs.get('petabox_webdata_secret', os.environ.get('PETABOX_WEBDATA_SECRET'))
        self.mime_filter = ['application/pdf']
        self.rstore = 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
        if not self.rstore:
            self.rstore = ResourceStore(loaderfactory=CDXLoaderFactory(
                webdata_secret=self.petabox_webdata_secret,
                download_base_url=self.options.warc_uri_prefix))
        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

        # Convert TEI XML to JSON
        try:
            info['grobid0:tei_json'] = teixml2json(info['grobid0:tei_xml'], encumbered=True)
        except xml.etree.ElementTree.ParseError:
            info['grobid0:status'] = dict(status="fail", reason="GROBID 200 XML parse error")
            return info, info['grobid0:status']
        except ValueError:
            info['grobid0:status'] = dict(status="fail", reason="GROBID 200 XML non-TEI content")
            return info, info['grobid0:status']

        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
        info['grobid0:status'] = {'status': 'success'}

        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']
        if key in KEY_DENYLIST:
            self.increment_counter('lines', 'denylist')
            yield _, dict(status='denylist', key=key)
            return

        # 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
                and not self.options.force_existing):
            # 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()