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
|
import io
import json
import mrjob
import pytest
import struct
import responses
import happybase_mock
import wayback.exception
from unittest import mock
from extraction_cdx_grobid import MRExtractCdxGrobid, Resource
FAKE_PDF_BYTES = b"%PDF SOME JUNK" + struct.pack("!q", 112853843)
OK_CDX_LINE = b"""com,sagepub,cep)/content/28/9/960.full.pdf 20170705062200 http://cep.sagepub.com/content/28/9/960.full.pdf application/pdf 200 ABCDEF12345Q2MSVX7XZKYAYSCX5QBYJ - - 401 313356621 CITESEERX-CRAWL-2017-06-20-20170705061647307-00039-00048-wbgrp-svc284/CITESEERX-CRAWL-2017-06-20-20170705062052659-00043-31209~wbgrp-svc284.us.archive.org~8443.warc.gz"""
@pytest.fixture
def job():
"""
Note: this mock only seems to work with job.run_mapper(), not job.run();
the later results in a separate instantiation without the mock?
"""
job = MRExtractCdxGrobid(['--no-conf', '-'])
conn = happybase_mock.Connection()
conn.create_table('wbgrp-journal-extract-test',
{'file': {}, 'grobid0': {}, 'f': {}})
job.hb_table = conn.table('wbgrp-journal-extract-test')
return job
@mock.patch('extraction_cdx_grobid.MRExtractCdxGrobid.fetch_warc_content', return_value=(FAKE_PDF_BYTES, None))
@responses.activate
def test_mapper_lines(mock_fetch, job):
with open('tests/files/23b29ea36382680716be08fc71aa81bd226e8a85.xml', 'r') as f:
real_tei_xml = f.read()
responses.add(responses.POST, 'http://localhost:8070/api/processFulltextDocument', status=200,
body=real_tei_xml, content_type='text/xml')
raw = io.BytesIO(b"""
com,sagepub,cep)/content/28/9/960.full.pdf 20170705062200 http://cep.sagepub.com/content/28/9/960.full.pdf application/pdf 301 3I42H3S6NNFQ2MSVX7XZKYAYSCX5QBYJ - - 401 313356621 CITESEERX-CRAWL-2017-06-20-20170705061647307-00039-00048-wbgrp-svc284/CITESEERX-CRAWL-2017-06-20-20170705062052659-00043-31209~wbgrp-svc284.us.archive.org~8443.warc.gz
eu,eui,cadmus)/bitstream/handle/1814/36635/rscas_2015_03.pdf;jsessionid=761393014319a39f40d32ae3eb3a853f?sequence=1 20170705062202 http://cadmus.eui.eu/bitstream/handle/1814/36635/RSCAS_2015_03.pdf%3Bjsessionid%3D761393014319A39F40D32AE3EB3A853F?sequence%3D1 application/PDF 200 MPCXVWMUTRUGFP36SLPHKDLY6NGU4S3J - - 854156 328850624 CITESEERX-CRAWL-2017-06-20-20170705061647307-00039-00048-wbgrp-svc284/CITESEERX-CRAWL-2017-06-20-20170705062052659-00043-31209~wbgrp-svc284.us.archive.org~8443.warc.gz
com,pbworks,educ333b)/robots.txt 20170705063311 http://educ333b.pbworks.com/robots.txt text/plain 200 6VAUYENMOU2SK2OWNRPDD6WTQTECGZAD - - 638 398190140 CITESEERX-CRAWL-2017-06-20-20170705062707827-00049-00058-wbgrp-svc284/CITESEERX-CRAWL-2017-06-20-20170705063158203-00053-31209~wbgrp-svc284.us.archive.org~8443.warc.gz
""")
output = io.BytesIO()
job.sandbox(stdin=raw, stdout=output)
job.run_mapper()
# for debugging tests
#print(output.getvalue().decode('utf-8'))
#print(list(job.hb_table.scan()))
# wayback gets FETCH 1x times
mock_fetch.assert_called_once_with(
"CITESEERX-CRAWL-2017-06-20-20170705061647307-00039-00048-wbgrp-svc284/CITESEERX-CRAWL-2017-06-20-20170705062052659-00043-31209~wbgrp-svc284.us.archive.org~8443.warc.gz",
328850624,
854156)
# grobid gets POST 1x times
assert len(responses.calls) == 1
# HBase
assert job.hb_table.row(b'1') == {}
# HTTP 301
assert job.hb_table.row(b'sha1:3I42H3S6NNFQ2MSVX7XZKYAYSCX5QBYJ') == {}
# valid
assert job.hb_table.row(b'sha1:MPCXVWMUTRUGFP36SLPHKDLY6NGU4S3J') != {}
# text/plain
assert job.hb_table.row(b'sha1:6VAUYENMOU2SK2OWNRPDD6WTQTECGZAD') == {}
# Saved extraction info
row = job.hb_table.row(b'sha1:MPCXVWMUTRUGFP36SLPHKDLY6NGU4S3J')
assert struct.unpack("!q", row[b'file:size'])[0] == len(FAKE_PDF_BYTES)
assert row[b'file:mime'] == b"application/pdf"
assert struct.unpack("!q", row[b'grobid0:status_code'])[0] == 200
# TODO: assert row[b'grobid0:quality'] == None
status = json.loads(row[b'grobid0:status'].decode('utf-8'))
assert type(status) == type(dict())
assert row[b'grobid0:tei_xml'].decode('utf-8') == real_tei_xml
tei_json = json.loads(row[b'grobid0:tei_json'].decode('utf-8'))
metadata = json.loads(row[b'grobid0:metadata'].decode('utf-8'))
assert tei_json['title'] == metadata['title']
assert 'body' in tei_json
assert 'body' not in metadata
def test_parse_cdx_invalid(job):
print("valid")
raw = "com,sagepub,cep)/content/28/9/960.full.pdf 20170705062200 http://cep.sagepub.com/content/28/9/960.full.pdf application/pdf 200 3I42H3S6NNFQ2MSVX7XZKYAYSCX5QBYJ - - 401 313356621 CITESEERX-CRAWL-2017-06-20-20170705061647307-00039-00048-wbgrp-svc284/CITESEERX-CRAWL-2017-06-20-20170705062052659-00043-31209~wbgrp-svc284.us.archive.org~8443.warc.gz"
info, status = job.parse_line(raw)
assert status is None
print("space-prefixed line")
raw = " com,sagepub,cep)/content/28/9/960.full.pdf 20170705062200 http://cep.sagepub.com/content/28/9/960.full.pdf application/pdf 200 3I42H3S6NNFQ2MSVX7XZKYAYSCX5QBYJ - - 401 313356621 CITESEERX-CRAWL-2017-06-20-20170705061647307-00039-00048-wbgrp-svc284/CITESEERX-CRAWL-2017-06-20-20170705062052659-00043-31209~wbgrp-svc284.us.archive.org~8443.warc.gz"
info, status = job.parse_line(raw)
assert info is None
assert status['status'] == "invalid"
assert 'prefix' in status['reason']
print("commented line")
raw = "#com,sagepub,cep)/content/28/9/960.full.pdf 20170705062200 http://cep.sagepub.com/content/28/9/960.full.pdf application/pdf 200 3I42H3S6NNFQ2MSVX7XZKYAYSCX5QBYJ - - 401 313356621 CITESEERX-CRAWL-2017-06-20-20170705061647307-00039-00048-wbgrp-svc284/CITESEERX-CRAWL-2017-06-20-20170705062052659-00043-31209~wbgrp-svc284.us.archive.org~8443.warc.gz"
info, status = job.parse_line(raw)
assert info is None
assert status['status'] == "invalid"
assert 'prefix' in status['reason']
print("wrong column count")
raw = "a b c d"
info, status = job.parse_line(raw)
assert info is None
assert status['status'] == "invalid"
assert 'parse' in status['reason']
print("missing mimetype")
raw = "com,sagepub,cep)/content/28/9/960.full.pdf 20170705062200 http://cep.sagepub.com/content/28/9/960.full.pdf - 200 3I42H3S6NNFQ2MSVX7XZKYAYSCX5QBYJ - - 401 313356621 CITESEERX-CRAWL-2017-06-20-20170705061647307-00039-00048-wbgrp-svc284/CITESEERX-CRAWL-2017-06-20-20170705062052659-00043-31209~wbgrp-svc284.us.archive.org~8443.warc.gz"
info, status = job.parse_line(raw)
assert info is None
print(status)
assert status['status'] == "invalid"
assert 'parse' in status['reason']
print("HTTP status")
raw = "com,sagepub,cep)/content/28/9/960.full.pdf 20170705062200 http://cep.sagepub.com/content/28/9/960.full.pdf application/pdf 501 3I42H3S6NNFQ2MSVX7XZKYAYSCX5QBYJ - - 401 313356621 CITESEERX-CRAWL-2017-06-20-20170705061647307-00039-00048-wbgrp-svc284/CITESEERX-CRAWL-2017-06-20-20170705062052659-00043-31209~wbgrp-svc284.us.archive.org~8443.warc.gz"
info, status = job.parse_line(raw)
assert info is None
assert status['status'] == "invalid"
print("datetime")
raw = "com,sagepub,cep)/content/28/9/960.full.pdf 20170705 http://cep.sagepub.com/content/28/9/960.full.pdf application/pdf 501 3I42H3S6NNFQ2MSVX7XZKYAYSCX5QBYJ - - 401 313356621 CITESEERX-CRAWL-2017-06-20-20170705061647307-00039-00048-wbgrp-svc284/CITESEERX-CRAWL-2017-06-20-20170705062052659-00043-31209~wbgrp-svc284.us.archive.org~8443.warc.gz"
info, status = job.parse_line(raw)
assert info is None
assert status['status'] == "invalid"
def test_parse_cdx_skip(job):
job.mapper_init()
print("warc format")
raw = "com,sagepub,cep)/content/28/9/960.full.pdf 20170705062200 http://cep.sagepub.com/content/28/9/960.full.pdf application/pdf 200 3I42H3S6NNFQ2MSVX7XZKYAYSCX5QBYJ - - 401 313356621 CITESEERX-CRAWL-2017-06-20-20170705062052659-00043-31209~wbgrp-svc284.us.archive.org~8443.warc.gz"
info, status = job.mapper(None, raw).__next__()
assert info is None
assert status['status'] == "skip"
assert 'WARC' in status['reason']
print("mimetype")
raw = "com,sagepub,cep)/content/28/9/960.full.pdf 20170705062200 http://cep.sagepub.com/content/28/9/960.full.pdf text/html 200 3I42H3S6NNFQ2MSVX7XZKYAYSCX5QBYJ - - 401 313356621 CITESEERX-CRAWL-2017-06-20-20170705061647307-00039-00048-wbgrp-svc284/CITESEERX-CRAWL-2017-06-20-20170705062052659-00043-31209~wbgrp-svc284.us.archive.org~8443.warc.gz"
info, status = job.mapper(None, raw).__next__()
assert info is None
assert status['status'] == "skip"
assert 'mimetype' in status['reason']
@mock.patch('extraction_cdx_grobid.MRExtractCdxGrobid.fetch_warc_content', return_value=(FAKE_PDF_BYTES, None))
@responses.activate
def test_grobid_503(mock_fetch, job):
status = b'{"status": "done broke due to 503"}'
responses.add(responses.POST, 'http://localhost:8070/api/processFulltextDocument', status=503,
body=status)
output = io.BytesIO()
job.sandbox(stdin=io.BytesIO(OK_CDX_LINE), stdout=output)
job.run_mapper()
row = job.hb_table.row(b'sha1:ABCDEF12345Q2MSVX7XZKYAYSCX5QBYJ')
status = json.loads(row[b'grobid0:status'].decode('utf-8'))
assert json.loads(row[b'grobid0:status'].decode('utf-8')) == status
@mock.patch('extraction_cdx_grobid.MRExtractCdxGrobid.fetch_warc_content', return_value=(FAKE_PDF_BYTES, None))
@responses.activate
def test_grobid_not_xml(mock_fetch, job):
payload = b'this is not XML'
responses.add(responses.POST, 'http://localhost:8070/api/processFulltextDocument', status=200,
body=payload)
output = io.BytesIO()
job.sandbox(stdin=io.BytesIO(OK_CDX_LINE), stdout=output)
job.run_mapper()
row = job.hb_table.row(b'sha1:ABCDEF12345Q2MSVX7XZKYAYSCX5QBYJ')
assert struct.unpack("!q", row[b'grobid0:status_code'])[0] == 200
assert row[b'grobid0:tei_xml'] == payload
assert b'grobid0:tei_json' not in row
@mock.patch('extraction_cdx_grobid.MRExtractCdxGrobid.fetch_warc_content', return_value=(FAKE_PDF_BYTES, None))
def test_grobid_invalid_connection(mock_fetch, job):
status = b'{"status": "done broke"}'
job.options.grobid_uri = 'http://host.invalid:8070/api/processFulltextDocument'
output = io.BytesIO()
job.sandbox(stdin=io.BytesIO(OK_CDX_LINE), stdout=output)
job.run_mapper()
output = output.getvalue().decode('utf-8')
assert 'error' in output
assert 'GROBID' in output
assert job.hb_table.row(b'sha1:ABCDEF12345Q2MSVX7XZKYAYSCX5QBYJ') == {}
def test_wayback_failure(job):
job.options.warc_uri_prefix = 'http://host.invalid/'
output = io.BytesIO()
job.sandbox(stdin=io.BytesIO(OK_CDX_LINE), stdout=output)
job.run_mapper()
output = output.getvalue().decode('utf-8')
assert 'error' in output
assert 'wayback' in output
assert job.hb_table.row(b'sha1:ABCDEF12345Q2MSVX7XZKYAYSCX5QBYJ') == {}
@mock.patch('extraction_cdx_grobid.ResourceStore')
def test_wayback_not_found(mock_rs, job):
# This is... a little convoluded. Basically creating a 404 situation for
# reading a wayback resource.
mock_resource = mock.MagicMock()
mock_resource.get_status.return_value = (404, "Not Found")
mock_rso = mock.MagicMock()
mock_rso.load_resource.return_value = mock_resource
mock_rs.return_value = mock_rso
print(mock_rs().load_resource().get_status())
job.options.warc_uri_prefix = 'http://dummy-archive.org/'
output = io.BytesIO()
job.sandbox(stdin=io.BytesIO(OK_CDX_LINE), stdout=output)
job.run_mapper()
output = output.getvalue().decode('utf-8')
print(output)
assert 'error' in output
assert 'not 200' in output
assert job.hb_table.row(b'sha1:ABCDEF12345Q2MSVX7XZKYAYSCX5QBYJ') == {}
@mock.patch('extraction_cdx_grobid.MRExtractCdxGrobid.fetch_warc_content', return_value=(FAKE_PDF_BYTES, None))
@responses.activate
def test_mapper_rerun(mock_fetch, job):
responses.add(responses.POST, 'http://localhost:8070/api/processFulltextDocument', status=200,
body=b"FAKE", content_type='text/xml')
output1 = io.BytesIO()
job.sandbox(stdin=io.BytesIO(OK_CDX_LINE), stdout=output1)
job.run_mapper()
output1 = output1.getvalue().decode('utf-8')
# wayback gets FETCH 1x times
assert mock_fetch.call_count == 1
# grobid gets POST 1x times
assert len(responses.calls) == 1
# HBase
assert job.hb_table.row(b'sha1:ABCDEF12345Q2MSVX7XZKYAYSCX5QBYJ') != {}
assert 'success' in output1
# Run again, same line
output2 = io.BytesIO()
job.sandbox(stdin=io.BytesIO(OK_CDX_LINE), stdout=output2)
job.run_mapper()
output2 = output2.getvalue().decode('utf-8')
# wayback still only FETCH 1x times
assert mock_fetch.call_count == 1
# grobid still only POST 1x times
assert len(responses.calls) == 1
assert 'existing' in output2
|
