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
|
import io
import json
import mrjob
import pytest
import struct
import responses
import happybase_mock
import wayback.exception
from unittest import mock
from common import parse_ungrobided_line
from extraction_ungrobided import MRExtractUnGrobided
FAKE_PDF_BYTES = b"%PDF SOME JUNK" + struct.pack("!q", 112853843)
OK_UNGROBIDED_LINE = b"\t".join((
b"sha1:3I42H3S6NNFQ2MSVX7XZKYAYSCX5QBYJ",
b"""{"c": 1, "d": "2017-07-06T07:54:11", "f": "CITESEERX-CRAWL-2017-06-20-20170706075012840-00388-3671~wbgrp-svc285.us.archive.org~8443.warc.gz", "o": 914718776, "u": "http://www.ibc7.org/article/file_down.php?mode%3Darticle_print%26pid%3D250"}""",
b"application/pdf",
b"""{"c_size": 501, "dt": "20170706075411", "offset": 914718776, "surt": "org,ibc7)/article/file_down.php?mode=article_print&pid=250", "url": "http://www.ibc7.org/article/file_down.php?mode%3Darticle_print%26pid%3D250", "warc": "CITESEERX-CRAWL-2017-06-20-20170706074206206-00379-00388-wbgrp-svc285/CITESEERX-CRAWL-2017-06-20-20170706075012840-00388-3671~wbgrp-svc285.us.archive.org~8443.warc.gz"}""",
))
with open('tests/files/23b29ea36382680716be08fc71aa81bd226e8a85.xml', 'r') as f:
REAL_TEI_XML = f.read()
@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 = MRExtractUnGrobided(['--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_ungrobided.MRExtractUnGrobided.fetch_warc_content', return_value=(FAKE_PDF_BYTES, None))
@responses.activate
def test_mapper_single_line(mock_fetch, job):
responses.add(responses.POST, 'http://localhost:8070/api/processFulltextDocument', status=200,
body=REAL_TEI_XML, content_type='text/xml')
raw = io.BytesIO(OK_UNGROBIDED_LINE)
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-2017-06-20-20170706074206206-00379-00388-wbgrp-svc285/CITESEERX-CRAWL-2017-06-20-20170706075012840-00388-3671~wbgrp-svc285.us.archive.org~8443.warc.gz",
914718776,
501)
# grobid gets POST 1x times
assert len(responses.calls) == 1
# HBase
assert job.hb_table.row(b'1') == {}
# Saved extraction info
row = job.hb_table.row(b'sha1:3I42H3S6NNFQ2MSVX7XZKYAYSCX5QBYJ')
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
@mock.patch('extraction_ungrobided.MRExtractUnGrobided.fetch_warc_content', return_value=(FAKE_PDF_BYTES, None))
@responses.activate
def test_mapper_lines(mock_fetch, job):
responses.add(responses.POST, 'http://localhost:8070/api/processFulltextDocument', status=200,
body=REAL_TEI_XML, content_type='text/xml')
raw = io.BytesIO(b"""sha1:23PTUXWSNSVE4HS5J7ELDUUG63J2FPCI\t{"c": 1, "d": "2016-06-09T00:27:36", "f": "WIDE-20160609001810-06993.warc.gz", "o": 287880616, "u": "http://www.case-research.eu/sites/default/files/publications/18092393_E-brief_Dabrowski_Monetary_Policy_final_0.pdf"}\tapplication/pdf\t{"c_size": 68262, "dt": "20160609002736", "offset": 287880616, "surt": "eu,case-research)/sites/default/files/publications/18092393_e-brief_dabrowski_monetary_policy_final_0.pdf", "url": "http://www.case-research.eu/sites/default/files/publications/18092393_E-brief_Dabrowski_Monetary_Policy_final_0.pdf", "warc": "WIDE-20160609000312-crawl427/WIDE-20160609001810-06993.warc.gz"}
sha1:23PW2APYHNBPIBRIVNQ6TMKUNY53UL3D\t{"c": 1, "d": "2016-01-07T03:29:03", "f": "MUSEUM-20160107025230-02354.warc.gz", "o": 413484441, "u": "http://www.portlandoregon.gov/fire/article/363695"}\tapplication/pdf\t{"c_size": 44600, "dt": "20160107032903", "offset": 413484441, "surt": "gov,portlandoregon)/fire/article/363695", "url": "http://www.portlandoregon.gov/fire/article/363695", "warc": "MUSEUM-20160107004301-crawl891/MUSEUM-20160107025230-02354.warc.gz"}
sha1:23RJIHUIOYY5747CR6YYCTMACXDCFYTT\t{"c": 1, "d": "2014-06-07T18:00:56", "f": "ARCHIVEIT-219-QUARTERLY-20047-20140607125555378-00017-wbgrp-crawl051.us.archive.org-6442.warc.gz", "o": 720590380, "u": "https://www.indiana.edu/~orafaq/faq/pdf.php?cat=36&id=264&artlang=en"}\tapplication/pdf\t{"c_size": 3727, "dt": "20140607180056", "offset": 720590380, "surt": "edu,indiana)/~orafaq/faq/pdf.php?artlang=en&cat=36&id=264", "url": "https://www.indiana.edu/~orafaq/faq/pdf.php?cat=36&id=264&artlang=en", "warc": "ARCHIVEIT-219-QUARTERLY-20047-00001/ARCHIVEIT-219-QUARTERLY-20047-20140607125555378-00017-wbgrp-crawl051.us.archive.org-6442.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()))
# grobid gets POST 3x times
assert len(responses.calls) == 3
# wayback gets FETCH 3x times
mock_fetch.assert_has_calls((
mock.call("WIDE-20160609000312-crawl427/WIDE-20160609001810-06993.warc.gz", 287880616, 68262),
mock.call("MUSEUM-20160107004301-crawl891/MUSEUM-20160107025230-02354.warc.gz", 413484441, 44600),
mock.call("ARCHIVEIT-219-QUARTERLY-20047-00001/ARCHIVEIT-219-QUARTERLY-20047-20140607125555378-00017-wbgrp-crawl051.us.archive.org-6442.warc.gz", 720590380, 3727),
))
# Saved extraction info
assert job.hb_table.row(b'sha1:3I42H3S6NNFQ2MSVX7XZKYAYSCX5QBYJ') == {}
assert job.hb_table.row(b'sha1:23PTUXWSNSVE4HS5J7ELDUUG63J2FPCI') != {}
assert job.hb_table.row(b'sha1:23PW2APYHNBPIBRIVNQ6TMKUNY53UL3D') != {}
assert job.hb_table.row(b'sha1:23RJIHUIOYY5747CR6YYCTMACXDCFYTT') != {}
row = job.hb_table.row(b'sha1:23RJIHUIOYY5747CR6YYCTMACXDCFYTT')
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
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_ungrobided_invalid(job):
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_ungrobided_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_ungrobided_line(raw)
assert info is None
assert status['status'] == "invalid"
assert 'prefix' in status['reason']
print("wrong column count")
raw = "a b c d e"
info, status = job.parse_ungrobided_line(raw)
assert info is None
assert status['status'] == "invalid"
assert 'parse' in status['reason']
print("CDX line, somehow")
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_ungrobided_line(raw)
assert info is None
print(status)
assert status['status'] == "invalid"
assert 'parse' in status['reason']
def test_parse_ungrobided_valid():
parsed = parse_ungrobided_line(OK_UNGROBIDED_LINE.decode('utf-8'))
assert parsed['key'] == "sha1:3I42H3S6NNFQ2MSVX7XZKYAYSCX5QBYJ"
assert parsed['f:c']['u'] == "http://www.ibc7.org/article/file_down.php?mode%3Darticle_print%26pid%3D250"
assert parsed['file:mime'] == "application/pdf"
assert parsed['file:cdx']['c_size'] == 501
assert parsed['file:cdx']['dt'] == "20170706075411"
|
