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import io
import json
import mrjob
import pytest
import struct
import responses
import happybase_mock
from unittest import mock
from extraction_cdx_grobid import MRExtractCdxGrobid
FAKE_PDF_BYTES = b"%PDF SOME JUNK" + struct.pack("!q", 112853843)
@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)
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 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""")
output = io.BytesIO()
job.sandbox(stdin=raw, 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)
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 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""")
output = io.BytesIO()
job.sandbox(stdin=raw, 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))
@responses.activate
def test_grobid_invalid_connection(mock_fetch, job):
status = b'{"status": "done broke"}'
job.options.grobid_uri = 'http://host.invalid:8070/api/processFulltextDocument'
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 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""")
output = io.BytesIO()
job.sandbox(stdin=raw, stdout=output)
#with pytest.raises...
job.run_mapper()
assert job.hb_table.row(b'sha1:ABCDEF12345Q2MSVX7XZKYAYSCX5QBYJ') == {}
# TODO: failure to fetch from wayback
|
