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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)
# file:mime should actually not get clobbered by GROBID updater
#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)
# file:mime should actually not get clobbered by GROBID updater
#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"
|
