diff options
Diffstat (limited to 'python_hadoop/tests/test_extraction_ungrobided.py')
| -rw-r--r-- | python_hadoop/tests/test_extraction_ungrobided.py | 178 |
1 files changed, 178 insertions, 0 deletions
diff --git a/python_hadoop/tests/test_extraction_ungrobided.py b/python_hadoop/tests/test_extraction_ungrobided.py new file mode 100644 index 0000000..cb46d29 --- /dev/null +++ b/python_hadoop/tests/test_extraction_ungrobided.py @@ -0,0 +1,178 @@ + +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" |