diff options
Diffstat (limited to 'mapreduce/tests/test_extraction_cdx_grobid.py')
| -rw-r--r-- | mapreduce/tests/test_extraction_cdx_grobid.py | 319 |
1 files changed, 0 insertions, 319 deletions
diff --git a/mapreduce/tests/test_extraction_cdx_grobid.py b/mapreduce/tests/test_extraction_cdx_grobid.py deleted file mode 100644 index 1bf2420..0000000 --- a/mapreduce/tests/test_extraction_cdx_grobid.py +++ /dev/null @@ -1,319 +0,0 @@ - -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""" - -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 = 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): - - 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() - output = output.getvalue().decode('utf-8') - 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 - assert "XML parse error" in output - - -@mock.patch('extraction_cdx_grobid.MRExtractCdxGrobid.fetch_warc_content', return_value=(FAKE_PDF_BYTES, None)) -@responses.activate -def test_grobid_not_tei(mock_fetch, job): - - payload = b'<xml></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() - output = output.getvalue().decode('utf-8') - 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 - assert "non-TEI content" in output - - -@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=REAL_TEI_XML, 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 - -@mock.patch('extraction_cdx_grobid.MRExtractCdxGrobid.fetch_warc_content', return_value=(FAKE_PDF_BYTES, None)) -@responses.activate -def test_mapper_previously_backfilled(mock_fetch, job): - - responses.add(responses.POST, 'http://localhost:8070/api/processFulltextDocument', status=200, - body=REAL_TEI_XML, content_type='text/xml') - - job.hb_table.put(b'sha1:ABCDEF12345Q2MSVX7XZKYAYSCX5QBYJ', - {b'f:c': b'{"some": "dict"}', b'file:col': b'bogus'}) - assert job.hb_table.row(b'sha1:ABCDEF12345Q2MSVX7XZKYAYSCX5QBYJ') != {} - - 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 - assert 'success' in output1 |