refactor old python hadoop code into new directory

1 files changed, 0 insertions, 319 deletions

diff --git a/python/tests/test_extraction_cdx_grobid.py b/python/tests/test_extraction_cdx_grobid.py
deleted file mode 100644
index 471d94a..0000000
--- a/python/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
-
-
-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