refactor old python hadoop code into new directory

4 files changed, 0 insertions, 591 deletions

diff --git a/python/tests/files/example_ungrobided.tsv b/python/tests/files/example_ungrobided.tsv
deleted file mode 100644
index 9263b6f..0000000
--- a/python/tests/files/example_ungrobided.tsv
+++ /dev/null
@@ -1,20 +0,0 @@
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-sha1:23OUFX3ZYMF53HY4RUONR5PKN4HXN4O3	{"c": 1, "d": "2004-05-26T06:45:34", "f": "DW_crawl10.20040526064432.arc.gz", "o": 67593910, "u": "http://207.36.165.114:80/NewOrleans/Papers/1301466.pdf"}	application/pdf	{"c_size": 306879, "dt": "20040526064534", "offset": 67593910, "surt": "114,165,36,207)/neworleans/papers/1301466.pdf", "url": "http://207.36.165.114:80/NewOrleans/Papers/1301466.pdf", "warc": "DW_crawl10.20040525230808-c/DW_crawl10.20040526064432.arc.gz"}
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-sha1:23PRILJUIQUKHRYQIUYAKSBFPH53FOGT	{"c": 1, "d": "2017-07-14T18:51:38", "f": "WIDE-20170714181144-06521.warc.gz", "o": 820382225, "u": "http://carsandracingstuff.com/library/articles/32538.pdf"}	application/pdf	{"c_size": 125426, "dt": "20170714185138", "offset": 820382225, "surt": "com,carsandracingstuff)/library/articles/32538.pdf", "url": "http://carsandracingstuff.com/library/articles/32538.pdf", "warc": "WIDE-20170714174218-crawl426/WIDE-20170714181144-06521.warc.gz"}
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diff --git a/python/tests/test_backfill_hbase_from_cdx.py b/python/tests/test_backfill_hbase_from_cdx.py
deleted file mode 100644
index 070662b..0000000
--- a/python/tests/test_backfill_hbase_from_cdx.py
+++ /dev/null
@@ -1,74 +0,0 @@
-"""
-TODO: could probably refactor to use unittest.mock.patch('happybase')
-"""
-
-import io
-import json
-import pytest
-import mrjob
-import happybase_mock
-from backfill_hbase_from_cdx import MRCDXBackfillHBase
-
-@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 = MRCDXBackfillHBase(['--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
-
-
-def test_some_lines(job):
-
-    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
-""")
-
-    job.sandbox(stdin=raw)
-    job.run_mapper()
-
-    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') == {}
-
-    row = job.hb_table.row(b'sha1:MPCXVWMUTRUGFP36SLPHKDLY6NGU4S3J')
-    assert row[b'file:mime'] == b"application/pdf"
-
-    file_cdx = json.loads(row[b'file:cdx'].decode('utf-8'))
-    assert int(file_cdx['offset']) == 328850624
-
-    f_c = json.loads(row[b'f:c'].decode('utf-8'))
-    assert f_c['u'] == "http://cadmus.eui.eu/bitstream/handle/1814/36635/RSCAS_2015_03.pdf%3Bjsessionid%3D761393014319A39F40D32AE3EB3A853F?sequence%3D1"
-    assert b'i' not in f_c
-
-def test_parse_cdx_skip(job):
-
-    job.mapper_init()
-
-    print("CDX prefix")
-    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'] == "invalid"
-    assert 'prefix' 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']
-
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
diff --git a/python/tests/test_extraction_ungrobided.py b/python/tests/test_extraction_ungrobided.py
deleted file mode 100644
index cb46d29..0000000
--- a/python/tests/test_extraction_ungrobided.py
+++ /dev/null
@@ -1,178 +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 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"