Merge branch 'bnewbold-ungrobided'

2 files changed, 196 insertions, 0 deletions

diff --git a/python/tests/files/example_ungrobided.tsv b/python/tests/files/example_ungrobided.tsv
new file mode 100644
index 0000000..9263b6f
--- /dev/null
+++ b/python/tests/files/example_ungrobided.tsv
@@ -0,0 +1,20 @@
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diff --git a/python/tests/test_extraction_ungrobided.py b/python/tests/test_extraction_ungrobided.py
new file mode 100644
index 0000000..366d392
--- /dev/null
+++ b/python/tests/test_extraction_ungrobided.py
@@ -0,0 +1,176 @@
+
+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)
+    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)
+    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"