more WIP on extractor

1 files changed, 169 insertions, 0 deletions

diff --git a/extraction/tests/test_extraction_cdx_grobid.py b/extraction/tests/test_extraction_cdx_grobid.py
new file mode 100644
index 0000000..71b55a3
--- /dev/null
+++ b/extraction/tests/test_extraction_cdx_grobid.py
@@ -0,0 +1,169 @@
+
+import io
+import json
+import pytest
+import mrjob
+import responses
+import happybase_mock
+from extraction_cdx_grobid import MRExtractCDXGROBID
+
+
+
+def test_parse_cdx_line():
+
+    raw = "edu,upenn,ldc)/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf 20170828233154 https://www.ldc.upenn.edu/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf application/pdf 200 WL3FEA62TEU4F52Y5DOVQ62VET4QJW7G - - 210251 931661233 SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828231135742-00000-00009-wbgrp-svc284/SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828232253025-00005-3480~wbgrp-svc284.us.archive.org~8443.warc.gz"
+    correct = {
+        'key': "sha1:WL3FEA62TEU4F52Y5DOVQ62VET4QJW7G",
+        'file:mime': "application/pdf",
+        'file:cdx': {
+            'surt': "edu,upenn,ldc)/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf",
+            'url': "https://www.ldc.upenn.edu/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf",
+            'dt': "20170828233154",
+            'warc': "SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828231135742-00000-00009-wbgrp-svc284/SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828232253025-00005-3480~wbgrp-svc284.us.archive.org~8443.warc.gz",
+            'offset': 931661233,
+            'c_size': 210251,
+        },
+        'f:c': {
+            'u': "https://www.ldc.upenn.edu/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf",
+            'd': "2017-08-28T23:31:54",
+            'f': "SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828232253025-00005-3480~wbgrp-svc284.us.archive.org~8443.warc.gz",
+            'o': 931661233,
+            'c': 1,
+        }
+    }
+
+    assert transform_line(raw) == correct
+    assert transform_line(raw + "\n") == correct
+    assert transform_line(raw + " extra_field") == correct
+
+@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?
+    """
+    conn = happybase_mock.Connection()
+    conn.create_table('wbgrp-journal-extract-test',
+        {'file': {}, 'grobid0': {}, 'f': {}})
+    table = conn.table('wbgrp-journal-extract-test')
+
+    job = MRCDXBackfillHBase(['--no-conf', '-'], hb_table=table)
+    return job
+
+
+@responses.activate
+def test_mapper_lines(job):
+
+    fake_grobid = {}
+    responses.add(responses.POST, 'http://localhost:9070/api/processFulltextDocument', status=200,
+        body=json.dumps(fake_grobid), content_type='application/json')
+
+    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()
+
+    # wayback gets FETCH 1x times
+
+    # grobid gets POST 3x times
+
+    # 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') == {}
+
+    row = job.hb_table.row(b'sha1:MPCXVWMUTRUGFP36SLPHKDLY6NGU4S3J')
+
+    assert struct.unpack("", row[b'file:size']) == 12345
+    assert row[b'file:mime'] == b"application/pdf"
+    assert struct.unpack("", row[b'grobid0:status_code']) == 200
+    assert row[b'grobid0:quality'] == None # TODO
+    status = json.loads(row[b'grobid0:status'].decode('utf-8'))
+    assert type(row[b'grobid0:status']) == type(dict())
+    assert row[b'grobid0:tei_xml'] == "<xml><lorem>ipsum</lorem></xml>"
+    tei_json = json.loads(row[b'grobid0:tei_json'].decode('utf-8'))
+    metadata = json.loads(row[b'grobid0:metadata'].decode('utf-8'))
+
+def test_parse_cdx_invalid(job):
+
+    print("valid")
+    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 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 = 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 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 = 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 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 = io.BytesIO(b"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 = 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 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 'parse' in status['reason']
+
+    print("HTTP status")
+    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 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 = io.BytesIO(b"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):
+
+    print("warc format")
+    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 200 3I42H3S6NNFQ2MSVX7XZKYAYSCX5QBYJ - - 401 313356621 CITESEERX-CRAWL-2017-06-20-20170705062052659-00043-31209~wbgrp-svc284.us.archive.org~8443.warc.gz")
+    info, status = job.mapper(raw)
+    assert info is None
+    assert status['status'] == "skip"
+    assert 'WARC' in status['reason']
+
+    print("mimetype")
+    raw = io.BytesIO(b"com,sagepub,cep)/content/28/9/960.full.pdf 20170705 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.mapper(raw)
+    assert info is None
+    assert status['status'] == "skip"
+    assert 'mimetype' in status['reason']
+
+def test_tei_json_convert():
+    # TODO: load xml test vector, run it through
+    with open('tests/files/23b29ea36382680716be08fc71aa81bd226e8a85.xml', 'r') as f:
+        xml_content = f.read()
+    pass
+
+def test_tei_json_convert_invalid():
+    # TODO: pass in junk
+    pass