yet more test improvements

2 files changed, 61 insertions, 9 deletions

diff --git a/mapreduce/extraction_cdx_grobid.py b/mapreduce/extraction_cdx_grobid.py
index db36cac..c29b27e 100755
--- a/mapreduce/extraction_cdx_grobid.py
+++ b/mapreduce/extraction_cdx_grobid.py
@@ -189,8 +189,8 @@ class MRExtractCdxGrobid(MRJob):
         key = info['key']
 
         # Check if we've already processed this line
-        oldrow = self.hb_table.row(key, columns=[b'f', b'file',
-            b'grobid0:status_code'])
+        oldrow = self.hb_table.row(key,
+            columns=[b'f:c', b'file', b'grobid0:status_code'])
         if oldrow.get(b'grobid0:status_code', None) != None:
             # This file has already been processed; skip it
             self.increment_counter('lines', 'existing')
@@ -204,10 +204,11 @@ class MRExtractCdxGrobid(MRJob):
             status['key'] = key
             yield _, status
             return
+        extraction_status = status
 
         # Decide what to bother inserting back into HBase
         # Particularly: ('f:c', 'file:mime', 'file:size', 'file:cdx')
-        grobid_status = info.get('grobid0:status_code', None)
+        grobid_status_code = info.get('grobid0:status_code', None)
         for k in list(info.keys()):
             if k.encode('utf-8') in oldrow:
                 info.pop(k)
@@ -229,7 +230,14 @@ class MRExtractCdxGrobid(MRJob):
         self.hb_table.put(key, info)
         self.increment_counter('lines', 'success')
 
-        yield _, dict(status="success", grobid_status=grobid_status, key=key)
+        if extraction_status is not None:
+            yield _, dict(status="partial", key=key,
+                grobid_status_code=grobid_status_code,
+                reason=extraction_status['reason'])
+        else:
+            yield _, dict(status="success",
+                grobid_status_code=grobid_status_code, key=key,
+                extra=extraction_status)
 
 
 if __name__ == '__main__': # pragma: no cover
diff --git a/mapreduce/tests/test_extraction_cdx_grobid.py b/mapreduce/tests/test_extraction_cdx_grobid.py
index fa6f71f..1bf2420 100644
--- a/mapreduce/tests/test_extraction_cdx_grobid.py
+++ b/mapreduce/tests/test_extraction_cdx_grobid.py
@@ -14,6 +14,9 @@ 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():
     """
@@ -34,10 +37,8 @@ def job():
 @responses.activate
 def test_mapper_lines(mock_fetch, job):
 
-    with open('tests/files/23b29ea36382680716be08fc71aa81bd226e8a85.xml', 'r') as f:
-        real_tei_xml = f.read()
     responses.add(responses.POST, 'http://localhost:8070/api/processFulltextDocument', status=200,
-        body=real_tei_xml, content_type='text/xml')
+        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
@@ -81,7 +82,7 @@ com,pbworks,educ333b)/robots.txt 20170705063311 http://educ333b.pbworks.com/robo
     # 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
+    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']
@@ -183,10 +184,31 @@ def test_grobid_not_xml(mock_fetch, job):
     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))
@@ -247,7 +269,7 @@ def test_wayback_not_found(mock_rs, job):
 def test_mapper_rerun(mock_fetch, job):
 
     responses.add(responses.POST, 'http://localhost:8070/api/processFulltextDocument', status=200,
-        body=b"FAKE", content_type='text/xml')
+        body=REAL_TEI_XML, content_type='text/xml')
 
     output1 = io.BytesIO()
     job.sandbox(stdin=io.BytesIO(OK_CDX_LINE), stdout=output1)
@@ -273,3 +295,25 @@ def test_mapper_rerun(mock_fetch, job):
     # 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