extraction test fixes

2 files changed, 50 insertions, 27 deletions

diff --git a/mapreduce/extraction_cdx_grobid.py b/mapreduce/extraction_cdx_grobid.py
index bcb8663..9a0d795 100755
--- a/mapreduce/extraction_cdx_grobid.py
+++ b/mapreduce/extraction_cdx_grobid.py
@@ -18,6 +18,7 @@ Requires:
 
 import io
 import sys
+import xml
 import json
 import struct
 import requests
@@ -67,10 +68,6 @@ class MRExtractCdxGrobid(MRJob):
     def grobid_process_fulltext(self, content):
         r = requests.post(self.options.grobid_uri + "/api/processFulltextDocument",
             files={'input': content})
-        if r.status_code is not 200:
-            # if invalid file, get a 400 with JSON body with 'description' key (and others)
-            # XXX:
-            return None
         return r
 
     def mapper_init(self):
@@ -98,12 +95,10 @@ class MRExtractCdxGrobid(MRJob):
             return None, dict(status="invalid", reason="CDX parse")
 
         if info['file:mime'] not in self.mime_filter:
-            self.increment_counter('lines', 'skip')
             return None, dict(status="skip", reason="mimetype")
 
         # If warc is not item/file.(w)arc.gz form, skip it
         if len(info['file:cdx']['warc'].split('/')) != 2:
-            self.increment_counter('lines', 'skip')
             return None, dict(status="skip", reason="WARC path not petabox item/file")
 
         return info, None
@@ -114,13 +109,9 @@ class MRExtractCdxGrobid(MRJob):
             rstore = ResourceStore(loaderfactory=CDXLoaderFactory())
             gwb_record = rstore.load_resource(warc_uri, offset, c_size)
         except wayback.exception.ResourceUnavailable as err:
-            # XXX: during testing
-            raise err
-            self.increment_counter('lines', 'petabox_error')
             return None, dict(status="petabox_error", reason="failed to load file contents")
 
         if gwb_record.get_status()[0] != 200:
-            self.increment_counter('lines', 'error')
             return None, dict(status="error",
                 reason="archived HTTP response (WARC) was not 200",
                 warc_status=gwb_record.get_status()[0])
@@ -134,7 +125,6 @@ class MRExtractCdxGrobid(MRJob):
             info['file:cdx']['offset'],
             info['file:cdx']['c_size'])
         if status:
-            self.increment_counter('lines', status['status'])
             return None, status
 
         info['file:size'] = len(original_content)
@@ -142,20 +132,32 @@ class MRExtractCdxGrobid(MRJob):
         # Submit to GROBID
         try:
             grobid_response = self.grobid_process_fulltext(original_content)
-        except IOError as ioe:
-            raise ioe
-            # XXX: catch correct error
-            self.increment_counter('lines', 'fail')
-            return None, dict(status="fail", reason="GROBID connection")
+        except requests.exceptions.ConnectionError:
+            return None, dict(status="error", reason="connection to GROBID worker")
 
         info['grobid0:status_code'] = grobid_response.status_code
+        if grobid_response.status_code is not 200:
+            # response.text is .content decoded as utf-8
+            info['grobid0:status'] = json.loads(grobid_response.text)
+            return info, dict(status="error", reason="non-200 GROBID HTTP status",
+                extra=grobid_response.content)
+
+        info['grobid0:status'] = {}
         info['grobid0:tei_xml'] = grobid_response.content
-        info['grobid0:status'] = {} # TODO
 
         # Convert TEI XML to JSON
-        # TODO:
-        info['grobid0:tei_json'] = teixml2json(grobid_response.content, encumbered=True)
-        info['grobid0:metadata'] = teixml2json(grobid_response.content, encumbered=False)
+        try:
+            info['grobid0:tei_json'] = teixml2json(grobid_response.content, encumbered=True)
+        except xml.etree.ElementTree.ParseError:
+            return info, dict(status="fail", reason="GROBID 200 XML parse error")
+        except ValueError:
+            return info, dict(status="fail", reason="GROBID 200 XML non-TEI content")
+
+        tei_metadata = info['grobid0:tei_json'].copy()
+        for k in ('body', 'annex'):
+            # Remove fulltext (copywritted) content
+            tei_metadata.pop(k, None)
+        info['grobid0:metadata'] = tei_metadata
 
         # Determine extraction "quality"
         # TODO:
@@ -183,20 +185,22 @@ class MRExtractCdxGrobid(MRJob):
             self.increment_counter('lines', status['status'])
             yield _, status
             return
+        key = info['key']
 
         # Check if we've already processed this line
-        oldrow = self.hb_table.row(info['key'], columns=['f', 'file',
+        oldrow = self.hb_table.row(key, columns=['f', 'file',
             'grobid0:status_code'])
         if oldrow.get('grobid0:status', None):
             # This file has already been processed; skip it
             self.increment_counter('lines', 'existing')
-            yield _, dict(status="existing")
+            yield _, dict(status="existing", key=key)
             return
 
         # Do the extraction
         info, status = self.extract(info)
         if info is None:
             self.increment_counter('lines', status['status'])
+            status['key'] = key
             yield _, status
             return
 
@@ -224,7 +228,7 @@ class MRExtractCdxGrobid(MRJob):
         self.hb_table.put(key, info)
         self.increment_counter('lines', 'success')
 
-        yield _, dict(status="success", grobid_status=grobid_status)
+        yield _, dict(status="success", grobid_status=grobid_status, key=key)
 
 
 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 713e501..729e68b 100644
--- a/mapreduce/tests/test_extraction_cdx_grobid.py
+++ b/mapreduce/tests/test_extraction_cdx_grobid.py
@@ -158,7 +158,7 @@ def test_parse_cdx_skip(job):
 @responses.activate
 def test_grobid_503(mock_fetch, job):
 
-    status = b"{'status': 'done broke due to 503'}"
+    status = b'{"status": "done broke due to 503"}'
     responses.add(responses.POST, 'http://localhost:8070/api/processFulltextDocument', status=503,
         body=status)
 
@@ -176,9 +176,9 @@ def test_grobid_503(mock_fetch, job):
 @responses.activate
 def test_grobid_not_xml(mock_fetch, job):
 
-    status = b"{'status': 'done broke'}"
+    payload = b'this is not XML'
     responses.add(responses.POST, 'http://localhost:8070/api/processFulltextDocument', status=200,
-        body=status)
+        body=payload)
 
     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 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""")
 
@@ -186,5 +186,24 @@ def test_grobid_not_xml(mock_fetch, job):
     job.sandbox(stdin=raw, stdout=output)
     job.run_mapper()
     row = job.hb_table.row(b'sha1:ABCDEF12345Q2MSVX7XZKYAYSCX5QBYJ')
-    assert json.loads(row[b'grobid0:status'].decode('utf-8')) == status
+    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
+
+
+@mock.patch('extraction_cdx_grobid.MRExtractCdxGrobid.fetch_warc_content', return_value=(FAKE_PDF_BYTES, None))
+@responses.activate
+def test_grobid_invalid_connection(mock_fetch, job):
+
+    status = b'{"status": "done broke"}'
+    job.options.grobid_uri = 'http://host.invalid:8070/api/processFulltextDocument'
+
+    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 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""")
+
+    output = io.BytesIO()
+    job.sandbox(stdin=raw, stdout=output)
+    #with pytest.raises...
+    job.run_mapper()
+    assert job.hb_table.row(b'sha1:ABCDEF12345Q2MSVX7XZKYAYSCX5QBYJ') == {}
 
+# TODO: failure to fetch from wayback