extraction test fixes

1 files changed, 27 insertions, 23 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