Fix bug: Entry without comments causes exceptions

dbxref/retrieve/pfam.py

@@ -71,9 +71,13 @@ def read_annotation(entry):
     annotation = {
             'domain': entry.attrib['id'],
             'accession': entry.attrib['accession'],
-            'terms' : [],
-            'comment': entry.find('pfam:comment', ns).text.strip()
+            'terms' : []
             }
+
+    comment = entry.find('pfam:comment', ns)
+    if comment:
+      annotation['comment'] = comment.text.strip()
+
     go_terms = entry.find('pfam:go_terms', ns)
     if go_terms:
       categories = go_terms.findall('pfam:category', ns)

tests/test_pfam.py

 import unittest
-from dbxref import retriever, resolver
+from dbxref.retrieve import pfam
 
 class TestPfam(unittest.TestCase):
 
-    def test_no_go_terms(self):
-      '''regression test for missing go terms in pfam entry'''
-      documents = retriever.retrieve([{'db': 'pfam', 'id': 'PF10423.8'}])
+    def test_no_position(self):
+      '''regression test for missing comment in pfam entry'''
+      documents = pfam.retrieve([{'db': 'PFAM', 'id': 'PF00083.23'}])
       # this test failed due to an error due to missing None handling, 
       # so no assertions here. Once fixed. this should suffice