Replace single document handling with dictionary documents handling for dbxref resolver

psot/dbxref.py

-def dbxrefs_from(document):
+def dbxrefs_from_documents(documents):
+  refs = set()
+  for key in documents:
+    refs.update(dbxrefs_from_document(documents[key]))
+  return refs
+
+def dbxrefs_from_document(document):
   '''finds all dbxrefs in the document and returns a list of ids'''
   refs = []
   for c in document['computations']:
@@ -7,7 +13,11 @@ def dbxrefs_from(document):
             refs.append(r['target']['dbxref'])
   return set(refs)
 
-def combine(document, informations):
+def combine_with_documents(documents, informations):
+  for k in documents:
+    combine_with_document(documents[k], informations)
+
+def combine_with_document(document, informations):
   '''adds an information tag for each result that references a dbxref'''
   for c in document['computations']:
     for r in c['results']:

psot/scripts/resolve_dbxrefs.py

@@ -15,11 +15,11 @@ args = parser.parse_args()
 with open(args.input, 'r') as json_file: 
   j = json.load(json_file)
   # extract all dbxrefs
-  dbxrefs = dbxref.dbxrefs_from(j)
+  dbxrefs = dbxref.dbxrefs_from_documents(j)
   # retrieve information for dbxrefs
   entries = retrieve(convert_to_dbxrefs(sorted(dbxrefs)))
   # add information field to results
-  dbxref.combine(j, entries)
+  dbxref.combine_with_documents(j, entries)
   # write updated json
   with open(args.output, 'w') as o:
       json.dump(j, o)

tests/test_resolve_dbxrefs.py

@@ -25,7 +25,7 @@ class TestDbXrefs(unittest.TestCase):
         'text' : 'some text'
       }
     ]
-    dbxref.combine(test_data, test_information)
+    dbxref.combine_with_document(test_data, test_information)
     self.assertTrue('text' in test_data['computations'][0]['results'][0]['informations'])
     self.assertEqual(test_data['computations'][0]['results'][0]['informations']['text'], 'some text')
 
@@ -36,7 +36,7 @@ class TestDbXrefs(unittest.TestCase):
     with open(test_file, 'r') as f:
       data = json.load(f)
       # extract dbxrefs
-      dbxrefs = dbxref.dbxrefs_from(data)
+      dbxrefs = dbxref.dbxrefs_from_document(data)
       # test if all expected dbxrefs were found
       self.assertEqual(dbxrefs, set([
           "PFAM:PF01048.19",