indexing error in get_all_kegg

KarrLab · Mar 16, 2020 · 1d1cc01 · 1d1cc01
1 parent 17ea3f0
commit 1d1cc01
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Showing 2 changed files with 9 additions and 9 deletions.
diff --git a/datanator_query_python/query/query_protein.py b/datanator_query_python/query/query_protein.py
@@ -815,7 +815,7 @@ def get_all_kegg(self, ko, anchor, max_distance):
 
         Returns:
             (:obj:`list` of :obj:`dict`): list of result proteins and their info 
-            [{'distance': 0, 'documents': [{}]}
+            [
             {'distance': 1, 'documents': [{}, {}, {} ...]}, 
             {'distance': 2, 'documents': [{}, {}, {} ...]}, ...].
         '''
@@ -846,9 +846,9 @@ def get_all_kegg(self, ko, anchor, max_distance):
         for doc in docs:
             species = doc['species_name']
             obj = self.taxon_manager.get_canon_common_ancestor(anchor, species, org_format='tax_name')
-            distance = obj[anchor]            
+            distance = obj[species]            
             if distance != -1 and distance <= max_distance:
                 species_canon_ancestor = obj[species+'_canon_ancestors']
                 doc['canon_ancestors'] = species_canon_ancestor
-                result[distance]['documents'].append(doc)
+                result[distance-1]['documents'].append(doc)
         return result
diff --git a/tests/query/test_query_taxon_tree.py b/tests/query/test_query_taxon_tree.py
@@ -122,16 +122,16 @@ def test_get_canon_common_ancestor(self):
                                 'Candidatus Forterrea multitransposorum'],
                                 '743725': 1,
                                 '743725_canon_ancestors': ['Archaea']})
-        result = self.src.get_canon_common_ancestor('homo sapiens', 'gallus gallus', org_format='tax_name')
-        self.assertEqual(['Eukaryota', 'Metazoa','Chordata','Aves','Galliformes','Phasianidae','Gallus'], result['gallus gallus_canon_ancestors'])
+        result = self.src.get_canon_common_ancestor('escherichia coli', 'escherichia coli', org_format='tax_name')
+        self.assertEqual(result['escherichia coli'], 1)
         org_3 = 9606
         org_4 = 4932
         result = self.src.get_canon_common_ancestor(org_3, org_4)
         self.assertEqual(result, {'9606': 7, '4932': 7, '9606_canon_ancestors': ['Eukaryota', 'Metazoa', 'Chordata', 'Mammalia', 'Primates', 'Hominidae', 'Homo'], '4932_canon_ancestors': ['Eukaryota', 'Fungi', 'Ascomycota', 'Saccharomycetes', 'Saccharomycetales', 'Saccharomycetaceae', 'Saccharomyces']})
-        org_5 = 83333
-        org_6 = 562
-        result_0 = self.src.get_canon_common_ancestor(org_5, org_6)
-        print(result_0)
+        # org_5 = 83333
+        # org_6 = 562
+        # result_0 = self.src.get_canon_common_ancestor(org_5, org_6)
+        # print(result_0)
 
 
 class TestQueryTaxonTreeMock(unittest.TestCase):