Fixed test (#723)

src/oaklib/utilities/lexical/synonymizer.py

@@ -2,6 +2,7 @@
 from typing import Iterable, Iterator, List, Optional, Tuple
 
 from kgcl_schema.datamodel import kgcl
+from pronto import Definition
 
 from oaklib.datamodels.synonymizer_datamodel import RuleSet, Synonymizer
 from oaklib.datamodels.vocabulary import (
@@ -69,6 +70,8 @@ def apply_synonymizer_to_terms(
         if include_all:
             defn = adapter.definition(curie)
             if defn:
+                if isinstance(defn, Definition):
+                    defn = str(defn)
                 tvs.append(("definition", [defn]))
         for scope_pred, aliases in tvs:
             if aliases is not None:

tests/test_cli.py

@@ -934,10 +934,6 @@ def test_search_local_advanced(self):
                     logging.error(f"INPUT: {input_arg} code = {result.exit_code}")
                     logging.error(f"OUTPUT={out}")
                     logging.error(f"ERR={err}")
-                if result.exit_code == 1:
-                    import pdb
-
-                    pdb.set_trace()
                 self.assertEqual(0, result.exit_code)
                 logging.info(f"OUTPUT={out}")
                 logging.info(f"ERR={err}")

tests/test_implementations/test_robot_template.py

@@ -52,7 +52,6 @@ def test_basic_ontology_adapter(adapter):
     }
 
 
-@pytest.mark.skip("https://github.com/INCATools/kgcl/issues/64")
 def test_patcher(adapter):
     changes = [f"rename {BRAIN_SPECIMEN} from 'brain specimen' to 'brain sample'"]
     if not isinstance(adapter, PatcherInterface):
@@ -65,13 +64,12 @@ def test_patcher(adapter):
         assert isinstance(change_obj, kgcl.NodeRename)
         print("NEW:", change_obj.new_value)
         adapter.apply_patch(change_obj)
-    # adapter.set_label(BRAIN_SPECIMEN, "FOO")
-    assert adapter.label(BRAIN_SPECIMEN) == "FOO"
+    assert adapter.label(BRAIN_SPECIMEN) == "brain sample"
     if not isinstance(adapter, DumperInterface):
         raise ValueError("Adapter does not support dumping")
     adapter.dump(SAVED_TEMPLATES, clean=True)
     adapter2 = get_adapter(f"robottemplate:{SAVED_TEMPLATES}")
-    assert adapter2.label(BRAIN_SPECIMEN) == "FOO"
+    assert adapter2.label(BRAIN_SPECIMEN) == "brain sample"
 
 
 def test_set_label():

tests/test_utilities/test_synonymizer.py

@@ -81,6 +81,7 @@ def test_synonymizer(rule, input, expected):
                     "the plasma membrane and nucleus, but including other subcellular structures.' "
                     "to 'All of the contents of a cell excluding the plasma membrane and "
                     "NUCLEUS, but including other subcellular structures.'"
+
                 )
             ],
         ),
@@ -114,4 +115,5 @@ def test_syonymizer_on_terms(ruleset, include_all, terms, expected):
         change_str = render(change)
         print(change_str)
         changes_strs.append(change_str)
+
     assert set(changes_strs) == set(expected)