Update tests

biopragmatics · Nov 23, 2024 · 618804a · 618804a
1 parent 16a44c3
commit 618804a
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Showing 2 changed files with 31 additions and 12 deletions.
diff --git a/src/pyobo/reader.py b/src/pyobo/reader.py
@@ -548,7 +548,8 @@ def _handle_prop(
         datatype, strict=strict, ontology_prefix=ontology_prefix, node=node
     )
     if datatype_reference is None:
-        raise ValueError
+        logger.warning("[%s] had unparsable datatype %s", node.curie, prop_value_type)
+        return None
     return LiteralProperty(prop_reference, value, datatype_reference)
 
 

diff --git a/tests/test_reader.py b/tests/test_reader.py
@@ -258,6 +258,22 @@ def test_property_literal_typed(self) -> None:
         self.assertEqual("121.323", row["value"])
         self.assertEqual("xsd:decimal", row["datatype"])
 
+    def test_property_bad_datatype(self) -> None:
+        """Test parsing a property with an unparsable datatype."""
+        text = """\
+            ontology: chebi
+
+            [Term]
+            id: CHEBI:1234
+            property_value: mass "121.323" NOPE:NOPE
+        """
+        with self.assertRaises(ValueError):
+            _read(text)
+        ontology = _read(text, strict=False)
+        term = self.get_only_term(ontology)
+        self.assertEqual(0, len(term.annotations_literal))
+        self.assertEqual(0, len(term.annotations_object))
+
     def test_property_literal_url_questionable(self) -> None:
         """Test parsing a property with a literal object."""
         ontology = _read("""\
@@ -342,16 +358,18 @@ def test_property_literal_url(self) -> None:
 
     def test_property_unparsable_object(self) -> None:
         """Test when an object can't be parsed."""
-        ontology = _read(
-            """\
+        text = """\
             ontology: chebi
 
             [Term]
             id: CHEBI:1234
             property_value: https://w3id.org/biolink/vocab/something NOPE:NOPE
-            """,
-            strict=False,
-        )
+            """
+
+        with self.assertRaises(ValueError):
+            _read(text)
+
+        ontology = _read(text, strict=False)
         term = self.get_only_term(ontology)
         self.assertEqual(0, len(list(term.annotations_literal)))
         self.assertEqual(0, len(list(term.annotations_object)))
@@ -384,16 +402,16 @@ def test_property_literal_object(self) -> None:
         self.assertEqual("hgnc:1234", term.get_property(see_also))
 
     def test_node_unparsable(self) -> None:
-        """Test loading an ontology with unparsable nodes.."""
-        ontology = _read(
-            """\
+        """Test loading an ontology with unparsable nodes."""
+        text = """\
             ontology: chebi
 
             [Term]
             id: nope:1234
-        """,
-            strict=False,
-        )
+        """
+        with self.assertRaises(ValueError):
+            _read(text)
+        ontology = _read(text, strict=False)
         self.assertEqual(0, len(list(ontology.iter_terms())))
 
     def test_malformed_typedef(self) -> None: