Add additional test cases

src/biomappings/contribute/obo.py

@@ -31,16 +31,17 @@ def update_obo(*, prefix: str, path: Union[str, Path]) -> None:
         file.writelines(lines)
 
 
-def update_obo_lines(*, lines: List[str], mappings: List[Dict[str, Any]]) -> List[str]:
+def update_obo_lines(*, lines: List[str], mappings: List[Dict[str, Any]], progress: bool = True) -> List[str]:
     """Update the lines of an OBO file.
 
     :param mappings: Mappings to add
     :param lines: A list of lines of the file (still containing trailing newlines)
+    :param progress: Show a progress bar
     :returns: New lines. Does not modify the original list.
     """
     lines = deepcopy(lines)
 
-    for mapping in tqdm(mappings, unit="mapping", unit_scale=True):
+    for mapping in tqdm(mappings, unit="mapping", unit_scale=True, disable=not progress):
         target_prefix = mapping["target prefix"]
         target_prefix = bioregistry.get_preferred_prefix(target_prefix) or target_prefix
         target_identifier = standardize_identifier(target_prefix, mapping["target identifier"])

tests/test_contribute.py

@@ -9,8 +9,8 @@
 class TestContributeOBO(unittest.TestCase):
     """A test case for contributing to OBO flat files."""
 
-    def test_addition(self):
-        """Test adding a non-redundant mapping."""
+    def setUp(self) -> None:
+        """Set up the test case with a specific mapping."""
         mappings = get_curated_mappings("uberon")
         sources = {mapping["source identifier"] for mapping in mappings}
         self.assertIn("UBERON:0000018", sources, msg="Mappings are not loaded properly")
@@ -23,7 +23,10 @@ def test_addition(self):
             and mappings["target prefix"] == "idomal"
         ]
         self.assertEqual(1, len(mappings))
+        self.mappings = mappings
 
+    def test_addition(self):
+        """Test adding a non-redundant mapping."""
         original = dedent(
             """\
             [Term]
@@ -61,5 +64,53 @@ def test_addition(self):
         )
         self.assertEqual(
             expected.splitlines(),
-            update_obo_lines(mappings=mappings, lines=original.splitlines()),
+            update_obo_lines(mappings=self.mappings, lines=original.splitlines(), progress=False),
+        )
+
+    def test_skip_redundant_1(self):
+        """Test skipping adding a mapping that doesn't have metadata."""
+        original = dedent(
+            """\
+            [Term]
+            id: UBERON:0000018
+            name: compound eye
+            def: "A light sensing organ composed of ommatidia." [FB:gg, Wikipedia:Compound_eye]
+            subset: organ_slim
+            synonym: "adult compound eye" RELATED []
+            xref: BTO:0001921
+            xref: HAO:0000217
+            xref: IDOMAL:0002421
+            xref: TGMA:0000024
+            intersection_of: UBERON:0000970 ! eye
+            relationship: only_in_taxon NCBITaxon:6656 {source="PMID:21062451"} ! Arthropoda
+            property_value: seeAlso "https://github.com/obophenotype/uberon/issues/457" xsd:anyURI
+            """
+        )
+        self.assertEqual(
+            original.splitlines(),
+            update_obo_lines(mappings=self.mappings, lines=original.splitlines(), progress=False),
+        )
+
+    def test_skip_redundant_2(self):
+        """Test skipping adding a mapping that doesn't have metadata."""
+        original = dedent(
+            """\
+            [Term]
+            id: UBERON:0000018
+            name: compound eye
+            def: "A light sensing organ composed of ommatidia." [FB:gg, Wikipedia:Compound_eye]
+            subset: organ_slim
+            synonym: "adult compound eye" RELATED []
+            xref: BTO:0001921
+            xref: HAO:0000217
+            xref: IDOMAL:0002421 {dcterms:contributor="https://orcid.org/0000-0003-4423-4370"} ! compound eye
+            xref: TGMA:0000024
+            intersection_of: UBERON:0000970 ! eye
+            relationship: only_in_taxon NCBITaxon:6656 {source="PMID:21062451"} ! Arthropoda
+            property_value: seeAlso "https://github.com/obophenotype/uberon/issues/457" xsd:anyURI
+            """
+        )
+        self.assertEqual(
+            original.splitlines(),
+            update_obo_lines(mappings=self.mappings, lines=original.splitlines(), progress=False),
         )