Check unique genes in validator for any organism

src/cap_upload_validator/upload_validator.py

@@ -11,6 +11,7 @@
     MusMusculus,
     MultiSpecies,
     Organism,
+    UnsupportedOrganism,
     str_to_organism,
     ontology_id_to_organism,
 )
@@ -352,6 +353,12 @@ def _check_var_index(self, cap_adata: CapAnnData) -> Optional[pd.Series]:
         logger.debug(f"Organism(s) in dataset = {dataset_organisms}, known organisms = {known_organisms}")
 
         missing_genes_mask = None
+        if UnsupportedOrganism in dataset_organisms:
+            organism = (UnsupportedOrganism if len(dataset_organisms) == 1 else MultiSpecies)
+            self._organism = organism
+            logger.debug("Unknown organism found, skipping only known-gene validation.")
+            return missing_genes_mask
+
         # Check ENSEMBL ids for supported organism
         if len(dataset_organisms) == 1:
             organism = dataset_organisms[0]
@@ -361,7 +368,7 @@ def _check_var_index(self, cap_adata: CapAnnData) -> Optional[pd.Series]:
                 logger.debug("Single known organism found, validating gene IDs.")
                 missing_genes_mask = self._validate_gene_ids(clean_index, organism)
             else:
-                logger.debug("Unknown organism found, skipping gene validation.")
+                logger.debug("Organism has no known-gene validation rules, skipping that check.")
         elif len(dataset_organisms) > 1:
             logger.debug("There are multiple organisms in dataset")
             self._organism = MultiSpecies

test/test_upload_validator.py

@@ -33,6 +33,7 @@
     CSCMatrixInX,
     AnnDataMultipleOntologyIDs,
     AnnDataInvalidDiseaseOntologyForHuman,
+    AnnDataGeneIndexIsNotUnique,
 )
 
 TMP_DIR = Path(tempfile.mkdtemp())
@@ -189,6 +190,40 @@ def check_var_index():
         assert False, f"Unpredicted error: {e}"
 
 
+@pytest.mark.parametrize(
+    ("var_names", "should_fail"),
+    [
+        (["ENSG000001.1", "ENSG000001.2"], True),  # duplicate after removing version suffix
+        (["TP53", "TP53"], True),  # duplicate gene symbol
+        (["unknown_gene_1", "unknown_gene_2"], False),  # unique genes
+    ],
+)
+@pytest.mark.parametrize(
+    "organisms",
+    [
+        "unsupported organism",
+        [HomoSapiens.name, "unsupported organism"],  # mixed with unsupported organism
+    ],
+)
+def test_var_requires_unique_genes_for_any_unsupported_organism(
+    var_names,
+    should_fail,
+    organisms,
+):
+    adata = ad.AnnData(X=np.eye(len(var_names)))
+    adata.var_names = var_names
+    adata.obs[ORGANISM_COLUMN] = organisms
+
+    validator = UploadValidator(None)
+    validator._multi_exception.raise_on_append = True
+
+    if should_fail:
+        with pytest.raises(AnnDataGeneIndexIsNotUnique):
+            validator._check_var_index(adata)
+    else:
+        assert validator._check_var_index(adata) is None
+
+
 @pytest.mark.parametrize("set_organism", [False, True, "ont"])
 def test_validator(set_organism):
     x = np.eye(10) + 0.1  # not a counts