feat: validate raw matrix does not have more genes than raw var (#619)

* feat: validate raw matrix does not have more genes than raw var * only test raw matrix dimensionality if it exists * update tests to validate raw.var and raw.X dimension consistency if raw exists + add check if raw exists (#621) * remove unused imports --------- Co-authored-by: Nayib Gloria <[email protected]>
chanzuckerberg · Sep 15, 2023 · ccad8d9 · ccad8d9
1 parent 9bfa58c
commit ccad8d9
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Showing 2 changed files with 23 additions and 4 deletions.
diff --git a/cellxgene_schema_cli/cellxgene_schema/validate.py b/cellxgene_schema_cli/cellxgene_schema/validate.py
@@ -801,6 +801,14 @@ def _validate_seurat_convertibility(self):
 
                 self.is_seurat_convertible = False
 
+        if self.adata.raw and self.adata.raw.X.shape[1] != self.adata.raw.var.shape[0]:
+            self.warnings.append(
+                "This dataset cannot be converted to the .rds (Seurat v4) format. "
+                "There is a mismatch in the number of variables in the raw matrix and the raw var key-indexed "
+                "variables."
+            )
+            self.is_seurat_convertible = False
+
     def _validate_embedding_dict(self):
         """
         Validates the embedding dictionary -- it checks that all values of adata.obsm are numpy arrays with the correct

diff --git a/cellxgene_schema_cli/tests/test_validate.py b/cellxgene_schema_cli/tests/test_validate.py
@@ -54,16 +54,16 @@ def test_schema_definition(self):
             self.assertTrue("type" in self.schema_def["components"]["obs"]["columns"][i])
             if i == "curie":
                 self.assertIsInstance(
-                    self.schema_def["components"]["obs"]["columns"][i]["curie_constrains"],
+                    self.schema_def["components"]["obs"]["columns"][i]["curie_constraints"],
                     dict,
                 )
                 self.assertIsInstance(
-                    self.schema_def["components"]["obs"]["columns"][i]["curie_constrains"]["ontolgies"],
+                    self.schema_def["components"]["obs"]["columns"][i]["curie_constraints"]["ontolgies"],
                     list,
                 )
 
                 # Check that the allowed ontologies are in the ontology checker
-                for ontology_name in self.schema_def["components"]["obs"]["columns"][i]["curie_constrains"][
+                for ontology_name in self.schema_def["components"]["obs"]["columns"][i]["curie_constraints"][
                     "ontolgies"
                 ]:
                     self.assertTrue(self.OntologyChecker.is_valid_ontology(ontology_name))
@@ -281,8 +281,10 @@ def test__validate_with_h5ad_invalid_and_without_labels(self):
 
 
 class TestSeuratConvertibility(unittest.TestCase):
-    def validation_helper(self, matrix):
+    def validation_helper(self, matrix, raw=None):
         data = anndata.AnnData(X=matrix, obs=good_obs, uns=good_uns, obsm=good_obsm, var=good_var)
+        if raw:
+            data.raw = raw
         self.validator: Validator = Validator()
         self.validator._set_schema_def()
         self.validator.schema_def["max_size_for_seurat"] = 2**3 - 1  # Reduce size required to fail (faster tests)
@@ -319,3 +321,12 @@ def test_determine_seurat_convertibility(self):
         self.validator._validate_seurat_convertibility()
         self.assertTrue(len(self.validator.warnings) == 0)
         self.assertTrue(self.validator.is_seurat_convertible)
+
+        # h5ad where raw matrix variable count != length of raw var variables array is not Seurat-convertible
+        matrix = sparse.csr_matrix(np.zeros([good_obs.shape[0], good_var.shape[0]], dtype=np.float32))
+        raw = anndata.AnnData(X=matrix, var=good_var)
+        raw.var.drop("ENSSASG00005000004", axis=0, inplace=True)
+        self.validation_helper(matrix, raw)
+        self.validator._validate_seurat_convertibility()
+        self.assertTrue(len(self.validator.warnings) == 1)
+        self.assertFalse(self.validator.is_seurat_convertible)