feat: update validation for obs['is_primary_data'] to enforce False …

…if uns['spatial']['is_single'] is False (#865)

Co-authored-by: MillenniumFalconMechanic <[email protected]>

cellxgene_schema_cli/cellxgene_schema/validate.py

@@ -1386,6 +1386,20 @@ def _check_spatial_obs(self):
         # Validate cell type.
         self._validate_spatial_cell_type_ontology_term_id()
 
+        self._validate_spatial_is_primary_data()
+
+    def _validate_spatial_is_primary_data(self):
+        """
+        Validate is_primary_data for spatial datasets.
+        """
+        obs = getattr_anndata(self.adata, "obs")
+        if obs is None or "is_primary_data" not in obs:
+            return
+        if self._is_single() is False and obs["is_primary_data"].any():
+            self.errors.append(
+                "When uns['spatial']['is_single'] is False, obs['is_primary_data'] must be False for all rows."
+            )
+
     def _validate_spatial_cell_type_ontology_term_id(self):
         """
         Validate cell type ontology term id is "unknown" if Visium, is_single is True and in_tissue is 0.

cellxgene_schema_cli/tests/fixtures/examples_validate.py

@@ -240,6 +240,58 @@
 good_obs_slide_seqv2.loc[:, ["suspension_type"]] = good_obs_slide_seqv2.astype("category")
 good_obs_slide_seqv2.loc[:, ["tissue_type"]] = good_obs.astype("category")
 
+good_obs_visium_is_single_false = pd.DataFrame(
+    [
+        [
+            "CL:0000066",
+            "EFO:0010961",
+            "MONDO:0100096",
+            "NCBITaxon:9606",
+            "PATO:0000383",
+            "UBERON:0002048",
+            "tissue",
+            False,
+            "HANCESTRO:0575",
+            "HsapDv:0000003",
+            "donor_1",
+            "na",
+        ],
+        [
+            "CL:0000192",
+            "EFO:0010961",
+            "PATO:0000461",
+            "NCBITaxon:10090",
+            "unknown",
+            "CL:0000192",
+            "cell culture",
+            False,
+            "na",
+            "MmusDv:0000003",
+            "donor_2",
+            "na",
+        ],
+    ],
+    index=["X", "Y"],
+    columns=[
+        "cell_type_ontology_term_id",
+        "assay_ontology_term_id",
+        "disease_ontology_term_id",
+        "organism_ontology_term_id",
+        "sex_ontology_term_id",
+        "tissue_ontology_term_id",
+        "tissue_type",
+        "is_primary_data",
+        "self_reported_ethnicity_ontology_term_id",
+        "development_stage_ontology_term_id",
+        "donor_id",
+        "suspension_type",
+    ],
+)
+
+good_obs_visium_is_single_false.loc[:, ["donor_id"]] = good_obs_visium_is_single_false.astype("category")
+good_obs_visium_is_single_false.loc[:, ["suspension_type"]] = good_obs_visium_is_single_false.astype("category")
+good_obs_visium_is_single_false.loc[:, ["tissue_type"]] = good_obs_visium_is_single_false.astype("category")
+
 # ---
 # 2. Creating individual var components: valid object and valid object and with labels
 
@@ -327,6 +379,14 @@
     },
 }
 
+good_uns_with_is_single_false = {
+    "title": "A title",
+    "default_embedding": "X_umap",
+    "X_approximate_distribution": "normal",
+    "batch_condition": ["is_primary_data"],
+    "spatial": {"is_single": False},
+}
+
 good_uns_with_slide_seqV2_spatial = {
     "title": "A title",
     "default_embedding": "X_umap",
@@ -408,6 +468,14 @@
     var=good_var,
 )
 
+adata_spatial_is_single_false = anndata.AnnData(
+    X=sparse.csr_matrix(X),
+    obs=good_obs_visium_is_single_false,
+    uns=good_uns_with_is_single_false,
+    obsm=good_obsm_spatial,
+    var=good_var,
+)
+
 # anndata for testing migration
 unmigrated_obs = pd.DataFrame(
     [

cellxgene_schema_cli/tests/test_schema_compliance.py

@@ -63,6 +63,12 @@ def validator_with_adata_missing_raw(validator) -> Validator:
     return validator
 
 
+@pytest.fixture
+def validator_with_spatial_and_is_single_false(validator) -> Validator:
+    validator.adata = examples.adata_spatial_is_single_false.copy()
+    return validator
+
+
 @pytest.fixture
 def validator_with_visium_assay(validator) -> Validator:
     validator.adata = examples.adata_visium.copy()
@@ -1101,6 +1107,17 @@ def test_is_primary_data(self, validator_with_adata):
             "ERROR: Column 'is_primary_data' in dataframe 'obs' " "must be boolean, not 'object'."
         ]
 
+    def test_is_primary_data__spatial(self, validator_with_spatial_and_is_single_false):
+        """
+        is_primary_data	bool. This MUST be False if dataset has uns['spatial']['is_single'] == False
+        """
+        validator = validator_with_spatial_and_is_single_false
+        validator.adata.obs["is_primary_data"][0] = True
+        validator.validate_adata()
+        assert validator.errors == [
+            "ERROR: When uns['spatial']['is_single'] is False, obs['is_primary_data'] must be False for all rows."
+        ]
+
     def test_donor_id_must_be_categorical(self, validator_with_adata):
         """
         donor_id categorical with str categories. This MUST be free-text that identifies
@@ -1993,26 +2010,18 @@ def test_obsm_values_no_X_embedding__non_spatial_dataset(self, validator_with_ad
             "WARNING: Validation of raw layer was not performed due to current errors, try again after fixing current errors.",
         ]
 
-    @pytest.mark.parametrize(
-        "assay_ontology_term_id, adata_spatial",
-        [
-            ("EFO:0010961", examples.adata_visium),
-            ("EFO:0030062", examples.adata_slide_seqv2),
-        ],
-    )
-    def test_obsm_values_no_X_embedding__spatial_dataset(
-        self, validator_with_adata, assay_ontology_term_id, adata_spatial
-    ):
-        validator = validator_with_adata
-        validator.adata.obsm["harmony"] = validator.adata.obsm["X_umap"]
-        validator.adata.uns = adata_spatial.uns
-        validator.adata.uns["default_embedding"] = "harmony"
-        validator.adata.obsm["spatial"] = validator.adata.obsm["X_umap"]
+    def test_obsm_values_no_X_embedding__visium_dataset(self, validator_with_visium_assay):
+        validator = validator_with_visium_assay
+        validator.adata.uns["default_embedding"] = "spatial"
+        del validator.adata.obsm["X_umap"]
+        validator.validate_adata()
+        assert validator.errors == []
+        assert validator.is_spatial is True
+
+    def test_obsm_values_no_X_embedding__slide_seq_v2_dataset(self, validator_with_slide_seq_v2_assay):
+        validator = validator_with_slide_seq_v2_assay
+        validator.adata.uns["default_embedding"] = "spatial"
         del validator.adata.obsm["X_umap"]
-        validator.adata.obs = adata_spatial.obs
-        validator.adata.obs["assay_ontology_term_id"] = assay_ontology_term_id
-        validator.adata.obs["suspension_type"] = "na"
-        validator.adata.obs.loc[:, ["suspension_type"]] = validator.adata.obs.astype("category")
         validator.validate_adata()
         assert validator.errors == []
         assert validator.is_spatial is True
@@ -2025,24 +2034,9 @@ def test_obsm_values_spatial_embedding_missing__is_single_true(self, validator_w
             "ERROR: 'spatial' embedding is required in 'adata.obsm' if adata.uns['spatial']['is_single'] is True."
         ]
 
-    def test_obsm_values_spatial_embedding_missing__is_single_false(self, validator_with_visium_assay):
-        validator = validator_with_visium_assay
-        validator.adata.uns["spatial"] = {"is_single": False}
+    def test_obsm_values_spatial_embedding_missing__is_single_false(self, validator_with_spatial_and_is_single_false):
+        validator = validator_with_spatial_and_is_single_false
         del validator.adata.obsm["spatial"]
-        # Format adata.obs into valid shape for Visium and is_single False.
-        validator.adata.obs.pop("array_col")
-        validator.adata.obs.pop("array_row")
-        validator.adata.obs.pop("in_tissue")
-        validator.validate_adata()
-        assert validator.errors == []
-
-    def test_obsm_values_spatial_embedding_present__is_single_false(self, validator_with_visium_assay):
-        validator = validator_with_visium_assay
-        validator.adata.uns["spatial"] = {"is_single": False}
-        # Format adata.obs into valid shape for Visium and is_single False.
-        validator.adata.obs.pop("array_col")
-        validator.adata.obs.pop("array_row")
-        validator.adata.obs.pop("in_tissue")
         validator.validate_adata()
         assert validator.errors == []
 

cellxgene_schema_cli/tests/test_validate.py

@@ -23,6 +23,7 @@
 from fixtures.examples_validate import (
     adata_minimal,
     adata_slide_seqv2,
+    adata_spatial_is_single_false,
     adata_visium,
     adata_with_labels,
     good_obs,
@@ -333,6 +334,15 @@ def test__validate_spatial_slide_seqV2_ok(self):
         validator.validate_adata()
         assert not validator.errors
 
+    def test__validate_spatial_is_single_false_ok(self):
+        validator: Validator = Validator()
+        validator._set_schema_def()
+        validator.adata = adata_spatial_is_single_false.copy()
+
+        # Confirm spatial is valid.
+        validator.validate_adata()
+        assert not validator.errors
+
     def test__validate_spatial_forbidden_if_not_visium_or_slide_seqv2(self):
         validator: Validator = Validator()
         validator._set_schema_def()
@@ -708,6 +718,7 @@ def test__validate_tissue_position_forbidden(self, assay_ontology_term_id, is_si
         validator.adata = adata_visium.copy()
         validator.adata.obs.assay_ontology_term_id = assay_ontology_term_id
         validator.adata.uns["spatial"]["is_single"] = is_single
+        validator.adata.obs["is_primary_data"] = False
 
         # Confirm tissue positions are not allowed.
         validator._check_spatial_obs()
@@ -738,6 +749,7 @@ def test__validate_tissue_position_not_required(self):
         validator.adata = adata_slide_seqv2.copy()
         validator.adata.obs["assay_ontology_term_id"] = ["EFO:0010961", "EFO:0030062"]
         validator.adata.uns["spatial"]["is_single"] = False
+        validator.adata.obs["is_primary_data"] = False
 
         validator._check_spatial_obs()
         assert not validator.errors