chore: resolve/remove skipped tests (#1236)

Co-authored-by: Evan Molinelli <[email protected]>
chanzuckerberg · Jan 31, 2025 · 2aa2036 · 2aa2036
1 parent 0387a19
commit 2aa2036
Show file tree

Hide file tree

Showing 2 changed files with 0 additions and 57 deletions.
diff --git a/cellxgene_schema_cli/tests/test_map_species.py b/cellxgene_schema_cli/tests/test_map_species.py
@@ -57,9 +57,6 @@ def validator_with_adata(zebrafish_adata):
     return validator
 
 
-@pytest.mark.skip(
-    reason="Skipping this test as the schema its based on has changed and this command is being deprecated"
-)
 def test_map_species__valid_output(validator_with_adata):
     with TemporaryDirectory() as tmp:
         input_file = tmp + "input.h5ad"
@@ -109,9 +106,6 @@ def test_map_species_log_output_no_match(zebrafish_adata, caplog):
         assert "ZFA:0000047 has no closest match for UBERON in its ancestry tree." in caplog.text
 
 
-@pytest.mark.skip(
-    reason="Skipping this test as the schema its based on has changed and this command is being deprecated"
-)
 def test_map_species__with_existing_cols(validator_with_adata):
     obs = validator_with_adata.adata.obs
     obs["cell_type_ontology_term_id"] = ""

diff --git a/cellxgene_schema_cli/tests/test_schema_compliance.py b/cellxgene_schema_cli/tests/test_schema_compliance.py
@@ -2913,23 +2913,6 @@ def test_organism_cell_type_ontology_term_id__visium_in_tissue_0_invalid(
             in validator.errors[0]
         )
 
-    @pytest.mark.skip(
-        reason="Skipping this test to unblock downstream multispecies work. TODO: fix before 5.3.0 release"
-    )
-    def test_cell_type_ontology_term_id__visium_in_tissue_0__na(self, validator_with_visium_zebrafish_adata):
-        validator = validator_with_visium_zebrafish_adata
-        error_message = (
-            "ERROR: 'na' in 'cell_type_ontology_term_id' is not a valid ontology term id of 'ZFA'. "
-            "When 'organism_ontology_term_id' is 'NCBITaxon:7955' (Danio rerio), "
-            "'cell_type_ontology_term_id' MUST be a descendant term id of 'ZFA:0009000' (cell)."
-        )
-        obs = validator.adata.obs
-        obs.loc[obs.index[0], "in_tissue"] = 0
-        obs.loc[obs.index[0], "cell_type_ontology_term_id"] = "na"
-        validator.validate_adata()
-        # Passes visium check but fails cell_type_ontology_term_id check
-        assert validator.errors == [error_message]
-
     @pytest.mark.parametrize(
         "tissue_ontology_term_id",
         [
@@ -3105,23 +3088,6 @@ def test_organism_cell_type_ontology_term_id__visium_in_tissue_0_invalid(
             in validator.errors[0]
         )
 
-    @pytest.mark.skip(
-        reason="Skipping this test to unblock downstream multispecies work. TODO: fix before 5.3.0 release"
-    )
-    def test_cell_type_ontology_term_id__visium_in_tissue_0__na(self, validator_with_visium_fruitfly_adata):
-        validator = validator_with_visium_fruitfly_adata
-        error_message = (
-            "ERROR: 'na' in 'cell_type_ontology_term_id' is not a valid ontology term id of 'FBbt'. "
-            "When 'organism_ontology_term_id' is 'NCBITaxon:7227' (Drosophila melanogaster), "
-            "'cell_type_ontology_term_id' MUST be a descendant term id of 'FBbt:00007002' (cell)."
-        )
-        obs = validator.adata.obs
-        obs.loc[obs.index[0], "in_tissue"] = 0
-        obs.loc[obs.index[0], "cell_type_ontology_term_id"] = "na"
-        validator.validate_adata()
-        # Passes visium check but fails cell_type_ontology_term_id check
-        assert validator.errors == [error_message]
-
     @pytest.mark.parametrize(
         "tissue_ontology_term_id",
         [
@@ -3303,23 +3269,6 @@ def test_organism_cell_type_ontology_term_id__visium_in_tissue_0_invalid(
             in validator.errors[0]
         )
 
-    @pytest.mark.skip(
-        reason="Skipping this test to unblock downstream multispecies work. TODO: fix before 5.3.0 release"
-    )
-    def test_organism_cell_type_ontology_term_id__visium_in_tissue_0__na(self, validator_with_visium_roundworm_adata):
-        validator = validator_with_visium_roundworm_adata
-        error_message = (
-            "ERROR: 'na' in 'organism_cell_type_ontology_term_id' is not a valid ontology term id of 'WBbt'. "
-            "When 'organism_ontology_term_id' is 'NCBITaxon:6239' (Caenorhabditis elegans), "
-            "'organism_cell_type_ontology_term_id' MUST be a descendant term id of 'WBbt:0004017' (cell)."
-        )
-        obs = validator.adata.obs
-        obs.loc[obs.index[0], "in_tissue"] = 0
-        obs.loc[obs.index[0], "organism_cell_type_ontology_term_id"] = "na"
-        validator.validate_adata()
-        # Passes visium check but fails organism_cell_type_ontology_term_id check
-        assert validator.errors == [error_message]
-
     @pytest.mark.parametrize(
         "tissue_ontology_term_id",
         [