ran black

Author: andrewelamb

tests/integration/test_validate_manifest.py

@@ -1,3 +1,4 @@
+from typing import Any
 
 import pytest
 
@@ -7,6 +8,7 @@
 
 
 class TestValidateManifest:
+    """Tests for ValidateManifest class"""
 
     @pytest.mark.parametrize(
         ("manifest", "model", "root_node"),
@@ -16,47 +18,59 @@ class TestValidateManifest:
                 "example_test_nones.model.csv",
                 "MockComponent",
             ),
-            #(
-            #    "mock_manifests/Valid_Test_Manifest_with_nones.csv",
-            #    "example_test_nones.model2.csv",
-            #    "MockComponent",
-            #),
+            (
+                "mock_manifests/Invalid_Test_Manifest_with_nones.csv",
+                "example_test_nones.model.csv",
+                "MockComponent",
+            ),
         ],
     )
     def test_validate_manifest_values(
-        self, helpers, manifest, model, root_node
+        self, helpers: Any, manifest: str, model: str, root_node: str
     ):
+        """Tests for ValidateManifest.validate_manifest_values
+
+        Args:
+            helpers (Any): An object with helper functions
+            manifest (str): A path to the manifest to be tested
+            model (str): A path to the model to be tested
+            root_node (str): The name of the component to be tested
+        """
         # Get manifest and data model path
-        manifest_path = helpers.get_data_path(manifest)
-        model_path = helpers.get_data_path(model)
+        manifest_path: str = helpers.get_data_path(manifest)
+        model_path: str = helpers.get_data_path(model)
 
-        # Gather parmeters needed to run validate_manifest_rules
+        # Gather parameters needed to run validate_manifest_rules
         errors = []
         load_args = {
             "dtype": "string",
         }
 
         dmge = helpers.get_data_model_graph_explorer(path=model)
 
-        self.data_model_js = DataModelJSONSchema(
-            jsonld_path=model_path, graph=dmge.graph
-        )
-        json_schema = self.data_model_js.get_json_validation_schema(
+        data_model_js = DataModelJSONSchema(jsonld_path=model_path, graph=dmge.graph)
+        json_schema = data_model_js.get_json_validation_schema(
             root_node, root_node + "_validation"
         )
 
-        manifest = load_df(
+        manifest_df = load_df(
             manifest_path,
             preserve_raw_input=False,
             allow_na_values=True,
             **load_args,
         )
 
-        vm = ValidateManifest(errors, manifest, manifest_path, dmge, json_schema)
-        errors, warnings = vm.validate_manifest_values(manifest, json_schema, dmge)
-        import logging
+        vm = ValidateManifest(errors, manifest_df, manifest_path, dmge, json_schema)
+        errors, warnings = vm.validate_manifest_values(manifest_df, json_schema, dmge)
         assert not warnings
         assert errors
-        for error in errors:
-            logging.warning(error)
-        assert False
+
+        # Both manifests will have errors of type "<xxx> is not of type 'array'
+        # Only the invalid manifest will have errors of type "<xxx is not one of
+        #  ['Breast', 'None', 'Prostate', 'Colorectal', 'Skin', 'Lung']" in the
+        #  "Cancer Type" column.
+        error_attributes = [error[1] for error in errors]
+        if manifest == "mock_manifests/Valid_Test_Manifest_with_nones.csv":
+            assert "Cancer Type" not in error_attributes
+        else:
+            assert "Cancer Type" in error_attributes