add test_convert_nan_entries_to_empty_strings and stubs for additiona…

…l tests

tests/test_utils.py

@@ -19,6 +19,9 @@
 from pandas.testing import assert_frame_equal
 from synapseclient.core.exceptions import SynapseHTTPError
 
+from schematic.models.validate_manifest import ValidateManifest
+from schematic.models.metadata import MetadataModel
+
 from schematic.schemas.data_model_parser import DataModelParser
 from schematic.schemas.data_model_graph import DataModelGraph, DataModelGraphExplorer
 from schematic.schemas.data_model_jsonld import (
@@ -43,6 +46,7 @@
 )
 
 from schematic.utils import cli_utils, df_utils, general, io_utils, validate_utils
+from schematic.utils.df_utils import load_df
 from schematic.utils.general import (
     calculate_datetime,
     check_synapse_cache_size,
@@ -189,6 +193,14 @@
     (1073741825, 1073741824, 1181116006.4),
 ]
 
+def get_metadataModel(helpers, model_name:str):
+    metadataModel = MetadataModel(
+        inputMModelLocation=helpers.get_data_path(model_name),
+        inputMModelLocationType="local",
+        data_model_labels="class_label",
+    )
+    return metadataModel
+
 
 # create temporary files with various size based on request
 @pytest.fixture()
@@ -1060,6 +1072,76 @@ def test_validate_property_schema(self, helpers):
 
         assert error is None
 
+    @pytest.mark.parametrize(
+        ("manifest", "model", "root_node"),
+        [("mock_manifests/Patient_test_no_entry_for_cond_required_column.manifest.csv",
+            "example.model.csv", "Patient"),
+        ("mock_manifests/Valid_Test_Manifest_with_nones.csv",
+            "example_test_nones.model.csv", "MockComponent")]
+        )
+    def test_convert_nan_entries_to_empty_strings(
+            self, helpers, manifest, model, root_node):
+        # Get manifest and data model path
+        manifest_path = helpers.get_data_path(manifest)
+        model_path = helpers.get_data_path(model)
+
+        ## Gather parmeters 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(
+            root_node, root_node + "_validation"
+        )
+
+        manifest = load_df(
+            manifest_path,
+            preserve_raw_input=False,
+            allow_na_values=True,
+            **load_args,)
+
+        metadataModel = get_metadataModel(helpers, model)
+
+        # Instantiate Validate manifest, and run manifest validation
+        # In this step the manifest is modified while running rule 
+        # validation so need to do this step to get the updated manfest.
+        vm = ValidateManifest(
+                errors, manifest, manifest_path, dmge, json_schema)
+        manifest, vmr_errors, vmr_warnings = vm.validate_manifest_rules(
+            manifest, dmge, restrict_rules=False, project_scope=["syn54126707"],
+        )
+
+        # Run convert nan function
+        output = validate_utils.convert_nan_entries_to_empty_strings(
+            manifest=manifest
+        )
+
+        # Compare post rule validation manifest with output manifest looking
+        # for expected nan to empty string conversion
+        if root_node == 'Patient':
+            assert manifest['Family History'][0] == ['<NA>']
+            assert output['Family History'][0] == ['']
+        elif root_node == 'MockComponent':
+            assert manifest['Check List'][2] == ['<NA>']
+            assert manifest['Check List Like Enum'][2] == []
+            assert type(manifest['Check NA'][2]) == type(pd.NA)
+
+            assert output['Check List'][2] == ['']
+            assert output['Check List Like Enum'][2] == []
+
+
+    def test_get_list_robustness(self, helpers):
+        return
+
+    def parse_str_series_to_list(self, helpers):
+        return
+
     @pytest.mark.parametrize(
         "rule",
         [