Merge pull request #21 from InformaticsMatters/options-processing

Fixed failing decoder test

Author: alanbchristie

tests/test_decoder.py

@@ -235,7 +235,6 @@ def test_get_required_variable_names_for_simnple_python_molprops_with_options():
     assert "rdkitPropertyValue" in rqd_variables
 
 
-@pytest.mark.skip(reason="The decoder does not currently handle options processing")
 def test_set_variables_from_options_for_step_for_simnple_python_molprops_with_options():
     # Arrange
     variables = {
@@ -244,15 +243,14 @@ def test_set_variables_from_options_for_step_for_simnple_python_molprops_with_op
     }
 
     # Act
-    new_variables, error = decoder.set_variables_from_options_for_step(
+    new_variables = decoder.set_variables_from_options_for_step(
         _SIMPLE_PYTHON_MOLPROPS_WITH_OPTIONS_WORKFLOW,
         variables,
         "step1",
     )
 
     # Assert
-    assert error is None
-    assert len(new_variables) == 4
+    assert len(new_variables) == 2
     assert "name" in new_variables
     assert "value" in new_variables
     assert new_variables["name"] == "propertyName"

tests/test_workflow_engine_examples.py

@@ -313,7 +313,6 @@ def test_workflow_engine_simple_python_molprops(basic_engine):
     assert project_file_exists(output_file_2)
 
 
-# @pytest.mark.skip(reason="The engine does not currently create the required variables")
 def test_workflow_engine_simple_python_molprops_with_options(basic_engine):
     # Arrange
     da, md = basic_engine

workflow/decoder.py

@@ -111,13 +111,8 @@ def set_variables_from_options_for_step(
     assert isinstance(definition, dict)
     assert step_name
 
-    print("workflow", definition)
-    print("workflow_variables", variables)
-
     result = {}
     options = definition.get("variables", {}).get("options", [])
-    print("options", options)
-    print("variables", variables)
 
     for opt in options:
         for step_alias in opt["as"]: