feat: refactor definition of an output

Author: Alan Christie

tests/test_decoder.py

@@ -184,41 +184,3 @@ def test_get_workflow_steps():
     assert len(steps) == 2
     assert steps[0]["name"] == "step1"
     assert steps[1]["name"] == "step2"
-
-
-def test_get_step_input_variable_names_when_duplicates():
-    # Arrange
-    workflow_filename: str = os.path.join(
-        os.path.dirname(__file__),
-        "workflow-definitions",
-        "duplicate-step-input-output-variable-names.yaml",
-    )
-    with open(workflow_filename, "r", encoding="utf8") as wf_file:
-        definition: Dict[str, Any] = yaml.safe_load(wf_file)
-
-    # Act
-    inputs = decoder.get_step_input_variable_names(definition, "step-1")
-
-    # Assert
-    assert len(inputs) == 2
-    assert inputs[0] == "inputFile"
-    assert inputs[1] == "inputFile"
-
-
-def test_get_step_output_variable_names_when_duplicates():
-    # Arrange
-    workflow_filename: str = os.path.join(
-        os.path.dirname(__file__),
-        "workflow-definitions",
-        "duplicate-step-input-output-variable-names.yaml",
-    )
-    with open(workflow_filename, "r", encoding="utf8") as wf_file:
-        definition: Dict[str, Any] = yaml.safe_load(wf_file)
-
-    # Act
-    outputs = decoder.get_step_output_variable_names(definition, "step-2")
-
-    # Assert
-    assert len(outputs) == 2
-    assert outputs[0] == "outputFile"
-    assert outputs[1] == "outputFile"

tests/test_workflow_engine_examples.py

@@ -428,7 +428,7 @@ def test_workflow_engine_simple_python_split_combine(basic_engine):
         md,
         da,
         "simple-python-split-combine",
-        {"candidateMolecules": input_file_1},
+        {"candidateMolecules": input_file_1, "combination": "combination.smi"},
     )
 
     # Assert

tests/test_workflow_validator_for_run_level.py

@@ -215,27 +215,3 @@ def test_validate_simple_python_molprops_with_missing_input():
     assert error.error_msg == [
         "Missing workflow variable values for: candidateMolecules"
     ]
-
-
-def test_validate_duplicate_step_output_variable_names():
-    # Arrange
-    workflow_filename: str = os.path.join(
-        os.path.dirname(__file__),
-        "workflow-definitions",
-        "duplicate-step-input-output-variable-names.yaml",
-    )
-    with open(workflow_filename, "r", encoding="utf8") as workflow_file:
-        workflow: dict[str, Any] = yaml.load(workflow_file, Loader=yaml.FullLoader)
-    assert workflow
-
-    # Act
-    error = WorkflowValidator.validate(
-        level=ValidationLevel.TAG,
-        workflow_definition=workflow,
-    )
-
-    # Assert
-    assert error.error_num == 3
-    assert error.error_msg == [
-        "Duplicate step output variable: outputFile (step=step-2)"
-    ]

tests/test_workflow_validator_for_tag_level.py

@@ -149,27 +149,3 @@ def test_validate_simple_python_molprops_with_options():
     # Assert
     assert error.error_num == 0
     assert error.error_msg is None
-
-
-def test_validate_duplicate_step_output_variable_names():
-    # Arrange
-    workflow_filename: str = os.path.join(
-        os.path.dirname(__file__),
-        "workflow-definitions",
-        "duplicate-step-input-output-variable-names.yaml",
-    )
-    with open(workflow_filename, "r", encoding="utf8") as workflow_file:
-        workflow: dict[str, Any] = yaml.load(workflow_file, Loader=yaml.FullLoader)
-    assert workflow
-
-    # Act
-    error = WorkflowValidator.validate(
-        level=ValidationLevel.TAG,
-        workflow_definition=workflow,
-    )
-
-    # Assert
-    assert error.error_num == 3
-    assert error.error_msg == [
-        "Duplicate step output variable: outputFile (step=step-2)"
-    ]

tests/workflow-definitions/duplicate-step-input-output-variable-names.yaml

@@ -20,5 +20,5 @@ steps:
   - variable: smiles
     from-workflow:
       variable: smiles
-  out:
-  - outputFile
+  - variable: outputFile
+    to-project:

tests/workflow-definitions/example-smiles-to-file.yaml

@@ -38,5 +38,5 @@ steps:
     from-step:
       name: step-1
       variable: outputFile
-  out:
-  - outputFile
+  - variable: outputFile
+    to-project:

tests/workflow-definitions/replicate-using-undeclared-input.yaml

@@ -24,5 +24,5 @@ steps:
     from-step:
       name: example-1-step-1
       variable: outputFile
-  out:
-  - outputFile
+  - variable: outputFile
+    to-project:

tests/workflow-definitions/shortcut-example-1.yaml

@@ -41,5 +41,5 @@ steps:
   - variable: outputFile
     from-workflow:
       variable: clusteredMolecules
-  out:
-  - outputFile
+  - variable: outputFile
+    to-project:

tests/workflow-definitions/simple-python-molprops-with-options.yaml

@@ -37,5 +37,5 @@ steps:
   - variable: outputFile
     from-workflow:
       variable: clusteredMolecules
-  out:
-  - outputFile
+  - variable: outputFile
+    to-project: