feat: refactor definition of an output

Alan Christie · Alan Christie · commit f6707c8b4185 · 2025-09-02T16:36:46.000Z
diff --git a/tests/test_decoder.py b/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"
diff --git a/tests/test_workflow_engine_examples.py b/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
diff --git a/tests/test_workflow_validator_for_run_level.py b/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)"
-    ]
diff --git a/tests/test_workflow_validator_for_tag_level.py b/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)"
-    ]
diff --git a/tests/workflow-definitions/duplicate-step-input-output-variable-names.yaml b/tests/workflow-definitions/duplicate-step-input-output-variable-names.yaml
diff --git a/tests/workflow-definitions/example-smiles-to-file.yaml b/tests/workflow-definitions/example-smiles-to-file.yaml
@@ -20,5 +20,5 @@ steps:
   - variable: smiles
     from-workflow:
       variable: smiles
-  out:
-  - outputFile
+  - variable: outputFile
+    to-project:
diff --git a/tests/workflow-definitions/replicate-using-undeclared-input.yaml b/tests/workflow-definitions/replicate-using-undeclared-input.yaml
@@ -38,5 +38,5 @@ steps:
     from-step:
       name: step-1
       variable: outputFile
-  out:
-  - outputFile
+  - variable: outputFile
+    to-project:
diff --git a/tests/workflow-definitions/shortcut-example-1.yaml b/tests/workflow-definitions/shortcut-example-1.yaml
@@ -24,5 +24,5 @@ steps:
     from-step:
       name: example-1-step-1
       variable: outputFile
-  out:
-  - outputFile
+  - variable: outputFile
+    to-project:
diff --git a/tests/workflow-definitions/simple-python-molprops-with-options.yaml b/tests/workflow-definitions/simple-python-molprops-with-options.yaml
@@ -41,5 +41,5 @@ steps:
   - variable: outputFile
     from-workflow:
       variable: clusteredMolecules
-  out:
-  - outputFile
+  - variable: outputFile
+    to-project:
diff --git a/tests/workflow-definitions/simple-python-molprops.yaml b/tests/workflow-definitions/simple-python-molprops.yaml
@@ -37,5 +37,5 @@ steps:
   - variable: outputFile
     from-workflow:
       variable: clusteredMolecules
-  out:
-  - outputFile
+  - variable: outputFile
+    to-project:
diff --git a/tests/workflow-definitions/simple-python-parallel.yaml b/tests/workflow-definitions/simple-python-parallel.yaml
@@ -55,14 +55,14 @@ steps:
     collection: workflow-engine-unit-test-jobs
     job: concatenate
     version: "1.0.0"
-  inputs:
-  - input: inputFile
+  plumbing:
+  - variable: inputFile
     from:
       step: parallel-step-a
-      output: outputFile
-  - input: inputFile
+      variable: outputFile
+  - variable: inputFile
     from:
       step: parallel-step-b
-      output: outputFile
-  out:
-  - outputFile
+      variable: outputFile
+  - variable: outputFile
+    to-project:
diff --git a/tests/workflow-definitions/simple-python-split-combine.yaml b/tests/workflow-definitions/simple-python-split-combine.yaml
@@ -38,7 +38,7 @@ steps:
       variable: outputBase
 
 #- name: combine
-#  description: Add some params
+#  description: Combine the parallel files
 #  specification:
 #    collection: workflow-engine-unit-test-jobs
 #    job: concatenate
@@ -47,8 +47,11 @@ steps:
 #      outputFile: results.smi
 #  plumbing:
 #  - variable: inputFile
-#    from-step:
 #      variable: outputFile
+#    from-step:
 #      name: parallel
-  out:
-  - outputFile
+#  - variable: outputFile
+#    from-workflow:
+#      variable: combination
+#  - variable: outputFile
+#    to-project:
diff --git a/workflow/workflow-schema.yaml b/workflow/workflow-schema.yaml
@@ -102,6 +102,20 @@ definitions:
     - variable
     - from-workflow
 
+  # A Step variable
+  # (whose value is to be copied to the project directory)
+  step-variable-to-project:
+    type: object
+    additionalProperties: false
+    properties:
+      variable:
+        $ref: '#/definitions/variable-name'
+      to-project:
+        type: 'null'
+    required:
+    - variable
+    - to-project
+
   # A step specification variable
   # (there must be at least one if a variables block is defined).
   # Typical variable syntax based on Python's definition of a variable
@@ -167,23 +181,7 @@ definitions:
           anyOf:
           - $ref: "#/definitions/step-variable-from-step"
           - $ref: "#/definitions/step-variable-from-workflow"
-        minItems: 1
-      in:
-        # An optional list of the step variables that are inputs.
-        # These are typically files, expected to be present in the Project directory,
-        # that need to be copied (by the DM) into the step's instance directory.
-        type: array
-        items:
-          $ref: '#/definitions/variable-name'
-        minItems: 1
-      out:
-        # An optional list of the step variables that are outputs.
-        # These are typically files, expected to be present in the Step Instance directory,
-        # when it finished (successfully), that need to be copied (by the DM)
-        # into the Project directory via "realise_outputs()"
-        type: array
-        items:
-          $ref: '#/definitions/variable-name'
+          - $ref: "#/definitions/step-variable-to-project"
         minItems: 1
     required:
     - name

Original file line number	Diff line number	Diff line change
`@@ -428,7 +428,7 @@ def test_workflow_engine_simple_python_split_combine(basic_engine):`
`428`	`428`	`md,`
`429`	`429`	`da,`
`430`	`430`	`"simple-python-split-combine",`
`431`		`- {"candidateMolecules": input_file_1},`
	`431`	`+ {"candidateMolecules": input_file_1, "combination": "combination.smi"},`
`432`	`432`	`)`
`433`	`433`
`434`	`434`	`# Assert`