Merge pull request #14 from InformaticsMatters/prototype-work-alan

Method tweaks to simplify access to prior workflow step variables

Author: alanbchristie

tests/test_decoder.py

@@ -30,8 +30,21 @@
     _SIMPLE_PYTHON_MOLPROPS_WORKFLOW: Dict[str, Any] = yaml.safe_load(workflow_file)
 assert _SIMPLE_PYTHON_MOLPROPS_WORKFLOW
 
+_DUPLICATE_WORKFLOW_VARIABLE_NAMES_WORKFLOW_FILE: str = os.path.join(
+    os.path.dirname(__file__),
+    "workflow-definitions",
+    "duplicate-workflow-variable-names.yaml",
+)
+with open(
+    _DUPLICATE_WORKFLOW_VARIABLE_NAMES_WORKFLOW_FILE, "r", encoding="utf8"
+) as workflow_file:
+    _DUPLICATE_WORKFLOW_VARIABLE_NAMES_WORKFLOW: Dict[str, Any] = yaml.safe_load(
+        workflow_file
+    )
+assert _DUPLICATE_WORKFLOW_VARIABLE_NAMES_WORKFLOW
+
 
-def test_validate_minimal():
+def test_validate_schema_for_minimal():
     # Arrange
 
     # Act
@@ -41,7 +54,7 @@ def test_validate_minimal():
     assert error is None
 
 
-def test_validate_minimal_get_step_names():
+def test_minimal_get_step_names():
     # Arrange
 
     # Act
@@ -51,7 +64,7 @@ def test_validate_minimal_get_step_names():
     assert names == ["step-1"]
 
 
-def test_validate_without_name():
+def test_workflow_without_name():
     # Arrange
     workflow = _MINIMAL_WORKFLOW.copy()
     _ = workflow.pop("name", None)
@@ -63,7 +76,7 @@ def test_validate_without_name():
     assert error == "'name' is a required property"
 
 
-def test_validate_name_with_spaces():
+def test_workflow_name_with_spaces():
     # Arrange
     workflow = _MINIMAL_WORKFLOW.copy()
     workflow["name"] = "workflow with spaces"
@@ -77,7 +90,7 @@ def test_validate_name_with_spaces():
     )
 
 
-def test_validate_shortcut_example_1():
+def test_validate_schema_for_shortcut_example_1():
     # Arrange
 
     # Act
@@ -87,7 +100,7 @@ def test_validate_shortcut_example_1():
     assert error is None
 
 
-def test_validate_python_simple_molprops():
+def test_validate_schema_for_python_simple_molprops():
     # Arrange
 
     # Act
@@ -97,15 +110,16 @@ def test_validate_python_simple_molprops():
     assert error is None
 
 
-def test_get_workflow_variables():
+def test_get_workflow_variables_for_smiple_python_molprops():
     # Arrange
 
     # Act
     wf_variables = decoder.get_variable_names(_SIMPLE_PYTHON_MOLPROPS_WORKFLOW)
 
     # Assert
-    assert len(wf_variables) == 1
+    assert len(wf_variables) == 2
     assert "candidateMolecules" in wf_variables
+    assert "clusteredMolecules" in wf_variables
 
 
 def test_get_workflow_description():
@@ -138,3 +152,15 @@ def test_get_workflow_steps():
     assert len(steps) == 2
     assert steps[0]["name"] == "step1"
     assert steps[1]["name"] == "step2"
+
+
+def test_get_workflow_variables_for_duplicate_variables():
+    # Arrange
+
+    # Act
+    names = decoder.get_variable_names(_DUPLICATE_WORKFLOW_VARIABLE_NAMES_WORKFLOW)
+
+    # Assert
+    assert len(names) == 2
+    assert names[0] == "x"
+    assert names[1] == "x"

tests/test_test_api_adapter.py

@@ -267,6 +267,37 @@ def test_get_running_workflow_step():
     assert response["name"] == "step-1"
     assert not response["done"]
     assert response["running_workflow"]["id"] == rwfid
+    assert "prior_running_workflow_step" not in response
+
+
+def test_get_running_workflow_step_with_prior_step():
+    # Arrange
+    utaa = UnitTestWorkflowAPIAdapter()
+    response = utaa.create_workflow(workflow_definition={"name": "blah"})
+    wfid = response["id"]
+    response = utaa.create_running_workflow(
+        user_id="dlister",
+        workflow_id=wfid,
+        project_id=TEST_PROJECT_ID,
+        variables={},
+    )
+    rwfid = response["id"]
+    response, _ = utaa.create_running_workflow_step(
+        running_workflow_id=rwfid,
+        step="step-1",
+        prior_running_workflow_step_id="r-workflow-step-111",
+    )
+    rwfsid = response["id"]
+
+    # Act
+    response, _ = utaa.get_running_workflow_step(running_workflow_step_id=rwfsid)
+
+    # Assert
+    assert response["name"] == "step-1"
+    assert not response["done"]
+    assert response["running_workflow"]["id"] == rwfid
+    assert "prior_running_workflow_step" in response
+    assert response["prior_running_workflow_step"]["id"] == "r-workflow-step-111"
 
 
 def test_create_instance():
@@ -291,3 +322,69 @@ def test_create_and_get_instance():
 
     # Assert
     assert response["running_workflow_step_id"] == "r-workflow-step-000"
+
+
+def test_get_workflow_steps_driving_this_step_when_1st_step():
+    # Arrange
+    utaa = UnitTestWorkflowAPIAdapter()
+    response = utaa.create_workflow(
+        workflow_definition={
+            "name": "blah",
+            "steps": [{"name": "step-1"}, {"name": "step-2"}, {"name": "step-3"}],
+        }
+    )
+    response = utaa.create_running_workflow(
+        user_id="dlister",
+        workflow_id=response["id"],
+        project_id=TEST_PROJECT_ID,
+        variables={},
+    )
+    response, _ = utaa.create_running_workflow_step(
+        running_workflow_id=response["id"], step="step-1"
+    )
+    rwfs_id = response["id"]
+
+    # Act
+    response, _ = utaa.get_workflow_steps_driving_this_step(
+        running_workflow_step_id=rwfs_id
+    )
+
+    # Assert
+    assert response["caller_step_index"] == 0
+    assert len(response["steps"]) == 3
+    assert response["steps"][0]["name"] == "step-1"
+    assert response["steps"][1]["name"] == "step-2"
+    assert response["steps"][2]["name"] == "step-3"
+
+
+def test_get_workflow_steps_driving_this_step_when_2nd_step():
+    # Arrange
+    utaa = UnitTestWorkflowAPIAdapter()
+    response = utaa.create_workflow(
+        workflow_definition={
+            "name": "blah",
+            "steps": [{"name": "step-1"}, {"name": "step-2"}, {"name": "step-3"}],
+        }
+    )
+    response = utaa.create_running_workflow(
+        user_id="dlister",
+        workflow_id=response["id"],
+        project_id=TEST_PROJECT_ID,
+        variables={},
+    )
+    response, _ = utaa.create_running_workflow_step(
+        running_workflow_id=response["id"], step="step-2"
+    )
+    rwfs_id = response["id"]
+
+    # Act
+    response, _ = utaa.get_workflow_steps_driving_this_step(
+        running_workflow_step_id=rwfs_id
+    )
+
+    # Assert
+    assert response["caller_step_index"] == 1
+    assert len(response["steps"]) == 3
+    assert response["steps"][0]["name"] == "step-1"
+    assert response["steps"][1]["name"] == "step-2"
+    assert response["steps"][2]["name"] == "step-3"

tests/test_workflow_validator_for_create_level.py

@@ -64,7 +64,7 @@ def test_validate_example_smiles_to_file():
     assert error.error_msg is None
 
 
-def test_validate_example_tow_step_nop():
+def test_validate_example_two_step_nop():
     # Arrange
     workflow_file: str = os.path.join(
         os.path.dirname(__file__), "workflow-definitions", "example-two-step-nop.yaml"

tests/test_workflow_validator_for_run_level.py

@@ -29,6 +29,26 @@ def test_validate_example_nop_file():
     assert error.error_msg is None
 
 
+def test_validate_duplicate_step_names():
+    # Arrange
+    workflow_file: str = os.path.join(
+        os.path.dirname(__file__), "workflow-definitions", "duplicate-step-names.yaml"
+    )
+    with open(workflow_file, "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.RUN,
+        workflow_definition=workflow,
+    )
+
+    # Assert
+    assert error.error_num == 2
+    assert error.error_msg == ["Duplicate step names found: step-1"]
+
+
 def test_validate_example_smiles_to_file():
     # Arrange
     workflow_file: str = os.path.join(
@@ -49,7 +69,7 @@ def test_validate_example_smiles_to_file():
     assert error.error_msg is None
 
 
-def test_validate_example_tow_step_nop():
+def test_validate_example_two_step_nop():
     # Arrange
     workflow_file: str = os.path.join(
         os.path.dirname(__file__), "workflow-definitions", "example-two-step-nop.yaml"
@@ -87,3 +107,47 @@ def test_validate_shortcut_example_1():
     # Assert
     assert error.error_num == 0
     assert error.error_msg is None
+
+
+def test_validate_simple_python_molprops():
+    # Arrange
+    workflow_file: str = os.path.join(
+        os.path.dirname(__file__), "workflow-definitions", "simple-python-molprops.yaml"
+    )
+    with open(workflow_file, "r", encoding="utf8") as workflow_file:
+        workflow: dict[str, Any] = yaml.load(workflow_file, Loader=yaml.FullLoader)
+    assert workflow
+    variables = {"candidateMolecules": "input.sdf", "clusteredMolecules": "output.sdf"}
+
+    # Act
+    error = WorkflowValidator.validate(
+        level=ValidationLevel.RUN,
+        workflow_definition=workflow,
+        variables=variables,
+    )
+
+    # Assert
+    assert error.error_num == 0
+    assert error.error_msg is None
+
+
+def test_validate_duplicate_workflow_variable_names():
+    # Arrange
+    workflow_file: str = os.path.join(
+        os.path.dirname(__file__),
+        "workflow-definitions",
+        "duplicate-workflow-variable-names.yaml",
+    )
+    with open(workflow_file, "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 workflow variable names found: x"]