test: Add mock of step outputs

Author: Alan Christie

tests/test_test_api_adapter.py

@@ -443,19 +443,75 @@ def test_get_running_workflow_step_by_name():
     assert response["id"] == rwfs_id
 
 
-def test_basic_get_running_workflow_step_output_values_for_output_when_step_unknown():
+def test_mock_get_running_workflow_step_output_values_for_output():
     # Arrange
     utaa = UnitTestWorkflowAPIAdapter()
+    response = utaa.create_workflow(workflow_definition={"name": "blah"})
+    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"
+    )
 
     # Act
+    utaa.mock_get_running_workflow_step_output_values_for_output(
+        step_name="step-1", output_variable="results", output=["a", "b"]
+    )
+
+    # Assert
     response, _ = utaa.get_running_workflow_step_output_values_for_output(
         running_workflow_step_id="r-workflow-step-00000000-0000-0000-0000-000000000001",
-        output="outputFile",
+        output_variable="results",
+    )
+    assert "output" in response
+    assert len(response["output"]) == 2
+    assert "a" in response["output"]
+    assert "b" in response["output"]
+
+
+def test_basic_get_running_workflow_step_output_values_for_output_when_step_variable_name_unknown():
+    # Arrange
+    utaa = UnitTestWorkflowAPIAdapter()
+    response = utaa.create_workflow(workflow_definition={"name": "blah"})
+    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"
+    )
+
+    # Act
+    utaa.mock_get_running_workflow_step_output_values_for_output(
+        step_name="step-1", output_variable="results", output=["a", "b"]
     )
 
     # Assert
-    assert "outputs" in response
-    assert len(response["outputs"]) == 0
+    with pytest.raises(AssertionError):
+        _, _ = utaa.get_running_workflow_step_output_values_for_output(
+            running_workflow_step_id="r-workflow-step-00000000-0000-0000-0000-000000000001",
+            output_variable="unknownVariable",
+        )
+
+
+def test_basic_get_running_workflow_step_output_values_for_output_when_step_unknown():
+    # Arrange
+    utaa = UnitTestWorkflowAPIAdapter()
+
+    # Act
+    with pytest.raises(AssertionError):
+        _, _ = utaa.get_running_workflow_step_output_values_for_output(
+            running_workflow_step_id="r-workflow-step-00000000-0000-0000-0000-000000000001",
+            output_variable="outputFile",
+        )
+
+    # Assert
 
 
 def test_basic_realise():

tests/test_workflow_engine_examples.py

@@ -42,7 +42,7 @@ def basic_engine():
     print("Starting message queue...")
     message_queue.start()
 
-    yield [wapi_adapter, message_dispatcher]
+    yield [message_dispatcher, wapi_adapter]
 
     print("Stopping message queue...")
     message_queue.stop()
@@ -145,7 +145,7 @@ def wait_for_workflow(
 
 def test_workflow_engine_example_two_step_nop(basic_engine):
     # Arrange
-    da, md = basic_engine
+    md, da = basic_engine
 
     # Act
     r_wfid = start_workflow(md, da, "example-two-step-nop", {})
@@ -164,7 +164,7 @@ def test_workflow_engine_example_two_step_nop(basic_engine):
 
 def test_workflow_engine_example_nop_fail(basic_engine):
     # Arrange
-    da, md = basic_engine
+    md, da = basic_engine
 
     # Act
     r_wfid = start_workflow(md, da, "example-nop-fail", {})
@@ -181,7 +181,7 @@ def test_workflow_engine_example_nop_fail(basic_engine):
 
 def test_workflow_engine_example_smiles_to_file(basic_engine):
     # Arrange
-    da, md = basic_engine
+    md, da = basic_engine
     # Make sure a file that should be generated by the test
     # does not exist before we run the test.
     output_file = "ethanol.smi"
@@ -206,7 +206,7 @@ def test_workflow_engine_example_smiles_to_file(basic_engine):
 
 def test_workflow_engine_shortcut_example_1(basic_engine):
     # Arrange
-    da, md = basic_engine
+    md, da = basic_engine
     # Make sure files that should be generated by the test
     # do not exist before we run the test.
     output_file_a = "a.sdf"
@@ -234,7 +234,7 @@ def test_workflow_engine_shortcut_example_1(basic_engine):
 
 def test_workflow_engine_simple_python_molprops(basic_engine):
     # Arrange
-    da, md = basic_engine
+    md, da = basic_engine
     # Make sure files that should be generated by the test
     # do not exist before we run the test.
     output_file_1 = "step1.out.smi"
@@ -315,7 +315,7 @@ def test_workflow_engine_simple_python_molprops(basic_engine):
 
 def test_workflow_engine_simple_python_molprops_with_options(basic_engine):
     # Arrange
-    da, md = basic_engine
+    md, da = basic_engine
     # Make sure files that should be generated by the test
     # do not exist before we run the test.
     output_file_1 = "step1.out.smi"
@@ -403,7 +403,7 @@ def test_workflow_engine_simple_python_molprops_with_options(basic_engine):
 
 def test_workflow_engine_simple_python_parallel(basic_engine):
     # Arrange
-    da, md = basic_engine
+    md, da = basic_engine
     # Make sure files that should be generated by the test
     # do not exist before we run the test.
     output_file_first = "first-step.out.smi"

tests/wapi_adapter.py

@@ -15,6 +15,7 @@
 method.
 """
 
+import copy
 import os
 from http import HTTPStatus
 from multiprocessing import Lock
@@ -49,6 +50,7 @@
     f"{_PICKLE_DIRECTORY}/running-workflow-step.pickle"
 )
 _INSTANCE_PICKLE_FILE: str = f"{_PICKLE_DIRECTORY}/instance.pickle"
+_MOCK_STEP_OUTPUT_FILE: str = f"{_PICKLE_DIRECTORY}/mock-output.pickle"
 
 
 class UnitTestWorkflowAPIAdapter(WorkflowAPIAdapter):
@@ -73,12 +75,13 @@ def __init__(self):
             _RUNNING_WORKFLOW_PICKLE_FILE,
             _RUNNING_WORKFLOW_STEP_PICKLE_FILE,
             _INSTANCE_PICKLE_FILE,
+            _MOCK_STEP_OUTPUT_FILE,
         ]:
             with open(file, "wb") as pickle_file:
                 Pickler(pickle_file).dump({})
         UnitTestWorkflowAPIAdapter.lock.release()
 
-    def get_workflow(self, *, workflow_id: str) -> dict[str, Any]:
+    def get_workflow(self, *, workflow_id: str) -> tuple[dict[str, Any], int]:
         UnitTestWorkflowAPIAdapter.lock.acquire()
         with open(_WORKFLOW_PICKLE_FILE, "rb") as pickle_file:
             workflow = Unpickler(pickle_file).load()
@@ -138,7 +141,7 @@ def create_running_workflow_step(
         step: str,
         replica: int = 0,
         prior_running_workflow_step_id: str | None = None,
-    ) -> dict[str, Any]:
+    ) -> tuple[dict[str, Any], int]:
         if replica:
             assert replica > 0
 
@@ -172,7 +175,7 @@ def create_running_workflow_step(
 
     def get_running_workflow_step(
         self, *, running_workflow_step_id: str
-    ) -> dict[str, Any]:
+    ) -> tuple[dict[str, Any], int]:
         UnitTestWorkflowAPIAdapter.lock.acquire()
         with open(_RUNNING_WORKFLOW_STEP_PICKLE_FILE, "rb") as pickle_file:
             running_workflow_step = Unpickler(pickle_file).load()
@@ -188,7 +191,7 @@ def get_running_workflow_step(
 
     def get_running_workflow_step_by_name(
         self, *, name: str, running_workflow_id: str, replica: int = 0
-    ) -> dict[str, Any]:
+    ) -> tuple[dict[str, Any], int]:
         if replica:
             assert replica > 0
         UnitTestWorkflowAPIAdapter.lock.acquire()
@@ -293,7 +296,9 @@ def get_instance(self, *, instance_id: str) -> dict[str, Any]:
         response = {} if instance_id not in instances else instances[instance_id]
         return response, 0
 
-    def get_job(self, *, collection: str, job: str, version: str) -> dict[str, Any]:
+    def get_job(
+        self, *, collection: str, job: str, version: str
+    ) -> tuple[dict[str, Any], int]:
         assert collection == _JOB_DEFINITIONS["collection"]
         assert job in _JOB_DEFINITIONS["jobs"]
         assert version
@@ -391,14 +396,61 @@ def get_running_workflow_steps(self, *, running_workflow_id: str) -> dict[str, A
         return {"count": len(steps), "running_workflow_steps": steps}
 
     def get_running_workflow_step_output_values_for_output(
-        self, *, running_workflow_step_id: str, output: str
+        self, *, running_workflow_step_id: str, output_variable: str
     ) -> tuple[dict[str, Any], int]:
-        del running_workflow_step_id
-        del output
-        return {"outputs": []}, HTTPStatus.OK
+        """We use the 'mock' data to return output values, otherwise
+        we return an empty list. And we need to get the step in order to get its name.
+        """
+        # The RunningWorkflowStep must exist...
+        step, _ = self.get_running_workflow_step(
+            running_workflow_step_id=running_workflow_step_id
+        )
+        assert step
+        step_name: str = step["name"]
+        # Now we can inspect the 'mock' data...
+        UnitTestWorkflowAPIAdapter.lock.acquire()
+        with open(_MOCK_STEP_OUTPUT_FILE, "rb") as pickle_file:
+            mock_output = Unpickler(pickle_file).load()
+        UnitTestWorkflowAPIAdapter.lock.release()
+
+        if step_name not in mock_output:
+            return {"output": []}, 0
+        # The record's output variable must match (there's only one record per step atm)
+        assert mock_output[step_name]["output_variable"] == output_variable
+        # Now return what was provided to the mock method...
+        response = {"output": copy.copy(mock_output[step_name]["output"])}
+        return response, 0
 
     def realise_outputs(
         self, *, running_workflow_step_id: str
     ) -> tuple[dict[str, Any], int]:
         del running_workflow_step_id
         return {}, HTTPStatus.OK
+
+    # Custom (test) methods
+    # Methods not declared in the ABC
+
+    def mock_get_running_workflow_step_output_values_for_output(
+        self, *, step_name: str, output_variable: str, output: list[str]
+    ) -> None:
+        """Sets the output response for a step.
+        Limitation is that there can only be one record for each step name
+        so, for now, the output_variable is superfluous and only used
+        to check the output variable name matches."""
+        assert isinstance(step_name, str)
+        assert isinstance(output_variable, str)
+        assert isinstance(output, list)
+
+        UnitTestWorkflowAPIAdapter.lock.acquire()
+        with open(_MOCK_STEP_OUTPUT_FILE, "rb") as pickle_file:
+            mock_output = Unpickler(pickle_file).load()
+
+        record = {
+            "output_variable": output_variable,
+            "output": output,
+        }
+        mock_output[step_name] = record
+
+        with open(_MOCK_STEP_OUTPUT_FILE, "wb") as pickle_file:
+            Pickler(pickle_file).dump(mock_output)
+        UnitTestWorkflowAPIAdapter.lock.release()

workflow/workflow_abc.py

@@ -350,15 +350,15 @@ def get_job(
 
     @abstractmethod
     def get_running_workflow_step_output_values_for_output(
-        self, *, running_workflow_step_id: str, output: str
+        self, *, running_workflow_step_id: str, output_variable: str
     ) -> tuple[dict[str, Any], int]:
         """Gets the set of outputs generated for the output variable of a given step.
         The step must have stopped for this to return any meaningful value.
         Returned files might also include paths that are relative to the
         Step's instance directory."""
         # Should return a (possibly empty) list of paths and filenames:
         # {
-        #   "outputs": ["dir/file1.sdf", "dir/file2.sdf"]
+        #   "output": ["dir/file1.sdf", "dir/file2.sdf"]
         # }
 
     @abstractmethod