feat: Add smiles-to-file workflow (and test)

Author: Alan Christie

tests/instance_launcher.py

@@ -1,5 +1,6 @@
 import json
 import os
+import shutil
 import subprocess
 from datetime import datetime, timezone
 from subprocess import CompletedProcess
@@ -14,7 +15,16 @@
 from tests.message_dispatcher import UnitTestMessageDispatcher
 from workflow.workflow_abc import InstanceLauncher, LaunchResult
 
-_JOB_DIRECTORY: str = os.path.join(os.path.dirname(__file__), "jobs")
+# Full path to the 'jobs' directory
+_JOB_PATH: str = os.path.join(os.path.dirname(__file__), "jobs")
+# Relative path to the execution (project) directory
+_EXECUTION_DIRECTORY: str = os.path.join("tests", "project-root", TEST_PROJECT_ID)
+
+
+def project_file_exists(file_name: str) -> bool:
+    """A convenient test function to verify a file exists
+    in the execution (project) directory."""
+    return os.path.isfile(os.path.join(_EXECUTION_DIRECTORY, file_name))
 
 
 class UnitTestInstanceLauncher(InstanceLauncher):
@@ -43,6 +53,11 @@ def __init__(
         self._api_adapter = api_adapter
         self._msg_dispatcher = msg_dispatcher
 
+        # Every launcher starts with an empty execution directory...
+        print(f"Removing execution directory ({_EXECUTION_DIRECTORY})")
+        assert _EXECUTION_DIRECTORY.startswith("tests/project-root")
+        shutil.rmtree(_EXECUTION_DIRECTORY, ignore_errors=True)
+
     def launch(
         self,
         *,
@@ -60,6 +75,8 @@ def launch(
 
         assert project_id == TEST_PROJECT_ID
 
+        os.makedirs(_EXECUTION_DIRECTORY, exist_ok=True)
+
         # We're passed a RunningWorkflowStep ID but a record is expected to have been
         # created bt the caller, we simply create instance records.
         response = self._api_adapter.get_running_workflow_step(
@@ -74,10 +91,6 @@ def launch(
         response = self._api_adapter.create_task(instance_id=instance_id)
         task_id = response["id"]
 
-        # Where to run the job (i.e. in the test project directory)
-        execution_directory = f"tests/project-root/{project_id}"
-        os.makedirs(execution_directory, exist_ok=True)
-
         # Apply variables to the step's Job command.
         step_specification_map = json.loads(step_specification)
         job = self._api_adapter.get_job(
@@ -99,15 +112,15 @@ def launch(
         assert status
 
         # Now run the decoded command, which will be in the _JOB_DIRECTORY
-        command = f"{_JOB_DIRECTORY}/{decoded_command}"
+        command = f"{_JOB_PATH}/{decoded_command}"
         command_list = command.split()
         module = command_list[0]
         print(f"Module: {module}")
         assert os.path.isfile(module)
         subprocess_cmd: List[str] = ["python"] + command_list
         print(f"Subprocess command: {subprocess_cmd}")
         completed_process: CompletedProcess = subprocess.run(
-            subprocess_cmd, check=False, cwd=execution_directory
+            subprocess_cmd, check=False, cwd=_EXECUTION_DIRECTORY
         )
 
         # Simulate a PodMessage (that will contain the instance ID),

tests/test_workflow_engine_examples.py

@@ -12,7 +12,7 @@
 
 from tests.api_adapter import UnitTestAPIAdapter
 from tests.config import TEST_PROJECT_ID
-from tests.instance_launcher import UnitTestInstanceLauncher
+from tests.instance_launcher import UnitTestInstanceLauncher, project_file_exists
 from tests.message_dispatcher import UnitTestMessageDispatcher
 from tests.message_queue import UnitTestMessageQueue
 from workflow.workflow_engine import WorkflowEngine
@@ -148,3 +148,28 @@ def test_workflow_engine_example_nop_fail(basic_engine):
     assert response["count"] == 1
     assert response["running_workflow_steps"][0]["running_workflow_step"]["done"]
     assert not response["running_workflow_steps"][0]["running_workflow_step"]["success"]
+
+
+def test_workflow_engine_example_smiles_to_file(basic_engine):
+    # Arrange
+    da, md = 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"
+    assert not project_file_exists(output_file)
+
+    # Act
+    r_wfid = start_workflow(
+        md, da, "example-smiles-to-file", {"smiles": "CCO", "outputFile": output_file}
+    )
+
+    # Assert
+    wait_for_workflow(da, r_wfid)
+    # Additional, detailed checks...
+    # Check we only haver one step, and it failed
+    response = da.get_running_workflow_steps(running_workflow_id=r_wfid)
+    assert response["count"] == 1
+    assert response["running_workflow_steps"][0]["running_workflow_step"]["done"]
+    assert response["running_workflow_steps"][0]["running_workflow_step"]["success"]
+    # This test should generate some files now existing the project directory
+    assert project_file_exists(output_file)

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

@@ -0,0 +1,15 @@
+---
+kind: DataManagerWorkflow
+kind-version: "2024.1"
+name: smiles-to-file
+description: >-
+  A workflow with one step that uses variables.
+  The step takes an input string and the Job creates a file from it.
+steps:
+- name: step-1
+  specification: >-
+    {
+      "collection": "workflow-engine-unit-test-jobs",
+      "job": "smiles-to-file",
+      "version": "1.0.0"
+    }