test: Initial test material for shortcut example 1

Author: Alan Christie

tests/job-definitions/job-definitions.yaml

@@ -58,3 +58,52 @@ jobs:
           smiles:
             title: SMILES
             type: string
+
+  shortcut-example-1-process-a:
+    command: >-
+      shortcut-example-1-process-a.py --outputFile {{ outputFile }}
+    variables:
+      outputs:
+        type: object
+        properties:
+          title: Output file
+          mime-types:
+          - chemical/x-mdl-sdfile
+          - squonk/x-smiles
+          creates: '{{ outputFile }}'
+          type: file
+      options:
+        type: object
+        required:
+        - outputFile
+        properties:
+          outputFile:
+            title: Output file
+            type: string
+            default: clustered.sdf
+            pattern: "^[A-Za-z0-9_/\\.\\-]+\\.(smi|sdf)$"
+
+  shortcut-example-1-process-b:
+    command: >-
+      shortcut-example-1-process-b.py --inputFile {{ inputFile }}--outputFile {{ outputFile }}
+    variables:
+      outputs:
+        type: object
+        properties:
+          title: Output file
+          mime-types:
+          - chemical/x-mdl-sdfile
+          - squonk/x-smiles
+          creates: '{{ outputFile }}'
+          type: file
+      options:
+        type: object
+        required:
+        - outputFile
+        - inputFile
+        properties:
+          outputFile:
+            title: Output file
+            type: string
+            default: clustered.sdf
+            pattern: "^[A-Za-z0-9_/\\.\\-]+\\.(smi|sdf)$"

tests/jobs/shortcut-example-1-process-a.py

@@ -0,0 +1,58 @@
+import argparse
+
+_SDF_CONTENT: str = """
+O=C(CSCc1ccc(Cl)s1)N1CCC(O)CC1
+     RDKit          3D
+
+ 18 19  0  0  0  0  0  0  0  0999 V2000
+    8.7102   -1.3539   24.2760 O   0  0  0  0  0  0  0  0  0  0  0  0
+    9.4334   -2.1203   23.6716 C   0  0  0  0  0  0  0  0  0  0  0  0
+   10.3260   -1.7920   22.4941 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.5607   -0.5667   21.3699 S   0  0  0  0  0  0  0  0  0  0  0  0
+    7.9641   -1.3976   21.0216 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.1007   -0.5241   20.1671 C   0  0  0  0  0  0  0  0  0  0  0  0
+    5.7930   -0.1276   20.3932 C   0  0  0  0  0  0  0  0  0  0  0  0
+    5.2841    0.6934   19.3422 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.2234    0.8796   18.3624 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.0491    1.8209   16.9402 Cl  0  0  0  0  0  0  0  0  0  0  0  0
+    7.6812    0.0795   18.6678 S   0  0  0  0  0  0  0  0  0  0  0  0
+    9.5928   -3.4405   24.2306 N   0  0  0  0  0  0  0  0  0  0  0  0
+   10.8197   -3.4856   25.0609 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.0016   -4.9279   25.4571 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.9315   -5.2800   26.4615 C   0  0  0  0  0  0  0  0  0  0  0  0
+   10.3887   -4.7677   27.7090 O   0  0  0  0  0  0  0  0  0  0  0  0
+    8.5793   -4.6419   26.1747 C   0  0  0  0  0  0  0  0  0  0  0  0
+    8.3826   -4.0949   24.7695 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  2  0
+  2  3  1  0
+  2 12  1  0
+  3  4  1  0
+  4  5  1  0
+  5  6  1  0
+  6  7  2  0
+  7  8  1  0
+  8  9  2  0
+  9 10  1  0
+  9 11  1  0
+ 11  6  1  0
+ 12 13  1  0
+ 13 14  1  0
+ 14 15  1  0
+ 15 16  1  0
+ 15 17  1  0
+ 17 18  1  0
+ 18 12  1  0
+M  END
+
+$$$$
+"""
+
+parser = argparse.ArgumentParser(
+    prog="shortcut-example-1-process-a",
+    description="The Job for the first step in our Shortcut example 1",
+)
+parser.add_argument("-o", "--outputFile", required=True)
+args = parser.parse_args()
+
+with open(args.outputFile, "wt", encoding="utf8") as output_file:
+    output_file.write(_SDF_CONTENT)

tests/jobs/shortcut-example-1-process-b.py

@@ -0,0 +1,16 @@
+import argparse
+
+parser = argparse.ArgumentParser(
+    prog="shortcut-example-1-process-a",
+    description="The Job for the first step in our Shortcut example 1",
+)
+parser.add_argument("-i", "--inputFile", required=True)
+parser.add_argument("-o", "--outputFile", required=True)
+args = parser.parse_args()
+
+print(args)
+
+with open(args.inputFile, "rt", encoding="utf8") as input_file:
+    content = input_file.read()
+    with open(args.outputFile, "wt", encoding="utf8") as output_file:
+        output_file.write(content)

tests/test_workflow_engine_examples.py

@@ -1,6 +1,7 @@
 import os
 import time
 from datetime import datetime, timezone
+from typing import Any
 
 import pytest
 import yaml
@@ -40,7 +41,9 @@ def basic_engine():
     print("Stopped")
 
 
-def start_workflow(md, da, workflow_file_name, variables) -> str:
+def start_workflow(
+    md, da, workflow_file_name: str, variables: dict[str, Any] | None = None
+) -> str:
     """A convenience function to handle all the 'START' logic for a workflow.
     It is given the message dispatcher, data adapter, and the base-name of the
     workflow definition - i.e. the filename without the '.yaml' extension
@@ -177,9 +180,37 @@ def test_workflow_engine_example_smiles_to_file(basic_engine):
     # Additional, detailed checks...
     # Check we only have one RunningWorkflowStep, and it succeeded
     response = da.get_running_workflow_steps(running_workflow_id=r_wfid)
-    print(f"^^^^^^ response={response}")
     assert response["count"] == 1
     assert response["running_workflow_steps"][0]["done"]
     assert response["running_workflow_steps"][0]["success"]
     # This test should generate a file in the simulated project directory
     assert project_file_exists(output_file)
+
+
+@pytest.mark.skip(reason="The engine does not currently create the required variables")
+def test_workflow_engine_shortcut_example_1(basic_engine):
+    # Arrange
+    da, md = 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"
+    assert not project_file_exists(output_file_a)
+    output_file_b = "b.sdf"
+    assert not project_file_exists(output_file_b)
+
+    # Act
+    r_wfid = start_workflow(md, da, "shortcut-example-1", {})
+
+    # Assert
+    wait_for_workflow(da, r_wfid)
+    # Additional, detailed checks...
+    # Check we only have one RunningWorkflowStep, and it succeeded
+    response = da.get_running_workflow_steps(running_workflow_id=r_wfid)
+    assert response["count"] == 2
+    assert response["running_workflow_steps"][0]["done"]
+    assert response["running_workflow_steps"][0]["success"]
+    assert response["running_workflow_steps"][1]["done"]
+    assert response["running_workflow_steps"][1]["success"]
+    # This test should generate a file in the simulated project directory
+    assert project_file_exists(output_file_a)
+    assert project_file_exists(output_file_b)

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

@@ -1,17 +1,28 @@
 ---
 kind: DataManagerWorkflow
 kind-version: "2024.1"
-name: experimental-workflow
-description: An experimental workflow
+name: shortcut-example-1
+description: The shortcut example 1 workflow
 steps:
-- name: step-1
+- name: example-1-step-1
   description: The first step
-  specification: '{"collection":"im-test","job":"process-a","version":"1.0.0", "variables":{"x": 7}}'
+  specification: >-
+    {
+      "collection": "workflow-engine-unit-test-jobs",
+      "job": "shortcut-example-1-process-a",
+      "version": "1.0.0"
+    }
   outputs:
   - output: 'outputFile'
     as: 'a.sdf'
-- name: step-2
-  specification: '{"collection":"im-test","job":"process-b","version":"1.0.0", "variables":{"y": 22}}'
+- name: example-1-step-2
+  description: The first step
+  specification: >-
+    {
+      "collection": "workflow-engine-unit-test-jobs",
+      "job": "shortcut-example-1-process-b",
+      "version": "1.0.0"
+    }
   inputs:
   - input: 'inputFile'
     from: