test: Add test for options example (skipped)

Author: Alan Christie

tests/test_workflow_engine_examples.py

@@ -232,7 +232,6 @@ def test_workflow_engine_shortcut_example_1(basic_engine):
     assert project_file_exists(output_file_b)
 
 
-# @pytest.mark.skip(reason="The engine does not currently create the required variables")
 def test_workflow_engine_simple_python_molprops(basic_engine):
     # Arrange
     da, md = basic_engine
@@ -312,3 +311,88 @@ def test_workflow_engine_simple_python_molprops(basic_engine):
     # This test should generate a file in the simulated project directory
     assert project_file_exists(output_file_1)
     assert project_file_exists(output_file_2)
+
+
+@pytest.mark.skip(reason="The engine does not currently create the required variables")
+def test_workflow_engine_simple_python_molprops_with_option(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_1 = "step1.out.smi"
+    assert not project_file_exists(output_file_1)
+    output_file_2 = "step2.out.smi"
+    assert not project_file_exists(output_file_2)
+    # And create the test's input file.
+    input_file_1 = "input1.smi"
+    input_file_1_content = """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
+
+    $$$$
+    """
+    with open(
+        f"{EXECUTION_DIRECTORY}/{input_file_1}", mode="wt", encoding="utf8"
+    ) as input_file:
+        input_file.writelines(input_file_1_content)
+
+    # Act
+    r_wfid = start_workflow(
+        md,
+        da,
+        "simple-python-molprops-with-options",
+        {"candidateMolecules": input_file_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_1)
+    assert project_file_exists(output_file_2)