@@ -232,7 +232,6 @@ def test_workflow_engine_shortcut_example_1(basic_engine):
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assert project_file_exists (output_file_b )
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- # @pytest.mark.skip(reason="The engine does not currently create the required variables")
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def test_workflow_engine_simple_python_molprops (basic_engine ):
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# Arrange
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da , md = basic_engine
@@ -312,3 +311,88 @@ def test_workflow_engine_simple_python_molprops(basic_engine):
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# This test should generate a file in the simulated project directory
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assert project_file_exists (output_file_1 )
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assert project_file_exists (output_file_2 )
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+
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+
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+ @pytest .mark .skip (reason = "The engine does not currently create the required variables" )
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+ def test_workflow_engine_simple_python_molprops_with_option (basic_engine ):
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+ # Arrange
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+ da , md = basic_engine
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+ # Make sure files that should be generated by the test
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+ # do not exist before we run the test.
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+ output_file_1 = "step1.out.smi"
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+ assert not project_file_exists (output_file_1 )
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+ output_file_2 = "step2.out.smi"
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+ assert not project_file_exists (output_file_2 )
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+ # And create the test's input file.
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+ input_file_1 = "input1.smi"
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+ input_file_1_content = """O=C(CSCc1ccc(Cl)s1)N1CCC(O)CC1
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+ RDKit 3D
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+
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+ 18 19 0 0 0 0 0 0 0 0999 V2000
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+ 8.7102 -1.3539 24.2760 O 0 0 0 0 0 0 0 0 0 0 0 0
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+ 9.4334 -2.1203 23.6716 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 10.3260 -1.7920 22.4941 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 9.5607 -0.5667 21.3699 S 0 0 0 0 0 0 0 0 0 0 0 0
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+ 7.9641 -1.3976 21.0216 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 7.1007 -0.5241 20.1671 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 5.7930 -0.1276 20.3932 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 5.2841 0.6934 19.3422 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 6.2234 0.8796 18.3624 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 6.0491 1.8209 16.9402 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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+ 7.6812 0.0795 18.6678 S 0 0 0 0 0 0 0 0 0 0 0 0
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+ 9.5928 -3.4405 24.2306 N 0 0 0 0 0 0 0 0 0 0 0 0
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+ 10.8197 -3.4856 25.0609 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 11.0016 -4.9279 25.4571 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 9.9315 -5.2800 26.4615 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 10.3887 -4.7677 27.7090 O 0 0 0 0 0 0 0 0 0 0 0 0
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+ 8.5793 -4.6419 26.1747 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 8.3826 -4.0949 24.7695 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 1 2 2 0
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+ 2 3 1 0
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+ 2 12 1 0
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+ 3 4 1 0
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+ 4 5 1 0
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+ 5 6 1 0
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+ 6 7 2 0
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+ 7 8 1 0
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+ 8 9 2 0
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+ 9 10 1 0
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+ 9 11 1 0
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+ 11 6 1 0
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+ 12 13 1 0
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+ 13 14 1 0
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+ 14 15 1 0
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+ 15 16 1 0
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+ 15 17 1 0
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+ 17 18 1 0
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+ 18 12 1 0
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+ M END
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+
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+ $$$$
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+ """
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+ with open (
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+ f"{ EXECUTION_DIRECTORY } /{ input_file_1 } " , mode = "wt" , encoding = "utf8"
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+ ) as input_file :
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+ input_file .writelines (input_file_1_content )
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+
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+ # Act
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+ r_wfid = start_workflow (
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+ md ,
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+ da ,
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+ "simple-python-molprops-with-options" ,
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+ {"candidateMolecules" : input_file_1 },
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+ )
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+
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+ # Assert
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+ wait_for_workflow (da , r_wfid )
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+ # Additional, detailed checks...
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+ # Check we only have one RunningWorkflowStep, and it succeeded
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+ response = da .get_running_workflow_steps (running_workflow_id = r_wfid )
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+ assert response ["count" ] == 2
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+ assert response ["running_workflow_steps" ][0 ]["done" ]
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+ assert response ["running_workflow_steps" ][0 ]["success" ]
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+ assert response ["running_workflow_steps" ][1 ]["done" ]
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+ assert response ["running_workflow_steps" ][1 ]["success" ]
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+ # This test should generate a file in the simulated project directory
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+ assert project_file_exists (output_file_1 )
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+ assert project_file_exists (output_file_2 )
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