toil.test.wdl.builtinTest
¶
Module Contents¶
Classes¶
A set of test cases for toil's wdl functions. |
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A set of test cases for toil's conformance with WDL. |
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A set of test cases for toil's conformance with the WDL language specification: |
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A set of test cases for toil's conformance with the WDL built-in standard library: |
- class toil.test.wdl.builtinTest.WdlStandardLibraryFunctionsTest(methodName='runTest')[source]¶
Bases:
digraph inheritance8fd7d2b8d9 { bgcolor=transparent; rankdir=LR; size="8.0, 12.0"; "TestCase" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",tooltip="A class whose instances are single test cases."]; "ToilTest" [URL="../../index.html#toil.test.ToilTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A common base class for Toil tests."]; "TestCase" -> "ToilTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "WdlStandardLibraryFunctionsTest" [URL="#toil.test.wdl.builtinTest.WdlStandardLibraryFunctionsTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A set of test cases for toil's wdl functions."]; "ToilTest" -> "WdlStandardLibraryFunctionsTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; }toil.test.ToilTest
A set of test cases for toil’s wdl functions.
- classmethod setUpClass()[source]¶
Hook method for setting up class fixture before running tests in the class.
- testFn_Ceil()[source]¶
Test the wdl built-in functional equivalent of ‘ceil()’, which converts a Float value into an Int by rounding up to the next higher integer
- class toil.test.wdl.builtinTest.WdlWorkflowsTest(methodName='runTest')[source]¶
Bases:
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A set of test cases for toil’s conformance with WDL.
All tests should include a simple wdl and json file for toil to run that checks the output.
- classmethod setUpClass()[source]¶
Hook method for setting up class fixture before running tests in the class.
- check_function(function_name, cases, json_file_name=None, expected_result=None, expected_exception=None)[source]¶
Run the given WDL workflow and check its output. The WDL workflow should store its output inside a ‘output.txt’ file that can be compared to expected_result.
If expected_exception is set, this test passes only when both the workflow fails and that the given expected_exception string is present in standard error.
- class toil.test.wdl.builtinTest.WdlLanguageSpecWorkflowsTest(methodName='runTest')[source]¶
Bases:
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A set of test cases for toil’s conformance with the WDL language specification:
https://github.com/openwdl/wdl/blob/main/versions/development/SPEC.md#language-specification
- classmethod setUpClass()[source]¶
Hook method for setting up class fixture before running tests in the class.
- test_v1_declaration()[source]¶
Basic declaration example modified from the WDL 1.0 spec:
https://github.com/openwdl/wdl/blob/main/versions/1.0/SPEC.md#declarations
- class toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest(methodName='runTest')[source]¶
Bases:
digraph inheritance46d7eae5a6 { bgcolor=transparent; rankdir=LR; size="8.0, 12.0"; "TestCase" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",tooltip="A class whose instances are single test cases."]; "ToilTest" [URL="../../index.html#toil.test.ToilTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A common base class for Toil tests."]; "TestCase" -> "ToilTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "WdlStandardLibraryWorkflowsTest" [URL="#toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A set of test cases for toil's conformance with the WDL built-in standard library:"]; "WdlWorkflowsTest" -> "WdlStandardLibraryWorkflowsTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "WdlWorkflowsTest" [URL="#toil.test.wdl.builtinTest.WdlWorkflowsTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A set of test cases for toil's conformance with WDL."]; "ToilTest" -> "WdlWorkflowsTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; }WdlWorkflowsTest
A set of test cases for toil’s conformance with the WDL built-in standard library:
https://github.com/openwdl/wdl/blob/main/versions/development/SPEC.md#standard-library