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')¶
Bases:
toil.test.ToilTest
A set of test cases for toil’s wdl functions.
- setUp()¶
Runs anew before each test to create farm fresh temp dirs.
- classmethod setUpClass()¶
Hook method for setting up class fixture before running tests in the class.
- tearDown()¶
Clean up outputs.
- testFn_Sub()¶
Test the wdl built-in functional equivalent of ‘sub()’.
- testFn_Ceil()¶
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
- testFn_Floor()¶
Test the wdl built-in functional equivalent of ‘floor()’, which converts a Float value into an Int by rounding down to the next lower integer
- testFn_ReadLines()¶
Test the wdl built-in functional equivalent of ‘read_lines()’.
- testFn_ReadTsv()¶
Test the wdl built-in functional equivalent of ‘read_tsv()’.
- testFn_ReadJson()¶
Test the wdl built-in functional equivalent of ‘read_json()’.
- testFn_ReadMap()¶
Test the wdl built-in functional equivalent of ‘read_map()’.
- testFn_ReadInt()¶
Test the wdl built-in functional equivalent of ‘read_int()’.
- testFn_ReadString()¶
Test the wdl built-in functional equivalent of ‘read_string()’.
- testFn_ReadFloat()¶
Test the wdl built-in functional equivalent of ‘read_float()’.
- testFn_ReadBoolean()¶
Test the wdl built-in functional equivalent of ‘read_boolean()’.
- testFn_WriteLines()¶
Test the wdl built-in functional equivalent of ‘write_lines()’.
- testFn_WriteTsv()¶
Test the wdl built-in functional equivalent of ‘write_tsv()’.
- testFn_WriteJson()¶
Test the wdl built-in functional equivalent of ‘write_json()’.
- testFn_WriteMap()¶
Test the wdl built-in functional equivalent of ‘write_map()’.
- testFn_Transpose()¶
Test the wdl built-in functional equivalent of ‘transpose()’.
- testFn_Length()¶
Test the WDL ‘length()’ built-in.
- testFn_Zip()¶
Test the wdl built-in functional equivalent of ‘zip()’.
- testFn_Cross()¶
Test the wdl built-in functional equivalent of ‘cross()’.
- class toil.test.wdl.builtinTest.WdlWorkflowsTest(methodName='runTest')¶
Bases:
toil.test.ToilTest
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()¶
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)¶
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')¶
Bases:
WdlWorkflowsTest
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()¶
Hook method for setting up class fixture before running tests in the class.
- test_type_pair()¶
- test_v1_declaration()¶
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')¶
Bases:
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
- classmethod setUpClass()¶
Hook method for setting up class fixture before running tests in the class.
- test_sub()¶
- test_size()¶
- test_ceil()¶
- test_floor()¶
- test_round()¶
- test_stdout()¶
- test_read()¶
Test the set of WDL read functions.
- test_write()¶
Test the set of WDL write functions.
- test_range()¶
- test_transpose()¶
- test_length()¶
- test_zip()¶
- test_cross()¶
- test_as_pairs()¶
- test_as_map()¶
- test_keys()¶
- test_collect_by_key()¶
- test_flatten()¶