toil.test.utils.toilDebugTest

A set of test cases for toilwdl.py

Module Contents

Functions

workflow_debug_jobstore(tmp_path)

testJobStoreContents(workflow_debug_jobstore)

Test toilDebugFile.printContentsOfJobStore().

fetchFiles(symLink, jobStoreDir, outputDir)

Fn for testFetchJobStoreFiles() and testFetchJobStoreFilesWSymlinks().

testFetchJobStoreFiles(tmp_path, workflow_debug_jobstore)

Test toilDebugFile.fetchJobStoreFiles() without using symlinks.

testFetchJobStoreFilesWSymlinks(tmp_path, ...)

Test toilDebugFile.fetchJobStoreFiles() using symlinks.

Attributes

logger

toil.test.utils.toilDebugTest.logger
toil.test.utils.toilDebugTest.workflow_debug_jobstore(tmp_path)[source]
Parameters

tmp_path (pathlib.Path) –

Return type

str

toil.test.utils.toilDebugTest.testJobStoreContents(workflow_debug_jobstore)[source]

Test toilDebugFile.printContentsOfJobStore().

Runs a workflow that imports ‘B.txt’ and ‘mkFile.py’ into the jobStore. ‘A.txt’, ‘C.txt’, ‘ABC.txt’ are then created. This checks to make sure these contents are found in the jobStore and printed.

Parameters

workflow_debug_jobstore (str) –

toil.test.utils.toilDebugTest.fetchFiles(symLink, jobStoreDir, outputDir)[source]

Fn for testFetchJobStoreFiles() and testFetchJobStoreFilesWSymlinks().

Runs a workflow that imports ‘B.txt’ and ‘mkFile.py’ into the jobStore. ‘A.txt’, ‘C.txt’, ‘ABC.txt’ are then created. This test then attempts to get a list of these files and copy them over into our output diectory from the jobStore, confirm that they are present, and then delete them.

Parameters

jobStoreDir (str) –

toil.test.utils.toilDebugTest.testFetchJobStoreFiles(tmp_path, workflow_debug_jobstore)[source]

Test toilDebugFile.fetchJobStoreFiles() without using symlinks.

Parameters
Return type

None

Test toilDebugFile.fetchJobStoreFiles() using symlinks.

Parameters
Return type

None