toil.test.utils.toilDebugTest

Module Contents

Classes

DebugJobTest

Test the toil debug-job command.

Functions

workflow_debug_jobstore()

testJobStoreContents()

Test toilDebugFile.printContentsOfJobStore().

fetchFiles(symLink, jobStoreDir, outputDir)

Fn for testFetchJobStoreFiles() and testFetchJobStoreFilesWSymlinks().

testFetchJobStoreFiles()

Test toilDebugFile.fetchJobStoreFiles() symlinks.

Attributes

logger

toil.test.utils.toilDebugTest.logger
toil.test.utils.toilDebugTest.workflow_debug_jobstore()[source]
Return type:

str

toil.test.utils.toilDebugTest.testJobStoreContents()[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.

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:

  • symLink (bool)

  • jobStoreDir (str)

  • outputDir (str)

toil.test.utils.toilDebugTest.testFetchJobStoreFiles()[source]

Test toilDebugFile.fetchJobStoreFiles() symlinks.

Return type:

None

class toil.test.utils.toilDebugTest.DebugJobTest(methodName='runTest')[source]

Bases: toil.test.ToilTest

Test the toil debug-job command.

test_run_job()[source]

Make sure that we can use toil debug-job to try and run a job in-process.

test_print_job_info()[source]

Make sure that we can use –printJobInfo to get information on a job from a job store.