toil.test.utils.toilDebugTest

Attributes

logger

Classes

TestDebugJob

Test the toil debug-job command.

Functions

workflow_debug_jobstore(tmp_path)

testJobStoreContents(tmp_path)

Test toilDebugFile.printContentsOfJobStore().

fetchFiles(symLink, jobStoreDir, outputDir)

Fn for testFetchJobStoreFiles() and testFetchJobStoreFilesWSymlinks().

testFetchJobStoreFiles(tmp_path)

Test toilDebugFile.fetchJobStoreFiles() symlinks.

Module Contents

toil.test.utils.toilDebugTest.logger
toil.test.utils.toilDebugTest.workflow_debug_jobstore(tmp_path)
Parameters:

tmp_path (pathlib.Path)

Return type:

pathlib.Path

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

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:

tmp_path (pathlib.Path)

Return type:

None

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

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:
Return type:

None

toil.test.utils.toilDebugTest.testFetchJobStoreFiles(tmp_path)

Test toilDebugFile.fetchJobStoreFiles() symlinks.

Parameters:

tmp_path (pathlib.Path)

Return type:

None

class toil.test.utils.toilDebugTest.TestDebugJob

Test the toil debug-job command.

test_run_job(tmp_path)

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

Parameters:

tmp_path (pathlib.Path)

Return type:

None

test_print_job_info(tmp_path)

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

Parameters:

tmp_path (pathlib.Path)

Return type:

None

test_retrieve_task_directory(tmp_path)

Make sure that we can use –retrieveTaskDirectory to get the input files for a job.

Parameters:

tmp_path (pathlib.Path)

Return type:

None