goerz / clusterjob Goto Github PK

PythonAction Error
Traceback (most recent call last):
  File "/path/to/repo/virtualenv/lib/python3.6/site-packages/doit/action.py", line 403, in execute
    returned_value = self.py_callable(*self.args, **kwargs)
  File "/path/to/repo/utilities.py", line 117, in wait_for_clusterjob
    run.wait()
  File "/path/to/repo/virtualenv/lib/python3.6/site-packages/clusterjob/__init__.py", line 1013, in wait
    status = self.status
  File "/path/to/repo/virtualenv/lib/python3.6/site-packages/clusterjob/__init__.py", line 938, in status
    status = self.backend.get_status(response, finished=False)
  File "/path/to/repo/virtualenv/lib/python3.6/site-packages/clusterjob/backends/lsf.py", line 103, in get_status
    status = line[status_pos:].split()[0]
IndexError: list index out of range

yield {
    'name': f'submit_{accession}',
    'actions': [
        (submit_clusterjob, (command, accession), {})
    ]
}

yield {
    'name': f'wait_{accession}',
    'actions': [
        (wait_for_clusterjob, (accession,), {})
    ]
}

def submit_clusterjob(body, jobname, runfolder, jobargs=(), jobkwargs={}):

    jobscript = clusterjob.JobScript(
        body,
        jobname,
        *jobargs,
        **jobkwargs
    )

    run = jobscript.submit(force=True)
    run.dump(os.path.join(runfolder, jobname))


def wait_for_clusterjob(jobname, runfolder):

    run = clusterjob.AsyncResult.load(os.path.join(runfolder, jobname))
    run.wait()
    os.unlink(os.path.join(runfolder, jobname))
    return run.successful()