Copy of files for a failed job not working in lie_md

[marcvdijk]

In lie_md a MD job failed (GROMACS issue) and was reported as such to lie_md by Cerise:

2019-02-07T10:04:13+0100 Job 48ebeb7e2ab011e9ba0a68fef707f509 has FAILED!
2019-02-07T10:04:13+0100 Check output at: /tmp/mdstudio/lie_md/tmpxwoiomlo
2019-02-07T10:04:13+0100 waiting for job
2019-02-07T10:04:13+0100 Cerise reported error: PermanentFailure
2019-02-07T10:04:13+0100 Cerise log stored at: /tmp/mdstudio/lie_md/tmpxwoiomlo/cerise.log

The temporary dir indeed contains output files created up to the point that GROMACS failed.
Subsequently a call to the lie_md WAMP endpoint: mdgroup.lie_md.endpoint.query_liemd_results failed with the message:

File "/Users/marcvandijk/Documents/WorkProjects/liestudio-master/lie_md/lie_md/wamp_services.py", line 45, in query_liemd_results
output = yield query_simulation_results(request, self.db)
File "/opt/local/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/twisted/internet/defer.py", line 1386, in _inlineCallbacks
result = g.send(result)
File "/Users/marcvandijk/Documents/WorkProjects/liestudio-master/lie_md/lie_md/cerise_interface.py", line 176, in query_simulation_results
output = wait_extract_clean(job, srv, srv_data['workdir'], srv_data['clean_remote'])
File "/Users/marcvandijk/Documents/WorkProjects/liestudio-master/lie_md/lie_md/cerise_interface.py", line 252, in wait_extract_clean
output = get_output(job, workdir)
File "/Users/marcvandijk/Documents/WorkProjects/liestudio-master/lie_md/lie_md/cerise_interface.py", line 463, in get_output
for key, fmt in file_formats.items() if key in job.outputs}
File "/Users/marcvandijk/Documents/WorkProjects/liestudio-master/lie_md/lie_md/cerise_interface.py", line 463, in
for key, fmt in file_formats.items() if key in job.outputs}
builtins.TypeError: argument of type 'NoneType' is not iterable

It seems that the cerise_interface aims to return any of the files that where created but fails querying the job.outputs object.

[LourensVeen]

I'd be interested in seeing the cerise.log for this one, could you mail it to me?

I think I've seen a similar issue actually, with job.output being None, but I don't remember if I found a cause and fixed it. Will have to check the commit log on that one.

[LourensVeen]

Hmm, looking at it again, if there are files in that temp dir, then lie_md did manage to download them, which suggests that it was given the files by Cerise Client. So this may be an lie_md issue. I need to work on both anyway, so let's leave this issue here and we'll see.