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Fail job if job output collection fails #5078

Merged
merged 4 commits into from Nov 28, 2017
Merged

Fail job if job output collection fails #5078

merged 4 commits into from Nov 28, 2017

Commits on Nov 23, 2017

  1. Fail job if job output collection fails 

    We now set a non-zero exit code to actually set a job to failed.
I belive this is a reasonable action, and it avoids green, empty datasets
with log messages like:
```
galaxy.jobs.runners ERROR 2017-11-14 13:32:06,469 (19020/860246.torque6.curie.fr) Job output not returned from cluster: [Errno 2] No such file or directory: '/data/users/mvandenb/gx
124/tmp_nfs/jwd/019/19020/galaxy_19020.o'
galaxy.jobs.runners DEBUG 2017-11-14 13:32:06,491 (19020/860246.torque6.curie.fr) Unable to cleanup /data/users/mvandenb/gx124/tmp_nfs/jwd/019/19020/galaxy_19020.o: [Errno 2] No suc
h file or directory: '/data/users/mvandenb/gx124/tmp_nfs/jwd/019/19020/galaxy_19020.o'
galaxy.jobs.runners DEBUG 2017-11-14 13:32:06,503 (19020/860246.torque6.curie.fr) Unable to cleanup /data/users/mvandenb/gx124/tmp_nfs/jwd/019/19020/galaxy_19020.e: [Errno 2] No suc
h file or directory: '/data/users/mvandenb/gx124/tmp_nfs/jwd/019/19020/galaxy_19020.e'
galaxy.jobs.runners DEBUG 2017-11-14 13:32:06,513 (19020/860246.torque6.curie.fr) Unable to cleanup /data/users/mvandenb/gx124/tmp_nfs/jwd/019/19020/galaxy_19020.ec: [Errno 2] No su
ch file or directory: '/data/users/mvandenb/gx124/tmp_nfs/jwd/019/19020/galaxy_19020.ec'
```
    @mvdbeek
    mvdbeek committed Nov 23, 2017
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Commits on Nov 27, 2017

  1. Fix undefined exit_code_str problem (thx @nsoranzo)

    @mvdbeek
    mvdbeek committed Nov 27, 2017
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Commits on Nov 28, 2017

  1. Mark job wrapper as failed in a more direct way

    @mvdbeek
    mvdbeek committed Nov 28, 2017
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  2. Add new runner state for 'Job output not returned from cluster' 

    This would allow adimns to write resubmit conditions for this specific failure.
    @mvdbeek
    mvdbeek committed Nov 28, 2017
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