Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b476cc4c57ad86c507eba22c88221584a62954a5 https://github.com/galaxyproject/galaxy/commit/b476cc4c57ad86c507eba22c88221... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-11-23 (Thu, 23 Nov 2017)

Changed paths: M lib/galaxy/jobs/runners/__init__.py

Log Message: ----------- 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' ```

Commit: 73454e12df8b8fe05aefc8ae120286e976985db8 https://github.com/galaxyproject/galaxy/commit/73454e12df8b8fe05aefc8ae12028... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-11-27 (Mon, 27 Nov 2017)

Changed paths: M lib/galaxy/jobs/runners/__init__.py

Log Message: ----------- Fix undefined exit_code_str problem (thx @nsoranzo)

Commit: cacd6eadc5b95686173c9394f635d5a25527f503 https://github.com/galaxyproject/galaxy/commit/cacd6eadc5b95686173c9394f635d... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-11-28 (Tue, 28 Nov 2017)

Changed paths: M lib/galaxy/jobs/runners/__init__.py

Log Message: ----------- Mark job wrapper as failed in a more direct way

Commit: 13f6eeecf099316acc586282773316f3858c0549 https://github.com/galaxyproject/galaxy/commit/13f6eeecf099316acc58628277331... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-11-28 (Tue, 28 Nov 2017)

Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py

Log Message: ----------- Add new runner state for 'Job output not returned from cluster'

This would allow adimns to write resubmit conditions for this specific failure.

Commit: fac65894d3efd339ae0449300fba162d177efaed https://github.com/galaxyproject/galaxy/commit/fac65894d3efd339ae0449300fba1... Author: John Chilton jmchilton@gmail.com Date: 2017-11-28 (Tue, 28 Nov 2017)

Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py

Log Message: ----------- Merge pull request #5078 from mvdbeek/fail_if_job_output_collection_fails

Fail job if job output collection fails

Compare: https://github.com/galaxyproject/galaxy/compare/c6c55e1046a7...fac65894d3ef