Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 024e296ea8fa6dc7c3b3da3e74ac9e520e8daf73 https://github.com/galaxyproject/galaxy/commit/024e296ea8fa6dc7c3b3da3e74ac9... Author: John Chilton jmchilton@gmail.com Date: 2017-03-20 (Mon, 20 Mar 2017)

Changed paths: M lib/galaxy/managers/datasets.py

Log Message: ----------- Re-use job.finish abstraction in dataset manager stop_creating_job.

It is used in purge a bit above and it is the better abstraction.

Commit: f153400e95ff3888fab1b6c0fb7be5686a882532 https://github.com/galaxyproject/galaxy/commit/f153400e95ff3888fab1b6c0fb7be... Author: John Chilton jmchilton@gmail.com Date: 2017-03-20 (Mon, 20 Mar 2017)

Changed paths: M test/api/test_jobs.py

Log Message: ----------- Rework jobs API to not use deprecated TestsDatasets mixin.

Commit: 009e2cbf5e9592fd8af782b2cde36d8d1687c003 https://github.com/galaxyproject/galaxy/commit/009e2cbf5e9592fd8af782b2cde36... Author: John Chilton jmchilton@gmail.com Date: 2017-03-20 (Mon, 20 Mar 2017)

Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/datasets.py M test/api/test_jobs.py M test/base/api_asserts.py M test/base/driver_util.py M test/base/populators.py M test/functional/tools/create_10.xml A test/functional/tools/create_2.xml M test/functional/tools/samples_tool_conf.xml

Log Message: ----------- Improve interaction between job state and purged datasets.

There are two basic behavior changes here and bunch of testing to verify the new behaviors.

1) Previously purging a dataset would cause a creating job to be cancelled but all outputs would need to be "deleted" in order to cause the creating job to be cancelled. After this change the behavior is the same for both deletion and purging - the job will run until all outputs are deleted or purged.

2) Previously Galaxy jobs wouldn't attempt to cleanup purged datasets that were created by a running tool - this cleanup now occurs.

These are tackled as a pair because I assume the difference in the behaviors between deletion and purging was a hack around tools populating datasets that had been purged while running. Cancelling the job wasn't a sure fix - but it would reduce the likelihood of such problems. I think the new approach is a bit more robust and explicit.

Commit: 967d0b6c0aef6fe331c4e9c92bc1b902363e660a https://github.com/galaxyproject/galaxy/commit/967d0b6c0aef6fe331c4e9c92bc1b... Author: Martin Cech marten@bx.psu.edu Date: 2017-03-27 (Mon, 27 Mar 2017)

Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/datasets.py M test/api/test_jobs.py M test/base/api_asserts.py M test/base/driver_util.py M test/base/populators.py M test/functional/tools/create_10.xml A test/functional/tools/create_2.xml M test/functional/tools/samples_tool_conf.xml

Log Message: ----------- Merge pull request #3619 from jmchilton/purge_jobs_rework

Improve interaction between job state and purged datasets.

Compare: https://github.com/galaxyproject/galaxy/compare/1c716eb9da35...967d0b6c0aef