Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c1614be1ef5abaab241bf9739fb99390a8954343 https://github.com/galaxyproject/galaxy/commit/c1614be1ef5abaab241bf9739fb99... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-05-31 (Thu, 31 May 2018)

Changed paths: M lib/galaxy/jobs/handler.py

Log Message: ----------- Pause jobs with invalid inputs

Otherwise these jobs may hang around forever/until the admin does a cleanup. This is probably preferable for users as well, as the pause message gives a hint of why their job didn't start running. Fixes https://github.com/galaxyproject/galaxy/issues/6022 and would minimize maintenance as outlined in https://github.com/galaxyproject/galaxy/issues/5944.

I'm working on tests, but one easy way to test this is create a collection through the list builder interface, then delete the source HDAs. Then run a workflow on the collection and without this commit the outputs get created but the job just hangs around indefinetely. With the PR the steps consuming the collection and the subsequent jobs will be paused.

Set to paused

Commit: 0e31f97269586b061ce58a9eac75743590e310a3 https://github.com/galaxyproject/galaxy/commit/0e31f97269586b061ce58a9eac757... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-05-31 (Thu, 31 May 2018)

Changed paths: M test/api/test_workflows.py

Log Message: ----------- Add a testcase for pausing jobs with deleted input

Fix test

Commit: ed0b087926c53f4c2c4293ff6443f997fafa9526 https://github.com/galaxyproject/galaxy/commit/ed0b087926c53f4c2c4293ff6443f... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-05-31 (Thu, 31 May 2018)

Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/model/__init__.py M test/api/test_workflows.py

Log Message: ----------- Fail jobs with purged inputs

We can't resume these jobs anyway, so better to set them to failed. Also resets the info field for datasets produced by resumed jobs.

Commit: f9a65a10eb10fd2942ca3306b461ba7dbae4aa09 https://github.com/galaxyproject/galaxy/commit/f9a65a10eb10fd2942ca3306b461b... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-05-31 (Thu, 31 May 2018)

Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js

Log Message: ----------- Display the info field for paused jobs

Commit: f8cc653b3051b93cea446317194fcdd88d1aa674 https://github.com/galaxyproject/galaxy/commit/f8cc653b3051b93cea446317194fc... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-05-31 (Thu, 31 May 2018)

Changed paths: M lib/galaxy/jobs/handler.py M test/api/test_workflows.py

Log Message: ----------- Pause job if input dataset state is paused

Commit: ca31222cf87a471648876575f068f4e5ac3cba92 https://github.com/galaxyproject/galaxy/commit/ca31222cf87a471648876575f068f... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-05-31 (Thu, 31 May 2018)

Changed paths: M lib/galaxy/model/__init__.py

Log Message: ----------- Optimize job resume function

Commit: c401f5a713c1774e2dd8d817de04d48e2864e40f https://github.com/galaxyproject/galaxy/commit/c401f5a713c1774e2dd8d817de04d... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-06-01 (Fri, 01 Jun 2018)

Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js

Log Message: ----------- Use info style when displaying the reason for pausing a dataset

Commit: a5594551c09250db0dac799711a0d5676817038c https://github.com/galaxyproject/galaxy/commit/a5594551c09250db0dac799711a0d... Author: Nate Coraor nate@bx.psu.edu Date: 2018-06-01 (Fri, 01 Jun 2018)

Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M lib/galaxy/jobs/handler.py M lib/galaxy/model/__init__.py M test/api/test_workflows.py

Log Message: ----------- Merge pull request #6036 from mvdbeek/kill_jobs_with_invalid_input

Pause jobs with invalid inputs

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