Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0dae3e7c687a943544ce590ab8790c43ca8e7801 https://github.com/galaxyproject/galaxy/commit/0dae3e7c687a943544ce590ab8790... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Fix job resume functionality for non-prefixed input data This should fix https://github.com/galaxyproject/galaxy/issues/5222. The problem was that HDA ids in nested parameters were not always being updated properly. In the case of bowtie2 the input dataset is provided via a conditional, but the conditional prefix is not being stored in the JobToInputDatasetAssociation, and so the `update_param` function was not able to update the dataset id in these instances. The approach now is to simply replace all occurences of the old dataset id with the new dataset id. TODO: tests, refactor the replacement functionality into a separate function and make this work for JobToInputDatasetCollectionAssociation. Commit: 39073b4b4c5cb7954310d9f7abbd2703b6e5d0ad https://github.com/galaxyproject/galaxy/commit/39073b4b4c5cb7954310d9f7abbd2... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Add test for resume job functionality This test runs a workflow whose first step fails, followed by a tool that uses the first step's output as an input, which is behind a nested conditional. This recapitulates the bug described in https://github.com/galaxyproject/galaxy/issues/5222. Commit: 26103416afe1843eb031586ef7bd3b896f1eb945 https://github.com/galaxyproject/galaxy/commit/26103416afe1843eb031586ef7bd3... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Move job remap functionality in separate function Commit: 9fdf0a62699b00e59da4cd0f0c275027b8603270 https://github.com/galaxyproject/galaxy/commit/9fdf0a62699b00e59da4cd0f0c275... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M test/api/test_workflows.py M test/functional/tools/job_properties.xml Log Message: ----------- Add job resume test with HDCA input to paused dataset I am slightly surprised that this worked without change, but it appears that the remapping occurs via the HDAs that the HDCA is composed of. Commit: c0dbace7bbf33da15ba1fdb9f69777a3c881cecd https://github.com/galaxyproject/galaxy/commit/c0dbace7bbf33da15ba1fdb9f6977... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M test/api/test_workflows.py M test/base/populators.py A test/functional/tools/fail_identifier.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Replace collection elements with re-run output This specifically addresses the problem where some jobs of a mapped-over collection have failed. Instead of filtering the failed collection and restarting the workflow at this position (involving a lot of copy-paste ...) the user can now limit the rerun to the problematic jobs and the workflow should resume from there. Should fix https://github.com/galaxyproject/galaxy/issues/2235. This is one possible implementation, it would also be feasible to not manipulate the original collection, but to copy the HDCA and then to replace collection elements and replace all references for jobs that depend on the HDCA, as we do for HDAs. This implementation seems simpler, but let me know if you see problems with this approach. Commit: 8e93c2e070af1263712d483d721d246e2f4356a1 https://github.com/galaxyproject/galaxy/commit/8e93c2e070af1263712d483d721d2... Author: John Chilton <jmchilton@gmail.com> Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/__init__.py M test/api/test_workflows.py M test/base/populators.py A test/functional/tools/fail_identifier.xml M test/functional/tools/job_properties.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #5247 from mvdbeek/job_rerun_fixes Fix and enhance job resume functionality Compare: https://github.com/galaxyproject/galaxy/compare/c78a23cb873c...8e93c2e070af