Fix and enhance job resume functionality #5247
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This should fix galaxyproject#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.
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 galaxyproject#5222.
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.
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 galaxyproject#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.
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Wow - this is totally awesome. Great fix and great feature to finally have some test coverage of - this is very exciting! Thanks so much @mvdbeek. |
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Replacing failed collection elements was already possible when dependent jobs were found (galaxyproject#5247). This commit restructures the remapping so that remapping is possible when no dependent jobs are available. This also simplifies the replacement of HDAs between old and new jobs.
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Replacing failed collection elements was already possible when dependent jobs were found (galaxyproject#5247). This commit restructures the remapping so that remapping is possible when no dependent jobs are available. This also simplifies the replacement of HDAs between old and new jobs.
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Replacing failed collection elements was already possible when dependent jobs were found (galaxyproject#5247). This commit restructures the remapping so that remapping is possible when no dependent jobs are available. This also simplifies the replacement of HDAs between old and new jobs.
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This should fix #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_paramfunction was not ableto 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.
The PR includes 2 testcases for this functionality, one for hda input and one for hdca input.
With this PR we also replace failed element of a collection with a job rerun (including a testcase), which fixes #2235.