On Tue, Mar 31, 2015 at 6:12 PM, John Chilton <jmchil...@gmail.com> wrote: > I think it is probably a pair of bugs you are seeing: >
Having tried the revert, yes, I think so too. > The wrong database being selected is probably this: > https://trello.com/c/72WuZ8mu. It would be interesting to know if > reverting this pull request > https://bitbucket.org/galaxy/galaxy-central/pull-request/433/fix-allow-editing-workflows-on-the-fly-for/diff > fixes it - that would be a good indication this is the problem. Looking at your comments on BitBucket, it was this commit in particular: https://bitbucket.org/galaxy/galaxy-central/commits/757412c63654ff16f6cd6a0b6ff776b25e0b5b03 i.e. The commit also known as: https://github.com/galaxyproject/galaxy/commit/667c04844e35e76a698161fff6c88cb03be8396a Unfortunately a clean revert is not possible, $ git revert -n 667c04844e35e76a698161fff6c88cb03be8396a warning: too many files (created: 778 deleted: 393), skipping inexact rename detection Automatic revert failed. After resolving the conflicts, mark the corrected paths with 'git add <paths>' or 'git rm <paths>' and commit the result. This seems to work (after resetting the symlink static/scripts/packed which seemed to have been a recent change): https://github.com/peterjc/galaxy/commit/d6a2ded29c2bc404a0375fe4f6111311eea8a412 i.e. With this change, my workflow trying to use "nr" no longer defaults to the first entry in blastdb_p.loc if "nr" was missing. Instead, as with an empty blastdb_p.loc, the workflow runs with an empty path for the database (and blastx fails cleanly). This is MUCH better, since the workflow now fails rather than runs and gives misleading data. > The tool running even though no valid inputs are found - is a sort of > known-ish issue but I cannot find any Trello card on it. I know I have > some WIP on a fix here: > https://github.com/jmchilton/galaxy/commit/900b7bbbf7f0084a86da9b737967fd8eb9d9f5fe > > ... and a related failing test case here. > https://github.com/galaxyproject/galaxy/blob/dev/test/api/test_tools.py#L223 > > The fix unfortunately is messy and will likely break stuff. > > -John Running tools anyway where the expected example.loc entry is missing is bad, but most tools would fail cleanly when given an empty path - so this is less critical than the first half of the bug. i.e. Can we address the side effects of Saket's commit?: https://github.com/galaxyproject/galaxy/commit/667c04844e35e76a698161fff6c88cb03be8396a https://bitbucket.org/galaxy/galaxy-central/commits/757412c63654ff16f6cd6a0b6ff776b25e0b5b03 Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/