On Tue, Mar 31, 2015 at 6:12 PM, John Chilton jmchilton@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-editi... 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/757412c63654ff16f6cd6a0b...
i.e. The commit also known as: https://github.com/galaxyproject/galaxy/commit/667c04844e35e76a698161fff6c88...
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/d6a2ded29c2bc404a0375fe4f6111311eea...
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/900b7bbbf7f0084a86da9b737967fd8eb...
... 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/667c04844e35e76a698161fff6c88... https://bitbucket.org/galaxy/galaxy-central/commits/757412c63654ff16f6cd6a0b...
Peter