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
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