On 1 April 2015 at 02:06, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> 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
>

Hi Peter,

Sorry, this really is a major bug. I agree this was pushed without
much testing. In fact, I did not at all consider the use case you just
pointed out. I can send a PR that simply reverts the change, since I
am not sure I will have enough time to look into it deeper.

Looks like I have broken more things than what I have contributed.

Saket

> Peter
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