Hi Peter,

On Jun 16, 2011, at 10:10 AM, Peter Cock wrote:

> On Thu, Jun 16, 2011 at 2:45 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>> Peter,
>> I've added comments to each of these issues in bitbucket, and have pated
>> them inline below as well.
>>> On Jun 16, 2011, at 5:03 AM, Peter Cock wrote:
>>> Hi all,
>>> I just tried updating one of my tools on the new hg based Galaxy Tool
>>> Shed and ran into some issues. I guess I'm the first person to try
>>> this...
>>> First of all, there is no clear "update" action like there used to me.
>>> Could that be restored please?
>>> https://bitbucket.org/galaxy/galaxy-central/issue/585/hg-tool-shed-lacks-update-tool-action
>> The requested functionality is currently possible using normal mercurial
>> features ( clone -> make changes to the cloned repo -> commit changes to the
>> cloned repo -> push changes to the tool shed repo ).
> Right, but not everyone wants to use hg for this.

I understand, and that is why I am working feverishly to add features that do 
not force the use of hg form the command line (I've got several features 
functional, but not everything yet).  The current tool shed requires some use 
of hg if you want to delete files from the repo, but other than that, hg is not 
really required.  

The current tool shed also provides some very useful features (e.g., browsing 
tool code files) that were not available in the old tool shed.  In addition, 
tool developers are no longer forced to to the extra work that was necessary in 
the old tool shed to add a tool (i.e., there is no longer a requirement for 
tool suite config definitions ).  My hope is that the current features make 
everyone happy enough that they will be able to wait for those messing featuers 
that are wanted, using the current features in the meantime.

>> It is also currently possible to upload a new tarball to any "upload point"
>> (position) in the tool shed repository by selecting the upload point in the
>> built-in repository file browser. - The hierarchy that the uploaded tarball
>> contains will be added to that upload point in the tool shed repository. -
>> Any files in the uploaded tarball that do not currently exist in the tool
>> shed repository will be added. - Any files that exist in the hierarchy of
>> the uploaded tarball that also exist in the same location of the hierarchy
>> of the repository relative to the upload point will be replaced in the
>> repository.
> Yes, I tried that and its broken (bug 586 below).

This is because you uploaded a gzipped tarball, which mercurial treats like a 
single file.  The current tool shed is based on mercurial, so mercurial's 
behavior is basically the tool shed's behavior.  It is on my list to determine 
if a file is compressed and if so uncompress it upon upload.  A potential 
problem with this is that some developers may not want their uploaded file 

>>> It is on my list to: Delete any files that do not exist in the uploaded
>>> tarball's hierarchy but that do existin the same position of the tool shed
>>> repository's hierarchy relative to the upload point. This feature will
>>> require clear documented communication to the user, which I've not yet had a
>>> chance to do, but will soon.
> That would be a change from "upload files" to "replace all the files",
> in line with the missing update tool functionality (#585). To me mixing
> these two is quite strange.

This should become more clear when the feature to delete files in the hierarchy 
is added.  

>>> I tried using the "upload files to repository" option, and picked my
>>> tarball. I did not pick a location since I wanted the tar ball
>>> unpacked at the repository root, but this isn't what happened:
>>> https://bitbucket.org/galaxy/galaxy-central/issue/586/hg-tool-shed-upload-files-to-repository
>> Peter, I believe this is a duplicate of # 584, correct?
> Not really, 584 is about deleting files via the web interface.
> Perhaps you regard 585 (missing tool update) and 586 (broken upload
> at root) as the same basic issue?

See above explanation.

>>> Finally, it seems there is currently no delete files action, so I
>>> can't fix this (delete the misplaced files) via the web interface.
>>> https://bitbucket.org/galaxy/galaxy-central/issue/584/cant-delete-files-in-new-hg-tool-shed
>> You can currently delete specific files by cloning the repository, making
>> any changes you want (including deleting), and committing and pushing the
>> changes using mercurial's command line.
> Again, I'd prefer not to have to do this.


>> I've added it to my list to provide a feature allowing a user to select a
>> specific file in the repository (hopefully using the built-in file browser)
>> and deleting the file in some way that doesn't require mercurial's command
>> line, but in the meantime, use the above existing feature.
>>> Are you expecting tool authors to work primarily at the hg level?
> You didn't answer that one ;)

Not necessarily, but hg is the basis for uploading and downloading tools.  I'm 
not sure if it will be possible to completely eliminate the requirement of a 
tool developer using hg, but we're making every attempt to do so.  Why are you 
so averse to using hg?

> Peter

Greg Von Kuster
Galaxy Development Team

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