Hi Lance,

I tried several scenarios today in an attempt to reproduce this but I was not 
able to.  Have you tried uninstalling the repository (check the checkbox to 
completely uninstall it) and then reinstall it?  I'm trying to reproduce this 
on a mac running mercurial version 2.2.3 and Python 2.5.  What's your 
environment?

Greg Von Kuster


On Dec 13, 2012, at 2:30 PM, Lance Parsons wrote:

> Since I've had issues with workflow and the toolshed in the past, I have 
> changed my workflow so that my only interaction with the toolshed is either 
> via uploading a tarball via the web interface or installing a tool into my 
> local Galaxy via the web interface (or occasionally just downloading 
> tarballs).
> 
> In this specific case, I uploaded a tar.gz file of the entire tool wrapper 
> directory.  I did NOT increment the tool version.  In the past, incrementing 
> the tool version has generally worked fine.  However, when I leave the tool 
> version the same, but change something (such as the help text for the tool), 
> and then upload a tarball to the toolshed, I am unable to pull updates into 
> my local galaxy instance.  I get an error similar to what I have described.
> 
> I hope this is enough information, but let me know if I can provide more 
> detail, etc.  I would very much like to get to the root of this issue, since 
> it has plagued my attempts to use the toolshed smoothly when (seemingly 
> inevitable) minor changes need to be made.  In the past I have just had to 
> wait until I update the tool version, as no changes can be made to the 
> installed revision in my production Galaxy instance.
> 
> Greg Von Kuster wrote:
>> 
>> Hi Lance,
>> 
>> What process did you use for updating the tool shed repository and how many 
>> separate repositories did you use?  You should not be updating a local 
>> repository, pushing the changes to the tool shed repository, and then 
>> attempting to pull the changes back to the same repository.  Your repository 
>> environment should be something like this:
>> 
>> DEV REPO ( all development updates are performed here, so this is where the 
>> tool version is incremented )
>>     |
>>    V
>> <pushed changeset>
>>    |
>>    V
>> EXISTING TOOL SHED REPO
>>    |
>>   V
>> <pulled changeset to some previously cloned repo>
>>    |
>>   V
>> PREVIOUSLY CLONED (possibly production) REPO
>> 
>> In other words, nothing should ever get pushed and pulled from the tool shed 
>> repo into the same repo.  If this is the process you used, it would 
>> undoubtedly result in the behavior you saw.  If you used separate repos as I 
>> describe above, we'll need more details as to the process you used in order 
>> to determine the cause of the problem.
>> 
>> Greg Von Kuster
>> 
>> 
>> On Dec 10, 2012, at 1:45 PM, Lance Parsons wrote:
>> 
>>> I recently updated the htseq-count tool in the Galaxy toolshed to version 
>>> 0.3.  This version has some functional changes and thus the tool version 
>>> was incremented.  I installed this new version of the tool in my local 
>>> Galaxy instance.
>>> 
>>> However, I realized later that I missed updating one part of the help text. 
>>> Today I fixed that text (but left the tool version the same), tarred up the 
>>> file, and uploaded it to the toolshed.  I then attempted to "Get Updates" 
>>> from my local Galaxy instances for that tool got the following error:
>>> 
>>> URL: 
>>> http://galaxy-dev.princeton.edu/admin_toolshed/update_to_changeset_revision?tool_shed_url=http://toolshed.g2.bx.psu.edu/&name=htseq_count&owner=lparsons&changeset_revision=5d969cb56112&latest_changeset_revision=f320093f1e8e&latest_ctx_rev=11
>>> File 
>>> '/data/galaxy-dev/galaxy-dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
>>>  line 364 in respond
>>> app_iter = self.application(environ, detect_start_response)
>>> File 
>>> '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py',
>>>  line 98 in __call__
>>> environ, self.app)
>>> File 
>>> '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', 
>>> line 539 in intercept_output
>>> app_iter = application(environ, replacement_start_response)
>>> File 
>>> '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', 
>>> line 80 in __call__
>>> return self.application(environ, start_response)
>>> File 
>>> '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/middleware/remoteuser.py',
>>>  line 91 in __call__
>>> return self.app( environ, start_response )
>>> File 
>>> '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
>>>  line 632 in __call__
>>> return self.application(environ, start_response)
>>> File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/base.py', line 
>>> 160 in __call__
>>> body = method( trans, **kwargs )
>>> File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/__init__.py', 
>>> line 206 in decorator
>>> return func( self, trans, *args, **kwargs )
>>> File 
>>> '/data/galaxy-dev/galaxy-dev/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
>>>  line 1677 in update_to_changeset_revision
>>> update_repository( repo, latest_ctx_rev )
>>> File '/data/galaxy-dev/galaxy-dev/lib/galaxy/util/shed_util_common.py', 
>>> line 1428 in update_repository
>>> rev=ctx_rev )
>>> File 
>>> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/commands.py',
>>>  line 5661 in update
>>> rev = scmutil.revsingle(repo, rev, rev).rev()
>>> File 
>>> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/scmutil.py',
>>>  line 515 in revsingle
>>> l = revrange(repo, [revspec])
>>> File 
>>> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/scmutil.py',
>>>  line 588 in revrange
>>> for r in m(repo, range(len(repo))):
>>> File 
>>> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py',
>>>  line 1414 in mfunc
>>> return getset(repo, subset, tree)
>>> File 
>>> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py',
>>>  line 156 in getset
>>> return methods[x[0]](repo, subset, *x[1:])
>>> File 
>>> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py',
>>>  line 171 in symbolset
>>> return stringset(repo, subset, x)
>>> File 
>>> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py',
>>>  line 161 in stringset
>>> x = repo[x].rev()
>>> File 
>>> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/localrepo.py',
>>>  line 235 in __getitem__
>>> return context.changectx(self, changeid)
>>> File 
>>> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/context.py',
>>>  line 103 in __init__
>>> _("unknown revision '%s'") % changeid)
>>> RepoLookupError: unknown revision '11'
>>> 
>>> 
>>> I believe this is because the revision I have installed (10) is not longer 
>>> considered a valid revision by the toolshed (I presume since it is an older 
>>> revision of with the same tool version).
>>> 
>>> Any help would be appreciated.  Thanks.
>>> 
>>> -- 
>>> Lance Parsons - Scientific Programmer
>>> 134 Carl C. Icahn Laboratory
>>> Lewis-Sigler Institute for Integrative Genomics
>>> Princeton University
>>> 
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
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>>> 
>>> http://lists.bx.psu.edu/
>> 
>> 
> 
> -- 
> Lance Parsons - Scientific Programmer
> 134 Carl C. Icahn Laboratory
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University
> 

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