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
>
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