Thanks Ira, I'll have this fixed tomorrow and let you know. Sorry for these glitches, we'll get these things ironed out rapidly. Thanks for helping! On Feb 7, 2012, at 7:40 PM, Ira Cooke wrote:

Dear Greg,

In the latest version of the galaxy-central code there seems to be a bug preventing me from updating my tools. When I go to update a tool I get the following error

URL: http://cookie.latrobe.edu.au:8300/admin_toolshed/browse_repositories?sort=name&f-deleted=False&operation=Get+updates&id=a3329e0bcb13f2c9 File '/var/www/galaxy/galaxyapp/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/var/www/galaxy/galaxyapp/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/var/www/galaxy/galaxyapp/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/var/www/galaxy/galaxyapp/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/var/www/galaxy/galaxyapp/lib/galaxy/web/framework/__init__.py', line 173 in decorator return func( self, trans, *args, **kwargs ) File '/var/www/galaxy/galaxyapp/lib/galaxy/web/controllers/admin_toolshed.py', line 96 in browse_repositories return self.check_for_updates( trans, **kwd ) File '/var/www/galaxy/galaxyapp/lib/galaxy/web/framework/__init__.py', line 173 in decorator return func( self, trans, *args, **kwargs ) File '/var/www/galaxy/galaxyapp/lib/galaxy/web/controllers/admin_toolshed.py', line 654 in check_for_updates ( tool_shed_url, url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) ValueError: unsupported format character '/' (0x2f) at index 1

Looking at the code there seems to be a typo on line 702 of admin_toolshed.py

It reads url = '%/srepository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \

But I think it should be url = '%s/repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \

When I change this though I still get further errors ... seems like a query to the database is not finding my toolshedrepository

The new error is

URL: http://127.0.0.1:8300/admin_toolshed/update_to_changeset_revision?tool_shed_url=http://127.0.0.1:9009/&name=protk&owner=iracooke&changeset_revision=21e996f8c650&latest_changeset_revision=21e996f8c650 File '/Users/iracooke/Sources/galaxy-proteomics/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/Users/iracooke/Sources/galaxy-proteomics/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/Users/iracooke/Sources/galaxy-proteomics/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/Users/iracooke/Sources/galaxy-proteomics/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/Users/iracooke/Sources/galaxy-proteomics/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/Users/iracooke/Sources/galaxy-proteomics/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/Users/iracooke/Sources/galaxy-proteomics/lib/galaxy/web/framework/__init__.py', line 173 in decorator return func( self, trans, *args, **kwargs ) File '/Users/iracooke/Sources/galaxy-proteomics/lib/galaxy/web/controllers/admin_toolshed.py', line 772 in update_to_changeset_revision id=trans.security.encode_id( repository.id ), AttributeError: 'NoneType' object has no attribute 'id'

If I browse my database I can find an entry in the tool_shed_repositories table which seems to have all the right data.

I'm getting these errors on the latest version of the galaxy-central code.

Ira