Hi Greg,

Thanks a lot for your help.

I still get the same error trying to reinstall the tool...

Here is the status of the DB:

mysql> select name,id,status,deleted,uninstalled from tool_shed_repository
where name = 'contra';
+--------+----+-------------+---------+-------------+
| name   | id | status      | deleted | uninstalled |
+--------+----+-------------+---------+-------------+
| contra |  9 | Uninstalled |       1 |           1 |
+--------+----+-------------+---------+-------------+
1 row in set (0.00 sec)

select name,status from tool_dependency where tool_shed_repository_id = 9;
+----------+-------------+
| name     | status      |
+----------+-------------+
| bedtools | Uninstalled |
+----------+-------------+
1 row in set (0.00 sec)

The shed_tool_conf has no Œcontra¹ entry...

A complete remove from the DB should help to solve it, but I don¹t want to
break possible relationship tables as I¹m not familiar with the schema..

Thanks,

Franco

On 7/12/12 1:01 AM, "Greg Von Kuster" <g...@bx.psu.edu> wrote:

> Hi Franco,
> 
> Sorry you're still seeing this issue.  I assume you updated your Galaxy to the
> dist release, so not sure how you have rev 8359 - we haven't even reached that
> rev in development yet.  However, since you've updated, the cause of the
> problem is narrowed down to likely being one of the weaknesses of the mysql
> database (this is why I always recommend using postgres over mysql).
> 
> We don't have a script to execute sql statements to correct problems like this
> because they do not occur very frequently and they usually turn out to be
> something very specific to the local environment,  However, looking at your
> contra repository, it looks like it attempts to install only 1 tool dependency
> (bedtools), so it should be fairly easy to fix manually.
> 
> Step 1:
> You need to get the record of the installed tool shed repository named contra
> from your Galaxy database (you'll need the value for Step 3).  This should do
> it for you.
> 
> select * from tool_shed_repository where name = 'contra';  (Keep track of the
> id column value for Step 3 below)
> 
> Step 2:
> Now update the row using the following sql statement:
> 
> update tool_shed_repository set deleted = True, uninstalled = True where name
> = 'contra';
> 
> Step 3:
> Using the value in the id column from Step 1, execute the following sql,
> substituting that value - capitalization in the status value is required, so
> use the exact value.
> 
> update tool_dependency set status = 'Uninstalled' where
> tool_shed_repository_id = <value of id column from Step 1>;
> 
> Step 4:
> Manually edit the shed_tool_conf.xml file to remove the entry for the contra
> repository
> 
> This should be all you need to do.  Let me know if you bump into additional
> issues.
> 
> Greg Von Kuster
> 
> 
> On Dec 6, 2012, at 2:08 AM, Franco Caramia wrote:
> 
>> Re: Re-installing error persists
>> Hi Greg,
>> 
>> We have now pulled the lastest revision 8359:c08a5d0d2a4f but the problem
>> persists. The stack trace remains the same...
>> Any ideas on what could be happening?
>> Ideally we would like to be able to fix the problem through the galaxy
>> interface, but in case we find no solution, do galaxy devs have some repo for
>> MySQL scripts to ³clean² the DB?? (ex. Complete delete of a toolshed tool)..
>> 
>> 
>> Thanks,  
>> 
>> 
>> On 5/12/12 9:10 PM, "Greg Von Kuster" <g...@bx.psu.edu
>> <x-msg://14/g...@bx.psu.edu> > wrote:
>> 
>>> If you have not yet updated your Galaxy instance to the revision from the
>>> galaxy-dist repository in bitbucket, then that is most likely the cause of
>>> the behavior you are seeing.
>>> 
>>> Greg Von Kuster
>>> 
>>> On Dec 5, 2012, at 12:52 AM, Franco Caramia wrote:
>>> 
>>>> Re-installing error persists
>>>> 
>>>> 
>>>> Hi Greg,
>>>> 
>>>> I have now modified the tool_dependencies.xml thank you for that..
>>>> 
>>>> I still have problems re-installing the tool... (need to reinstall to
>>>> update the tool dependency and test it correctly)
>>>> 
>>>> Is the reinstalling failure related to my galaxy version??
>>>> 
>>>> Here is the error:
>>>> Server Error
>>>>   URL: 
>>>> http://bioinf-galaxy/admin_toolshed/browse_repositories?operation=activate+
>>>> or+reinstall&id=88ee2d7021e4dc1a
>>>> Module paste.exceptions.errormiddleware:143 in __call__
>>>>>> >>   
>>>>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act
>>>>>> ivate+or+reinstall&id=88ee2d7021e4dc1a#> app_iter =
>>>>>> self.application(environ, start_response)
>>>> Module paste.debug.prints:98 in __call__
>>>>>> >>   
>>>>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act
>>>>>> ivate+or+reinstall&id=88ee2d7021e4dc1a#> environ, self.app)
>>>> Module paste.wsgilib:539 in intercept_output
>>>>>> >>   
>>>>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act
>>>>>> ivate+or+reinstall&id=88ee2d7021e4dc1a#> app_iter = application(environ,
>>>>>> replacement_start_response)
>>>> Module paste.recursive:80 in __call__
>>>>>> >>   
>>>>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act
>>>>>> ivate+or+reinstall&id=88ee2d7021e4dc1a#> return self.application(environ,
>>>>>> start_response)
>>>> Module paste.httpexceptions:632 in __call__
>>>>>> >>   
>>>>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act
>>>>>> ivate+or+reinstall&id=88ee2d7021e4dc1a#> return self.application(environ,
>>>>>> start_response)
>>>> Module galaxy.web.framework.base:160 in __call__
>>>>>> >>   
>>>>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act
>>>>>> ivate+or+reinstall&id=88ee2d7021e4dc1a#> body = method( trans, **kwargs )
>>>> Module galaxy.web.framework:184 in decorator
>>>>>> >>   
>>>>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act
>>>>>> ivate+or+reinstall&id=88ee2d7021e4dc1a#> return func( self, trans, *args,
>>>>>> **kwargs )
>>>> Module galaxy.web.controllers.admin_toolshed:350 in browse_repositories
>>>>>> >>   
>>>>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act
>>>>>> ivate+or+reinstall&id=88ee2d7021e4dc1a#> return
>>>>>> self.reselect_tool_panel_section( trans, **kwd )
>>>> Module galaxy.web.framework:184 in decorator
>>>>>> >>   
>>>>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act
>>>>>> ivate+or+reinstall&id=88ee2d7021e4dc1a#> return func( self, trans, *args,
>>>>>> **kwargs )
>>>> Module galaxy.web.controllers.admin_toolshed:1352 in
>>>> reselect_tool_panel_section
>>>>>> >>   
>>>>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act
>>>>>> ivate+or+reinstall&id=88ee2d7021e4dc1a#> status=status )
>>>> Module galaxy.web.framework:746 in fill_template
>>>>>> >>   
>>>>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act
>>>>>> ivate+or+reinstall&id=88ee2d7021e4dc1a#> return self.fill_template_mako(
>>>>>> filename, **kwargs )
>>>> Module galaxy.web.framework:757 in fill_template_mako
>>>>>> >>   
>>>>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act
>>>>>> ivate+or+reinstall&id=88ee2d7021e4dc1a#> return template.render( **data )
>>>> Module mako.template:296 in render
>>>>>> >>   
>>>>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act
>>>>>> ivate+or+reinstall&id=88ee2d7021e4dc1a#> return runtime._render(self,
>>>>>> self.callable_, args, data)
>>>> Module mako.runtime:660 in _render
>>>>>> >>   
>>>>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act
>>>>>> ivate+or+reinstall&id=88ee2d7021e4dc1a#>
>>>>>> **_kwargs_for_callable(callable_, data))
>>>> Module mako.runtime:692 in _render_context
>>>>>> >>   
>>>>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act
>>>>>> ivate+or+reinstall&id=88ee2d7021e4dc1a#> _exec_template(inherit,
>>>>>> lclcontext, args=args, kwargs=kwargs)
>>>> Module mako.runtime:718 in _exec_template
>>>>>> >>   
>>>>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act
>>>>>> ivate+or+reinstall&id=88ee2d7021e4dc1a#> callable_(context, *args,
>>>>>> **kwargs)
>>>> Module _base_mako:42 in render_body
>>>>>> >>   
>>>>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act
>>>>>> ivate+or+reinstall&id=88ee2d7021e4dc1a#> __M_writer(unicode(next.body()))
>>>> Module _admin_tool_shed_repository_reselect_tool_panel_section_mako:76 in
>>>> render_body
>>>>>> >>   
>>>>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act
>>>>>> ivate+or+reinstall&id=88ee2d7021e4dc1a#>
>>>>>> __M_writer(unicode(render_tool_dependency_section(
>>>>>> install_tool_dependencies_check_box, [ repo_info_dict ] )))
>>>> Module _admin_tool_shed_repository_common_mako:204 in
>>>> render_render_tool_dependency_section
>>>>>> >>   
>>>>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act
>>>>>> ivate+or+reinstall&id=88ee2d7021e4dc1a#> changeset_revision )
>>>> Module posixpath:67 in join
>>>>>> >>   
>>>>>> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act
>>>>>> ivate+or+reinstall&id=88ee2d7021e4dc1a#> elif path == '' or
>>>>>> path.endswith('/'):
>>>> AttributeError: 'NoneType' object has no attribute 'endswith'
>>>> 
>>>> Thanks, 
>>>> 
>>>> Franco
>>>> 
>>>> 
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>>> 
>>> 
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> 
> 



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