Hi Greg,
Sorry to dig up this unsolved thread from a few months back.
Recap of the bug: I have developed a small tool. I have put it in my
local Toolshed, and installed it. After applying some changes to the
tool, I 'hg push'ed the changes to my repository on my toolshed. I
uninstalled the tool, and reinstalled it. Since I work with job
handlers, I have to restart Galaxy. Since I had about ~4 committed
changes, I have repeated these steps about 4 times.
The bug: the tool appears multiple times in the tool management window.
2 times as new, and 1 time as uninstalled (since I uninstalled it). The
tool is still available in the toolbox, although it should not. The 2
installed tools have an option 'install', but when I click this I get an
internal server error 500.
Galaxy version:
*************
[galaxy@galaxy galaxy-dist]$ hg tip
changeset: 10411:c42567f43aa7
tag: tip
user: greg
date: Mon Aug 19 13:19:56 2013 -0400
summary: Filter invalid objects when generating the list of
repository_dependencies objects that are associated with a tool shed
repository installed into Galaxy.
*************
As per your request: the web log of this internal server error.
****************
193.191.128.2 - - [30/Sep/2013:13:15:19 +0200] "GET
/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.bits.vib.be/&repository_ids=968205d9ed31733d&changeset_revisions=e08a6d9e97a3
HTTP/1.1" 500 -
"http://galaxy.bits.vib.be/admin_toolshed/browse_repositories";
"Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
Ubuntu Chromium/28.0.1500.71 Chrome/28.0.1500.71 Safari/537.36"
Debug at: http://galaxy.bits.vib.be/_debug/view/1380535486
****************
The postgres database shows:
************************
galaxydb=> select id, tool_shed, name, owner,
installed_changeset_revision, status, error_message from
tool_shed_repository where name = 'transpose';
id | tool_shed | name | owner |
installed_changeset_revision | status | error_message
----+----------------------+-----------+---------+------------------------------+-------------+---------------
45 | toolshed.bits.vib.be | transpose | joachim |
cee0157acee1 | Uninstalled |
44 | toolshed.bits.vib.be | transpose | joachim |
2fa0462b9303 | New |
43 | toolshed.bits.vib.be | transpose | joachim |
e08a6d9e97a3 | New |
(3 rows)
************************
How should I proceed ?
This is the second time I experience this. On a last note: I have noted
also that I managed to get a repository with different branches in this
tool shed repository, by mixing 'hg push' and uploading a tarball. There
seems no easy way to fixing this.
Kind regards,
Joachim
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
On 06/14/2013 04:15 PM, Greg Von Kuster wrote:
Hello Joachim,
What version of Galaxy are your running?
What does the tool shed paster go show for the 500 Internal Server Error?
Also, run the following sql manually in your Galaxy database and send
the results.
select id, tool_shed, name, owner, installed_changeset_revision,
status, error_message from tool_shed_repository;
Thanks,
Greg Von Kuster
On Jun 14, 2013, at 3:41 AM, Joachim Jacob <joachim.ja...@gmail.com
<mailto:joachim.ja...@gmail.com>> wrote:
Hi all,
I have developed a tool in our local Galaxy, and imported it in a
local toolshed. I next removed the 'dev' version of the tool in
Galaxy, and installed it now via het Tool Shed Manager.
I got an error that the dependencies could not be installed. If
figured it out that it (needed to add an extra shell_command in the
tool_dependencies) (and the mount point on my system needs to have
exec permissions of course).
So I updated the tool in the toolshed. BUT, then I uninstalled the
tool from Galaxy, and reinstalled it from the Tool Shed ... instead
of just updating. Anyway, it has happened.
Now I have the tool listed in my 'Install Tool Shed Repositories',
and when I click on it, it says 'this tool is not installed'. The
only action I can apply on this installed tool shed repository is
'Install' (...). But clicking on that 'install' button, leads me to
an error page (http error 500).
******************************
URL:
http://localhost/admin_toolshed/prepare_for_install?tool_shed_url=http://localhost:9009/&repository_ids=84cbaf0b6bf7a1a9&changeset_revisions=fc2339abcab7
Module weberror.evalexception.middleware:364 in respond view
>> app_iter = self.application(environ, detect_start_response)
Module paste.recursive:84 in __call__ view
>> return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__ view
>> return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__ view
>> return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request view
>> body = method( trans, **kwargs )
Module galaxy.web.framework:221 in decorator view
>> return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.admin_toolshed:825 in
prepare_for_install view
>> raw_text = common_util.tool_shed_get( trans.app, tool_shed_url,
url )
Module tool_shed.util.common_util:110 in tool_shed_get view
>> response = urlopener.open( uri )
Module urllib2:397 in open view
>> response = meth(req, response)
Module urllib2:510 in http_response view
>> 'http', request, response, code, msg, hdrs)
Module urllib2:435 in error view
>> return self._call_chain(*args)
Module urllib2:369 in _call_chain view
>> result = func(*args)
Module urllib2:518 in http_error_default view
>> raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
HTTPError: HTTP Error 500: Internal Server Error
************************************
The same happens when I go to the Tool Shed, and try to install the
tool from there: Galaxy detects that the tool has been installed
before, and points me to that 500 error page.
Any help is heartily appreciated,
Thanks,
Joachim
--
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
--
@joachimjacob
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___________________________________________________________
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in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
