See attachment. Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 09/30/2013 02:15 PM, Peter Cock wrote:
On Mon, Sep 30, 2013 at 1:05 PM, Joachim Jacob | VIB | <joachim.jacob@vib.be> wrote:
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 Hmm - do these "New" entries show up in white on the "Manage installed tool shed repositories" admin page?
It sounds like a case of what was nicknamed "white ghosts", some causes of which have been fixed - but I don't think there was any automated removal of old "white ghosts" (I still have two on my test system).
Peter
