See attachment.

Joachim Jacob
Contact details:

On 09/30/2013 02:15 PM, Peter Cock wrote:
On Mon, Sep 30, 2013 at 1:05 PM, Joachim Jacob | VIB |
<> 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.

**************** - - [30/Sep/2013:13:15:19 +0200] "GET
HTTP/1.1" 500 -
""; "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:

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 | | transpose | joachim | cee0157acee1
| Uninstalled |
  44 | | transpose | joachim | 2fa0462b9303
| New         |
  43 | | 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,
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).


<<attachment: Selection_221.png>>

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