Re: [galaxy-dev] Toolshed error when browsing own repo's

Joachim Jacob Mon, 02 Apr 2012 08:13:39 -0700

Thanks for the suggestions, but no joy.

1. I have created hgweb.config like this in the main install dir
[galaxy@galaxy galaxy-dist]$ pwd
/home/galaxy/galaxy-dist
[galaxy@galaxy galaxy-dist]$ cat hgweb.config
[paths]


2. I have removed all repo directories from the toolshed database
[galaxy@galaxy 000]$ pwd
/home/galaxy/toolshed/database/community_files/000

3. I restart the toolshed with my modified init script (centos6.2)

4. I try to create a new repo (page loads)

5. I get to 'browse my repositories': again the page won't load, showingthe error from below.

Did I do something wrong, or are my steps from above not correct? Thanksfor the help!



Kind regards,
Joachim


On 04/02/2012 05:00 PM, Greg Von Kuster wrote:

This is the problem - it's unclear how your local tool shedenvironment is missing this file as it must have been generated thefirst time your started your tool shed application ( via shrun_community.sh ). Since this file does not exist, you must not yethave created any repositories, so manually create the file withcontents like this, and you should be able to create a repository.
[paths]
If you have created repositories in the past, then this file must havebeen inadvertently removed from disk, so you'll have to add entriesfor each repository you have on disk, something like this.
[paths]

repos/test/filter = database/community_files/000/repo_1
...
where "test" is replaced with your reppository owner, "filter" isreplaced with your repository name, and the path is replaced with yourrepository path.
If you don't care about keeping your repositories on disk (if you infact have any), you can delete them, and create the hgeweb.config filewith just the [paths] setting and no entries. This will result in anew, pristine tool shed environment.
Greg Von Kuster


On Apr 2, 2012, at 10:38 AM, Joachim Jacob wrote:
I am sorry, but I do not have a hgweb.config file in the install dir.

On 04/02/2012 04:23 PM, Greg Von Kuster wrote:
It should be in your Galaxy installation directory, and your on-diskrepositories will be in a directory under the setting you've definedfor the "file_path" configuration in your community_wsgi.ini file.
On Apr 2, 2012, at 10:17 AM, Joachim Jacob wrote:
Hi Greg,
If it is most likely a configuration error, I will check mysettings, and let you know my progress.
But one note: I do not have a hgweb.config file. Where is itsupposed to reside? I cannot find this info on the toolshed wiki.
Joachim


On 04/02/2012 03:30 PM, Greg Von Kuster wrote:
Hi Joachim,
I've not seen this in any of my tool shed developmentenvironments, nor using the test or main Galaxy tool sheds, so itis unlikely that this is a bug. It looks more likely to be aconfiguration problem in your local tool shed environment. Do therepositories defined in your hgweb.config match those you have ondisk?
Greg Von Kuster

On Apr 2, 2012, at 8:38 AM, Joachim Jacob wrote:
Hi all,
On a local Toolshed freshly installed, I got these errors whenbrowsing my repository.
Perhaps a bug?


Cheers,
Joachim


Server Error
URL:http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories>>>
Module paste.exceptions.errormiddleware:*143* in |__call__|
|>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>app_iter*=* self*.*application*(*environ*,* start_response*)*|
Module paste.debug.prints:*98* in |__call__|
|>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>environ*,*self*.*app*)*|
Module paste.wsgilib:*539* in |intercept_output|
|>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>app_iter*=* application*(*environ*,* replacement_start_response*)*|
Module paste.recursive:*80* in |__call__|
|>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>*return*self*.*application*(*environ*,* start_response*)*|
Module paste.httpexceptions:*632* in |__call__|
|>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>*return*self*.*application*(*environ*,* start_response*)*|
Module galaxy.web.framework.base:*160* in |__call__|
|>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>body*=* method*(* trans*,* ****kwargs *)*|Module galaxy.webapps.community.controllers.repository:*985* in|browse_repositories||>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>*return*self*.*repository_list_grid*(* trans*,* ****kwd *)*|
Module galaxy.web.framework.helpers.grids:*277* in |__call__|
|>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>kwargs*=*kwargs*)*|
Module galaxy.web.framework:*722* in |fill_template|
|>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>*return*self*.*fill_template_mako*(* filename*,* ****kwargs *)*|
Module galaxy.web.framework:*733* in |fill_template_mako|
|>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>*return*template*.*render*(* ****data *)*|
Module mako.template:*296* in |render|
|>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>*return*runtime*.*_render*(*self*,* self*.*callable_*,* args*,* data*)*|
Module mako.runtime:*660* in |_render|
|>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>****_kwargs_for_callable*(*callable_*,*data*)**)*|
Module mako.runtime:*692* in |_render_context|
|>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>_exec_template*(*inherit*,*lclcontext*,* args*=*args*,* kwargs*=*kwargs*)*|
Module mako.runtime:*718* in |_exec_template|
|>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>callable_*(*context*,****args*,* ****kwargs*)*|
Module _base_mako:*42* in |render_body|
|>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>__M_writer*(*unicode*(*next*.*body*(**)**)**)*|
Module _grid_base_mako:*119* in |render_body|
|>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>__M_writer*(*unicode*(*self*.*grid_body*(*grid *)**)**)*|
Module _grid_base_mako:*790* in |render_grid_body|
|>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>__M_writer*(*unicode*(*self*.*make_grid*(*grid *)**)**)*|
Module _grid_base_mako:*819* in |render_make_grid|
|>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>__M_writer*(*unicode*(*self*.*render_grid_table*(*grid*,* show_item_checkboxes *)**)**)*|
Module _grid_base_mako:*768* in |render_render_grid_table|
|>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>__M_writer*(*unicode*(*render_grid_table_body_contents*(*grid*,* show_item_checkboxes *)**)**)*|
Module _grid_base_mako:*664* in |render_grid_table_body_contents|
|>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>*return*render_render_grid_table_body_contents*(*context*,*grid*,*show_item_checkboxes*)*|Module _grid_base_mako:*322* in|render_render_grid_table_body_contents||>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>value*=* column*.*get_value*(* trans*,* grid*,* item *)*|Module galaxy.webapps.community.controllers.repository:*84* in|get_value||>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>select_field*=* build_changeset_revision_select_field*(* trans*,* repository *)*|Module galaxy.webapps.community.controllers.common:*992* in|build_changeset_revision_select_field||>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>repo*=* hg*.*repository*(* get_configured_ui*(**)**,*repository*.*repo_path *)*|Module galaxy.webapps.community.controllers.common:*757* in|get_configured_ui||>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>_ui*.*setconfig*(*'ui'*,* 'quiet'*,* True *)*|
Module mercurial.ui:*113* in |setconfig|
|>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>self*.*fixconfig*(**)*|
Module mercurial.ui:*100* in |fixconfig|
|>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>self*.*quiet*=* *not* self*.*debugflag *and* self*.*configbool*(*'ui'*,*'quiet'*)*|
Module mercurial.ui:*134* in |configbool|
|>><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#><http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#<http://192.168.10.26:9009/repository/browse_repositories?webapp=community&operation=my_repositories#>>>*if*v*.*lower*(**)* *not* *in* _booleans*:*|
*AttributeError: 'bool' object has no attribute 'lower'
*

--
Joachim Jacob, PhD

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib


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Re: [galaxy-dev] Toolshed error when browsing own repo's

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