Toolshed error when browsing own repo's
Hi all, On a local Toolshed freshly installed, I got these errors when browsing 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> Module paste.exceptions.errormiddleware:*143* in |__call__| |>> <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#>environ*,* self*.*app*)*| Module paste.wsgilib:*539* in |intercept_output| |>> <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#>*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#>*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#>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#>*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#>kwargs*=*kwargs *)*| Module galaxy.web.framework:*722* in |fill_template| |>> <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#>*return* template*.*render*(* ****data *)*| Module mako.template:*296* in |render| |>> <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#>****_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#>_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#>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#>__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#>__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#>__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#>__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#>__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#>*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#>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#>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#>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#>_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#>self*.*fixconfig*(**)*| Module mercurial.ui:*100* in |fixconfig| |>> <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#>*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
Hi Joachim, I've not seen this in any of my tool shed development environments, nor using the test or main Galaxy tool sheds, so it is unlikely that this is a bug. It looks more likely to be a configuration problem in your local tool shed environment. Do the repositories defined in your hgweb.config match those you have on disk? 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 when browsing 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> Module paste.exceptions.errormiddleware:*143* in |__call__| |>> <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#>environ*,* self*.*app*)*| Module paste.wsgilib:*539* in |intercept_output| |>> <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#>*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#>*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#>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#>*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#>kwargs*=*kwargs *)*| Module galaxy.web.framework:*722* in |fill_template| |>> <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#>*return* template*.*render*(* ****data *)*| Module mako.template:*296* in |render| |>> <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#>****_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#>_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#>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#>__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#>__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#>__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#>__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#>__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#>*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#>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#>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#>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#>_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#>self*.*fixconfig*(**)*| Module mercurial.ui:*100* in |fixconfig| |>> <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#>*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
___________________________________________________________ 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:
Hi Greg, If it is most likely a configuration error, I will check my settings, and let you know my progress. But one note: I do not have a hgweb.config file. Where is it supposed 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 development environments, nor using the test or main Galaxy tool sheds, so it is unlikely that this is a bug. It looks more likely to be a configuration problem in your local tool shed environment. Do the repositories defined in your hgweb.config match those you have on disk?
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 when browsing 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> Module paste.exceptions.errormiddleware:*143* in |__call__| |>> <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#>environ*,* self*.*app*)*| Module paste.wsgilib:*539* in |intercept_output| |>> <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#>*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#>*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#>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#>*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#>kwargs*=*kwargs *)*| Module galaxy.web.framework:*722* in |fill_template| |>> <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#>*return* template*.*render*(* ****data *)*| Module mako.template:*296* in |render| |>> <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#>****_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#>_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#>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#>__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#>__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#>__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#>__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#>__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#>*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#>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#>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#>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#>_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#>self*.*fixconfig*(**)*| Module mercurial.ui:*100* in |fixconfig| |>> <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#>*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
___________________________________________________________ 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:
It should be in your Galaxy installation directory, and your on-disk repositories will be in a directory under the setting you've defined for 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 my settings, and let you know my progress.
But one note: I do not have a hgweb.config file. Where is it supposed 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 development environments, nor using the test or main Galaxy tool sheds, so it is unlikely that this is a bug. It looks more likely to be a configuration problem in your local tool shed environment. Do the repositories defined in your hgweb.config match those you have on disk?
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 when browsing 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> Module paste.exceptions.errormiddleware:*143* in |__call__| |>> <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#>environ*,* self*.*app*)*| Module paste.wsgilib:*539* in |intercept_output| |>> <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#>*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#>*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#>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#>*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#>kwargs*=*kwargs *)*| Module galaxy.web.framework:*722* in |fill_template| |>> <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#>*return* template*.*render*(* ****data *)*| Module mako.template:*296* in |render| |>> <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#>****_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#>_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#>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#>__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#>__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#>__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#>__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#>__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#>*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#>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#>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#>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#>_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#>self*.*fixconfig*(**)*| Module mercurial.ui:*100* in |fixconfig| |>> <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#>*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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I am sorry, but I do not have a hgweb.config file in the install dir. My organisation: /home/galaxy/toolshed --> toolshed database for local repositories /home/galaxy/galaxy-dist --> main installation directory /home/galaxy/shed_tools --> dir for shed tools installed in galaxy Note: the page to create a new repo loads well. When I fill in the details and click 'save', the error described below appears. If more info is needed, please do not hesitate to ask. Joachim PS: for completeness, all files in my installation directory top :-p [galaxy@galaxy ~]$ ll -a galaxy-dist/ total 1716 drwxrwxr-x 19 galaxy galaxy 4096 Apr 2 15:57 . drwx------ 21 galaxy galaxy 4096 Apr 2 13:33 .. -rw-rw-r-- 1 galaxy galaxy 3994 Mar 27 17:04 buildbot_setup.sh -rw-rw-r-- 1 galaxy galaxy 2244 Mar 29 11:48 community.log -rw-rw-r-- 1 galaxy galaxy 116290 Apr 2 16:06 community_webapp.log -rw-rw-r-- 1 galaxy galaxy 4 Apr 2 15:57 community_webapp.pid -rw-rw-r-- 1 galaxy galaxy 2430 Apr 2 15:57 community_wsgi.ini -rw-rw-r-- 1 galaxy galaxy 2331 Mar 27 17:04 community_wsgi.ini.sample drwxrwxr-x 2 galaxy galaxy 4096 Mar 27 17:04 contrib -rwxrwxr-x 1 galaxy galaxy 60 Mar 27 17:04 create_db.sh drwxrwxr-x 2 galaxy galaxy 4096 Mar 27 17:04 cron drwxrwxr-x 9 nobody nobody 4096 Mar 29 11:43 database -rw-rw-r-- 1 galaxy galaxy 27442 Mar 27 17:04 datatypes_conf.xml -rw-rw-r-- 1 galaxy galaxy 27442 Mar 27 17:04 datatypes_conf.xml.sample -rw-rw-r-- 1 galaxy galaxy 1925 Mar 27 17:04 demo_sequencer_wsgi.ini.sample drwxrwxr-x 7 galaxy galaxy 4096 Mar 27 17:04 display_applications -rw-rw-r-- 1 galaxy galaxy 8965 Mar 27 17:04 dist-eggs.ini -rw-rw-r-- 1 galaxy galaxy 521 Mar 27 17:04 distributed_object_store_conf.xml.sample drwxrwxr-x 26 galaxy galaxy 4096 Mar 29 10:54 eggs -rw-rw-r-- 1 galaxy galaxy 1687 Mar 27 17:04 eggs.ini drwxrwxr-x 2 galaxy galaxy 4096 Mar 27 17:04 external_service_types -rw-rw-r-- 1 galaxy galaxy 234 Mar 27 17:04 external_service_types_conf.xml -rw-rw-r-- 1 galaxy galaxy 234 Mar 27 17:04 external_service_types_conf.xml.sample -rwxrwxr-x 1 galaxy galaxy 146 Mar 27 17:04 extract_dataset_parts.sh drwxrwxr-x 3 galaxy galaxy 4096 Mar 27 17:04 .hg -rw-rw-r-- 1 galaxy galaxy 579 Mar 27 17:04 .hgignore drwxrwxr-x 6 galaxy galaxy 4096 Apr 2 10:33 import -rw-r--r-- 1 galaxy galaxy 17751 Apr 2 13:42 integrated_tool_panel.xml drwxrwxr-x 4 galaxy galaxy 4096 Mar 27 17:04 lib -rw-rw-r-- 1 galaxy galaxy 1254 Mar 27 17:04 LICENSE.txt drwxrwxr-x 5 galaxy galaxy 4096 Mar 27 17:04 locale -rwxrwxr-x 1 galaxy galaxy 238 Mar 27 17:04 manage_db.sh -rw-rw-r-- 1 galaxy galaxy 63 Mar 27 17:04 manage_tools.sh -rw-rw-r-- 1 galaxy galaxy 68 Mar 27 17:04 migrated_tools_conf.xml -rw-rw-r-- 1 galaxy galaxy 68 Mar 27 17:04 migrated_tools_conf.xml.sample -rw-rw-r-- 1 galaxy galaxy 1088563 Apr 2 15:47 paster.log -rw-rw-r-- 1 galaxy galaxy 4 Apr 2 13:42 paster.pid -rw-rw-r-- 1 galaxy galaxy 820 Mar 27 17:04 README.txt -rw-rw-r-- 1 galaxy galaxy 2035 Mar 27 17:04 reports_wsgi.ini -rw-rw-r-- 1 galaxy galaxy 2035 Mar 27 17:04 reports_wsgi.ini.sample -rw-rw-r-- 1 galaxy galaxy 2244 Mar 28 09:41 run_community.log -rwxrwxr-x 1 galaxy galaxy 146 Mar 27 17:04 run_community.sh -rw-rw-r-- 1 galaxy galaxy 160 Mar 27 17:04 run_demo_sequencer.sh -rwxrwxr-x 1 galaxy galaxy 1913 Mar 27 17:04 run_functional_tests.sh -rw-rw-r-- 1 galaxy galaxy 153 Mar 27 17:04 run_galaxy_listener.sh -rw-rw-r-- 1 galaxy galaxy 140 Mar 27 17:04 run_reports.sh -rwxrwxr-x 1 galaxy galaxy 1437 Mar 27 17:04 run.sh -rwxrwxr-x 1 galaxy galaxy 349 Mar 27 17:04 run_unit_tests.sh drwxrwxr-x 15 galaxy galaxy 4096 Mar 27 17:05 scripts -rwxrwxr-x 1 galaxy galaxy 63 Mar 27 17:04 set_metadata.sh -rw-rw-r-- 1 galaxy galaxy 101 Mar 27 17:04 setup_rabbitmq.sh -rw-rw-r-- 1 galaxy galaxy 79 Apr 2 12:56 shed_tool_conf.xml -rw-rw-r-- 1 galaxy galaxy 69 Mar 27 17:04 shed_tool_conf.xml.sample drwxrwxr-x 16 galaxy galaxy 4096 Mar 27 17:04 static drwxrwxr-x 19 galaxy galaxy 4096 Mar 27 17:04 templates drwxrwxr-x 5 galaxy galaxy 4096 Mar 27 17:04 test drwxrwxr-x 18 galaxy galaxy 61440 Mar 27 17:04 test-data -rw-rw-r-- 1 galaxy galaxy 27345 Mar 27 17:04 tool_conf.xml -rw-rw-r-- 1 galaxy galaxy 21517 Mar 27 17:04 tool_conf.xml.main -rw-rw-r-- 1 galaxy galaxy 27345 Mar 27 17:04 tool_conf.xml.sample drwxrwxr-x 3 galaxy galaxy 4096 Mar 27 17:04 tool-data -rw-rw-r-- 1 galaxy galaxy 5226 Mar 27 17:04 tool_data_table_conf.xml -rw-rw-r-- 1 galaxy galaxy 3185 Mar 27 17:04 tool_data_table_conf.xml.oldlocstyle -rw-rw-r-- 1 galaxy galaxy 5226 Mar 27 17:04 tool_data_table_conf.xml.sample -rw-rw-r-- 1 galaxy galaxy 2618 Mar 27 17:04 tool_list.py drwxrwxr-x 45 galaxy galaxy 4096 Mar 27 17:04 tools -rw-rw-r-- 1 galaxy galaxy 291 Apr 2 12:57 tool_sheds_conf.xml -rw-rw-r-- 1 galaxy galaxy 219 Mar 27 17:04 tool_sheds_conf.xml.sample -rw-rw-r-- 1 galaxy galaxy 27983 Apr 2 15:55 universe_wsgi.ini -rw-rw-r-- 1 galaxy galaxy 27949 Mar 27 17:04 universe_wsgi.ini.sample On 04/02/2012 04:23 PM, Greg Von Kuster wrote:
It should be in your Galaxy installation directory, and your on-disk repositories will be in a directory under the setting you've defined for 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 my settings, and let you know my progress.
But one note: I do not have a hgweb.config file. Where is it supposed 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 development environments, nor using the test or main Galaxy tool sheds, so it is unlikely that this is a bug. It looks more likely to be a configuration problem in your local tool shed environment. Do the repositories defined in your hgweb.config match those you have on disk?
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 when browsing 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>> 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#>>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#>>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#>>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#>>*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#>>*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#>>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#>>*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#>>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#>>*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#>>*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#>>*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#>>****_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#>>_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#>>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#>>__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#>>__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#>>__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#>>__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#>>__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#>>*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#>>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#>>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#>>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#>>_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#>>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#>>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#>>*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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This is the problem - it's unclear how your local tool shed environment is missing this file as it must have been generated the first time your started your tool shed application ( via sh run_community.sh ). Since this file does not exist, you must not yet have created any repositories, so manually create the file with contents like this, and you should be able to create a repository. [paths] If you have created repositories in the past, then this file must have been inadvertently removed from disk, so you'll have to add entries for 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" is replaced with your repository name, and the path is replaced with your repository path. If you don't care about keeping your repositories on disk (if you in fact have any), you can delete them, and create the hgeweb.config file with just the [paths] setting and no entries. This will result in a new, 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-disk repositories will be in a directory under the setting you've defined for 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 my settings, and let you know my progress.
But one note: I do not have a hgweb.config file. Where is it supposed 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 development environments, nor using the test or main Galaxy tool sheds, so it is unlikely that this is a bug. It looks more likely to be a configuration problem in your local tool shed environment. Do the repositories defined in your hgweb.config match those you have on disk?
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 when browsing 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>> 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#>>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#>>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#>>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#>>*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#>>*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#>>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#>>*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#>>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#>>*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#>>*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#>>*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#>>****_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#>>_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#>>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#>>__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#>>__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#>>__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#>>__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#>>__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#>>*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#>>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#>>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#>>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#>>_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#>>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#>>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#>>*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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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, showing the error from below. Did I do something wrong, or are my steps from above not correct? Thanks for 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 shed environment is missing this file as it must have been generated the first time your started your tool shed application ( via sh run_community.sh ). Since this file does not exist, you must not yet have created any repositories, so manually create the file with contents like this, and you should be able to create a repository.
[paths]
If you have created repositories in the past, then this file must have been inadvertently removed from disk, so you'll have to add entries for 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" is replaced with your repository name, and the path is replaced with your repository path.
If you don't care about keeping your repositories on disk (if you in fact have any), you can delete them, and create the hgeweb.config file with just the [paths] setting and no entries. This will result in a new, 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-disk repositories will be in a directory under the setting you've defined for 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 my settings, and let you know my progress.
But one note: I do not have a hgweb.config file. Where is it supposed 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 development environments, nor using the test or main Galaxy tool sheds, so it is unlikely that this is a bug. It looks more likely to be a configuration problem in your local tool shed environment. Do the repositories defined in your hgweb.config match those you have on disk?
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 when browsing 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
___________________________________________________________ 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:
Try completely dropping and recreating your tool shed database. Also, what version of Galaxy are you running and what version of Python are you running? What database / version are you using? On Apr 2, 2012, at 11:13 AM, Joachim Jacob wrote:
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, showing the error from below.
Did I do something wrong, or are my steps from above not correct? Thanks for 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 shed environment is missing this file as it must have been generated the first time your started your tool shed application ( via sh run_community.sh ). Since this file does not exist, you must not yet have created any repositories, so manually create the file with contents like this, and you should be able to create a repository.
[paths]
If you have created repositories in the past, then this file must have been inadvertently removed from disk, so you'll have to add entries for 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" is replaced with your repository name, and the path is replaced with your repository path.
If you don't care about keeping your repositories on disk (if you in fact have any), you can delete them, and create the hgeweb.config file with just the [paths] setting and no entries. This will result in a new, 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-disk repositories will be in a directory under the setting you've defined for 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 my settings, and let you know my progress.
But one note: I do not have a hgweb.config file. Where is it supposed 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 development environments, nor using the test or main Galaxy tool sheds, so it is unlikely that this is a bug. It looks more likely to be a configuration problem in your local tool shed environment. Do the repositories defined in your hgweb.config match those you have on disk?
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 when browsing 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 > > > ___________________________________________________________ > 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/
Hi, I stopped toolshed, dropped the database, and recreated it. Relaunched toolshed without errors. I have create a login again, created a category (no problems), and tried to create a repo, which upon saving gives me the error again. Is it a problem that I use the same user for access to both the galaxy db and the toolshed db? My versions (excuse me for not posting this earlier): -- Python 2.6.6 -- Postgres version 8.4.9: bash-4.1$ psql -c "select version();" template1 version ----------------------------------------------------------------------------------------------------------------- PostgreSQL 8.4.9 on x86_64-redhat-linux-gnu, compiled by GCC gcc (GCC) 4.4.5 20110214 (Red Hat 4.4.5-6), 64-bit (1 row) -- Galaxy version: it is the latest update [galaxy@galaxy galaxy-dist]$ hg head changeset: 6799:40f1816d6857 tag: tip user: Greg Von Kuster <greg@bx.psu.edu> date: Wed Mar 07 13:35:34 2012 -0500 summary: Fix for populating the tool panel and generating the integrated_tool_panel.xml file. Joachim On 04/02/2012 05:16 PM, Greg Von Kuster wrote:
Try completely dropping and recreating your tool shed database. Also, what version of Galaxy are you running and what version of Python are you running? What database / version are you using?
On Apr 2, 2012, at 11:13 AM, Joachim Jacob wrote:
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, showing the error from below.
Did I do something wrong, or are my steps from above not correct? Thanks for 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 shed environment is missing this file as it must have been generated the first time your started your tool shed application ( via sh run_community.sh ). Since this file does not exist, you must not yet have created any repositories, so manually create the file with contents like this, and you should be able to create a repository.
[paths]
If you have created repositories in the past, then this file must have been inadvertently removed from disk, so you'll have to add entries for 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" is replaced with your repository name, and the path is replaced with your repository path.
If you don't care about keeping your repositories on disk (if you in fact have any), you can delete them, and create the hgeweb.config file with just the [paths] setting and no entries. This will result in a new, 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-disk repositories will be in a directory under the setting you've defined for 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 my settings, and let you know my progress.
But one note: I do not have a hgweb.config file. Where is it supposed 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 development environments, nor using the test or main Galaxy tool sheds, so it is unlikely that this is a bug. It looks more likely to be a configuration problem in your local tool shed environment. Do the repositories defined in your hgweb.config match those you have on disk? > > 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 when browsing 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 >> >> >> ___________________________________________________________ >> 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/
Hi Joachim, It's not a problem using the same user to access the tool shed db as you use to access the Galaxy db. However, you are using a completely separate database instance for the tool shed from the instance you have configured for Galaxy, correct? It's going to be tough for me to figure out what the problem in your environment is. Is your mercurial package correctly installed? Other things to consider are: 1. Repositories will be created on disk at the location you've specified in for your file_path setting in community_wsgi.ini. Is this directory writable by the user that starts up the tool shed? 2. The hgweb.config file should be automatically created in your Galaxy install directory when you start up your tool shed. Is this the case? If not, is your Galaxy install directory writable by the user that starts up the tool shed? From your paster log, it looks like line 757 of ~/lib/galaxy/webapps/community/controllers/common.py is this: _ui.setconfig( 'ui', 'quiet', True ) Comment out that line and see if any additinal helpful information is displayed in your paster log - the line is the one in th following complete method. def get_configured_ui(): # Configure any desired ui settings. _ui = ui.ui() # The following will suppress all messages. This is # the same as adding the following setting to the repo # hgrc file' [ui] section: # quiet = True _ui.setconfig( 'ui', 'quiet', True ) return _ui On Apr 3, 2012, at 3:32 AM, Joachim Jacob wrote:
Hi,
I stopped toolshed, dropped the database, and recreated it. Relaunched toolshed without errors. I have create a login again, created a category (no problems), and tried to create a repo, which upon saving gives me the error again.
Is it a problem that I use the same user for access to both the galaxy db and the toolshed db?
My versions (excuse me for not posting this earlier): -- Python 2.6.6 -- Postgres version 8.4.9: bash-4.1$ psql -c "select version();" template1 version ----------------------------------------------------------------------------------------------------------------- PostgreSQL 8.4.9 on x86_64-redhat-linux-gnu, compiled by GCC gcc (GCC) 4.4.5 20110214 (Red Hat 4.4.5-6), 64-bit (1 row)
-- Galaxy version: it is the latest update
[galaxy@galaxy galaxy-dist]$ hg head changeset: 6799:40f1816d6857 tag: tip user: Greg Von Kuster <greg@bx.psu.edu> date: Wed Mar 07 13:35:34 2012 -0500 summary: Fix for populating the tool panel and generating the integrated_tool_panel.xml file.
Joachim
On 04/02/2012 05:16 PM, Greg Von Kuster wrote:
Try completely dropping and recreating your tool shed database. Also, what version of Galaxy are you running and what version of Python are you running? What database / version are you using?
On Apr 2, 2012, at 11:13 AM, Joachim Jacob wrote:
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, showing the error from below.
Did I do something wrong, or are my steps from above not correct? Thanks for 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 shed environment is missing this file as it must have been generated the first time your started your tool shed application ( via sh run_community.sh ). Since this file does not exist, you must not yet have created any repositories, so manually create the file with contents like this, and you should be able to create a repository.
[paths]
If you have created repositories in the past, then this file must have been inadvertently removed from disk, so you'll have to add entries for 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" is replaced with your repository name, and the path is replaced with your repository path.
If you don't care about keeping your repositories on disk (if you in fact have any), you can delete them, and create the hgeweb.config file with just the [paths] setting and no entries. This will result in a new, 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-disk repositories will be in a directory under the setting you've defined for 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 my settings, and let you know my progress. > > But one note: I do not have a hgweb.config file. Where is it supposed 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 development environments, nor using the test or main Galaxy tool sheds, so it is unlikely that this is a bug. It looks more likely to be a configuration problem in your local tool shed environment. Do the repositories defined in your hgweb.config match those you have on disk? >> >> 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 when browsing 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 >>> >>> >>> ___________________________________________________________ >>> 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/
Hi Greg, - Toolshed uses a separate (from Galaxy) postgres database, called toolsheddb. - Mercurial has version 1.4. <--- THIS IS THE PROBLEM (default in the repo of Centos6.2) -- see below [quote] The hgweb.config file should be automatically created in your Galaxy install directory when you start up your tool shed. Is this the case? If not, is your Galaxy install directory writable by the user that starts up the tool shed? [/quote] ---> No, it does NOT! So I decided to remove the mercurial version 1.4 and do a source install of the latest version 2.1.2. After installing, as user Galaxy I confirm a correct installation with: [galaxy@galaxy galaxy-dist]$ hg debuginstall Checking encoding (UTF-8)... Checking installed modules (/usr/local/lib64/python2.6/site-packages/mercurial)... Checking templates (/usr/local/lib64/python2.6/site-packages/mercurial/templates)... Checking commit editor... Checking username... No problems detected I created a ~/.hgrc file with: [ui] username = joachim jacob <joachim.jacob@vib.be> However, after this I still have to set the PYTHONPATH variable (otherwise, python does not find mercurial): export PYTHONPATH=/usr/local/lib64/python2.6/site-packages/:${PYTHONPATH} Starting run_community.sh still fails, but the error log now reports the lack of an 'hgweb.conf' file. Now it was easy. $echo "[path]" >~/galaxy-dist/hgweb.conf And our toolshed runs now, without errors. :-D Thanks for you interest and support, Greg! Can I make a suggestion: I think the galaxy community would hugely benefit from having a forum. Cheers! Joachim --- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 04/03/2012 03:53 PM, Greg Von Kuster wrote:
Hi Joachim,
It's not a problem using the same user to access the tool shed db as you use to access the Galaxy db. However, you are using a completely separate database instance for the tool shed from the instance you have configured for Galaxy, correct?
It's going to be tough for me to figure out what the problem in your environment is. Is your mercurial package correctly installed?
Other things to consider are: 1. Repositories will be created on disk at the location you've specified in for your file_path setting in community_wsgi.ini. Is this directory writable by the user that starts up the tool shed? 2. The hgweb.config file should be automatically created in your Galaxy install directory when you start up your tool shed. Is this the case? If not, is your Galaxy install directory writable by the user that starts up the tool shed?
From your paster log, it looks like line 757 of ~/lib/galaxy/webapps/community/controllers/common.py is this:
_ui.setconfig( 'ui', 'quiet', True )
Comment out that line and see if any additinal helpful information is displayed in your paster log - the line is the one in th following complete method.
def get_configured_ui(): # Configure any desired ui settings. _ui = ui.ui() # The following will suppress all messages. This is # the same as adding the following setting to the repo # hgrc file' [ui] section: # quiet = True _ui.setconfig( 'ui', 'quiet', True ) return _ui
On Apr 3, 2012, at 3:32 AM, Joachim Jacob wrote:
Hi,
I stopped toolshed, dropped the database, and recreated it. Relaunched toolshed without errors. I have create a login again, created a category (no problems), and tried to create a repo, which upon saving gives me the error again.
Is it a problem that I use the same user for access to both the galaxy db and the toolshed db?
My versions (excuse me for not posting this earlier): -- Python 2.6.6 -- Postgres version 8.4.9: bash-4.1$ psql -c "select version();" template1 version ----------------------------------------------------------------------------------------------------------------- PostgreSQL 8.4.9 on x86_64-redhat-linux-gnu, compiled by GCC gcc (GCC) 4.4.5 20110214 (Red Hat 4.4.5-6), 64-bit (1 row)
-- Galaxy version: it is the latest update
[galaxy@galaxy galaxy-dist]$ hg head changeset: 6799:40f1816d6857 tag: tip user: Greg Von Kuster <greg@bx.psu.edu <mailto:greg@bx.psu.edu>> date: Wed Mar 07 13:35:34 2012 -0500 summary: Fix for populating the tool panel and generating the integrated_tool_panel.xml file.
Joachim
On 04/02/2012 05:16 PM, Greg Von Kuster wrote:
Try completely dropping and recreating your tool shed database. Also, what version of Galaxy are you running and what version of Python are you running? What database / version are you using?
On Apr 2, 2012, at 11:13 AM, Joachim Jacob wrote:
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, showing the error from below.
Did I do something wrong, or are my steps from above not correct? Thanks for 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 shed environment is missing this file as it must have been generated the first time your started your tool shed application ( via sh run_community.sh ). Since this file does not exist, you must not yet have created any repositories, so manually create the file with contents like this, and you should be able to create a repository.
[paths]
If you have created repositories in the past, then this file must have been inadvertently removed from disk, so you'll have to add entries for 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" is replaced with your repository name, and the path is replaced with your repository path.
If you don't care about keeping your repositories on disk (if you in fact have any), you can delete them, and create the hgeweb.config file with just the [paths] setting and no entries. This will result in a new, 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-disk repositories will be in a directory under the setting > you've defined for 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 my >> settings, and let you know my progress. >> >> But one note: I do not have a hgweb.config file. Where is it >> supposed 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 development >>> environments, nor using the test or main Galaxy tool sheds, so >>> it is unlikely that this is a bug. It looks more likely to be >>> a configuration problem in your local tool shed environment. >>> Do the repositories defined in your hgweb.config match those >>> you have on disk? >>> >>> 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 >>>> when browsing 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<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#<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#<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#<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#<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#<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#<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#<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#<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#<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#<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#<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#<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#<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#<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#<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#<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#<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#<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#<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#<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#<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#<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#<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#<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#<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#<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#<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 >>>> >>>> >>>> ___________________________________________________________ >>>> 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/
participants (2)
-
Greg Von Kuster -
Joachim Jacob