Re: [galaxy-dev] Toolshed error when browsing own repo's
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 g...@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=communityoperation=my_repositorieshttp://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=my_repositorieshttp://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=my_repositories
Re: [galaxy-dev] Toolshed error when browsing own repo's
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=communityoperation=my_repositorieshttp://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=my_repositories Module paste.exceptions.errormiddleware:*143* in |__call__| | http://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=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=communityoperation=my_repositories#environ*,* self*.*app*)*| Module paste.wsgilib:*539* in |intercept_output| | http://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=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=communityoperation=my_repositories#*return* self*.*application*(*environ*,* start_response*)*| Module paste.httpexceptions:*632* in |__call__| | http://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=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=communityoperation=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=communityoperation=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=communityoperation=my_repositories#kwargs*=*kwargs *)*| Module galaxy.web.framework:*722* in |fill_template| | http://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=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=communityoperation=my_repositories#*return* template*.*render*(* data *)*| Module mako.template:*296* in |render| | http://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=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=communityoperation=my_repositories#_kwargs_for_callable*(*callable_*,* data*)**)*| Module mako.runtime:*692* in |_render_context| | http://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=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=communityoperation=my_repositories#callable_*(*context*,* ***args*,* kwargs*)*| Module _base_mako:*42* in |render_body| | http://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=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=communityoperation=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=communityoperation=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=communityoperation=my_repositories#__M_writer*(*unicode*(*self*.*render_grid_table*(* grid*,* show_item_checkboxes *)**)**)*| Module _grid_base_mako:*768* in |render_render_grid_table| |
Re: [galaxy-dev] Toolshed error when browsing own repo's
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=communityoperation=my_repositorieshttp://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=my_repositories Module paste.exceptions.errormiddleware:*143* in |__call__| | http://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=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=communityoperation=my_repositories#environ*,* self*.*app*)*| Module paste.wsgilib:*539* in |intercept_output| | http://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=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=communityoperation=my_repositories#*return* self*.*application*(*environ*,* start_response*)*| Module paste.httpexceptions:*632* in |__call__| | http://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=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=communityoperation=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=communityoperation=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=communityoperation=my_repositories#kwargs*=*kwargs *)*| Module galaxy.web.framework:*722* in |fill_template| | http://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=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=communityoperation=my_repositories#*return* template*.*render*(* data *)*| Module mako.template:*296* in |render| | http://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=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=communityoperation=my_repositories#_kwargs_for_callable*(*callable_*,* data*)**)*| Module mako.runtime:*692* in |_render_context| | http://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=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=communityoperation=my_repositories#callable_*(*context*,* ***args*,* kwargs*)*| Module _base_mako:*42* in |render_body| | http://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=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=communityoperation=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=communityoperation=my_repositories#__M_writer*(*unicode*(*self*.*make_grid*(* grid *)**)**)*| Module
Re: [galaxy-dev] Toolshed error when browsing own repo's
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=communityoperation=my_repositorieshttp://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=my_repositories http://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=my_repositories http://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=my_repositories http://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=my_repositories Module paste.exceptions.errormiddleware:*143* in |__call__| | http://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=my_repositories# http://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=my_repositories# http://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=my_repositories# http://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=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=communityoperation=my_repositories# http://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=my_repositories# http://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=my_repositories# http://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=my_repositories#environ*,*
