Adam, Thank you for the information you provided, this error has been fixed in changeset 8338:42a6e3f82c0d, which will be included in the next Galaxy distribution release. The problem was that the .tar.gz you were uploading contains a tool wrapper XML, specifically rgGLM.xml, with invalid parameter definitions. These definitions were not being processed correctly, causing the error you reported. --Dave B. On 12/5/12 12:00:18.000, Adam Carr (NBI) wrote:
Sorry Greg, I hadn’t spotted your other questions there.
I’m fairly certain this must be a problem with the repository download I took as a .tar.gz from the main Galaxy Tool Shed: http://toolshed.g2.bx.psu.edu/repository/view_repository?id=ecc93bc8f0382e9e&changeset_revision=c2a356708570
I have tested this on a prior revision and the same error reoccurs.
I’m installing this clean for each test, to walk you through my process…
su – postgres
psql
postgres=# DROP DATABASE toolshed;
postgres=# CREATE DATABASE toolshed OWNER galaxy TEMPLATE template0;
postgres=# \q
exit
su – galaxy
cd toolshed/
hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
cd galaxy-dist/
hg pull –u
cp ../../community_wsgi.ini .
chmod a+x ./*run*
./run.sh --daemon start; tail -F paster.log
./run.sh --daemon stop
./run_community.sh --daemon start; tail -F community_webapp.log
I access the Tool Shed and register my account, I access the Admin menu and create a category. I create a new repository and from there attempt to upload files to repository, selecting the .tar.gz previously downloaded from the link above. This is when I receive the error:
Module paste.exceptions.errormiddleware:*143* in |__call__| |>> <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583>app_iter *=* self*.*application*(*environ*,* start_response*)*| Module paste.debug.prints:*98* in |__call__| |>> <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583>environ*,* self*.*app*)*| Module paste.wsgilib:*539* in |intercept_output| |>> <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583>app_iter *=* application*(*environ*,* replacement_start_response*)*| Module paste.recursive:*80* in |__call__| |>> <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583>*return* self*.*application*(*environ*,* start_response*)*| Module paste.httpexceptions:*632* in |__call__| |>> <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583>*return* self*.*application*(*environ*,* start_response*)*| Module galaxy.web.framework.base:*160* in |__call__| |>> <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583>body *=* method*(* trans*,* ****kwargs *)*| Module galaxy.web.framework:*94* in |decorator| |>> <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583>*return* func*(* self*,* trans*,* ***args*,* ****kwargs *)*| Module galaxy.webapps.community.controllers.upload:*184* in |upload| |>> <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583>set_repository_metadata_due_to_new_tip*(* trans*,* repository*,* content_alert_str*=*content_alert_str*,* ****kwd *)*| Module galaxy.webapps.community.controllers.common:*884* in |set_repository_metadata_due_to_new_tip| |>> <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583>error_message*,* status *=* set_repository_metadata*(* trans*,* repository*,* content_alert_str*=*content_alert_str*,* ****kwd *)*| Module galaxy.webapps.community.controllers.common:*833* in |set_repository_metadata| |>> <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583>updating_installed_repository*=*False *)*| Module galaxy.util.shed_util:*706* in |generate_metadata_for_changeset_revision| |>> <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583>invalid_files_and_errors_tups *=* check_tool_input_params*(* app*,* files_dir*,* name*,* tool*,* sample_file_metadata_paths *)*| Module galaxy.util.shed_util:*310* in |check_tool_input_params| |>> <http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583>*if* options*.*tool_data_table *or* options*.*missing_tool_data_table_name*:*| *AttributeError: 'str' object has no attribute 'tool_data_table'*
*From:*Greg Von Kuster [mailto:greg@bx.psu.edu] *Sent:* 05 December 2012 13:43 *To:* Adam Carr (NBI) *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] Main toolshed broken??
ok, I'll wait on the additional information I requested.
On Dec 5, 2012, at 6:56 AM, Adam Carr (NBI) wrote:
Hi Greg,
Thank you for helping me out here.
I’m running on the galaxy-dist branch, changeset 8285:f364d992270c.
Many Thanks,
Adam.
*From:*Greg Von Kuster [mailto:greg@bx.psu.edu] *Sent:*05 December 2012 11:20 *To:*Adam Carr (NBI) *Cc:*galaxy-dev@lists.bx.psu.edu <mailto:galaxy-dev@lists.bx.psu.edu> *Subject:*Re: [galaxy-dev] Main toolshed broken??
Hi Adam,
I cannot help with this new issue without more information from you. What version of Galaxy are you running?
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