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:g...@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:g...@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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