Re: [galaxy-dev] Main toolshed broken??
Hi, I hadn't caught this as I posted my query to the list, I'm having trouble uploading to a brand new repository. Could my issue described here: http://dev.list.galaxyproject.org/Tool-Shed-Upload-Files-To-Repository-Crash..., be related? Many Thanks, Adam. --- Adam Carr Linux Support & Developmnent E adam.carr@nbi.ac.uk T +44 1603 450161 W jic.ac.uk ifr.ac.uk tgac.ac.uk tsl.ac.uk NBI Partnership Ltd Norwich Research Park Norwich NR4 7UH The NBI Partnership Ltd provides non-scientific services to the Institute of Food Research, the John Innes Centre, The Genome Analysis Centre and The Sainsbury Laboratory -----Original Message-----
Hi list,
Trying to upload, delete, update files from a repository I own in the toolshed I keep getting Server Error..
This is the repo: http://fcaramia@.../repos/fcaramia/methylation_analysis_bismark
Is anyone having the same issues?? I could just delete the repository but no option for that is given..
Thanks,
Franco
Hi Adam, I believe this is related to the invalid xml definition in your repository's tool_data_table_conf.xml.sample file which I discussed in a previous reply. Greg Von Kuster On Dec 4, 2012, at 8:08 AM, Adam Carr (NBI) wrote:
Hi,
I hadn't caught this as I posted my query to the list, I'm having trouble uploading to a brand new repository. Could my issue described here: http://dev.list.galaxyproject.org/Tool-Shed-Upload-Files-To-Repository-Crash..., be related?
Many Thanks, Adam.
--- Adam Carr Linux Support & Developmnent E adam.carr@nbi.ac.uk T +44 1603 450161 W jic.ac.uk ifr.ac.uk tgac.ac.uk tsl.ac.uk
NBI Partnership Ltd Norwich Research Park Norwich NR4 7UH
The NBI Partnership Ltd provides non-scientific services to the Institute of Food Research, the John Innes Centre, The Genome Analysis Centre and The Sainsbury Laboratory
-----Original Message-----
Hi list,
Trying to upload, delete, update files from a repository I own in the toolshed I keep getting Server Error..
This is the repo: http://fcaramia@.../repos/fcaramia/methylation_analysis_bismark
Is anyone having the same issues?? I could just delete the repository but no option for that is given..
Thanks,
Franco
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Hi Greg, Thank you for your reply. I have checked on my tool_data_table_conf.xml.sample and tool_data_table_conf.xml files and they look to be correctly formatted with <tables> tags at their beginnings and ends. However, I noticed that this file is already populated, should that be the case with a fresh newly installed Tool Shed? My issue doesn't occur when I'm importing a tool from the Tool Shed to Galaxy, but when I'm uploading a tool that I've downloaded from the Galaxy Tool Shed to my Tool Shed. The last of the errors reported after I attempt an upload being: Module galaxy.util.shed_util:336 in check_tool_input_params
<http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=9ed9121ed2b0078e> if options.tool_data_table or options.missing_tool_data_table_name: AttributeError: 'str' object has no attribute 'tool_data_table'
Many Thanks, Adam. -----Original Message----- From: Greg Von Kuster [mailto:greg@bx.psu.edu] Sent: 04 December 2012 16:40 To: Adam Carr (NBI) Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Main toolshed broken?? Hi Adam, I believe this is related to the invalid xml definition in your repository's tool_data_table_conf.xml.sample file which I discussed in a previous reply. Greg Von Kuster On Dec 4, 2012, at 8:08 AM, Adam Carr (NBI) wrote:
Hi,
I hadn't caught this as I posted my query to the list, I'm having trouble uploading to a brand new repository. Could my issue described here: http://dev.list.galaxyproject.org/Tool-Shed-Upload-Files-To-Repository-Crash..., be related?
Many Thanks,
Adam.
---
Adam Carr
Linux Support & Developmnent
E adam.carr@nbi.ac.uk<mailto:adam.carr@nbi.ac.uk>
T +44 1603 450161
W jic.ac.uk ifr.ac.uk tgac.ac.uk tsl.ac.uk
NBI Partnership Ltd
Norwich Research Park
Norwich NR4 7UH
The NBI Partnership Ltd provides non-scientific services to the
Institute of Food Research, the John Innes Centre, The Genome Analysis
Centre and The Sainsbury Laboratory
-----Original Message-----
Hi list,
Trying to upload, delete, update files from a repository I own in the toolshed I keep getting Server Error..
This is the repo:
http://fcaramia@.../repos/fcaramia/methylation_analysis_bismark
Is anyone having the same issues?? I could just delete the repository but no option for that is given..
Thanks,
Franco
___________________________________________________________
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 Adam, I cannot help with this new issue without more information from you. What version of Galaxy are you running? On Dec 5, 2012, at 5:44 AM, Adam Carr (NBI) wrote:
Hi Greg,
Thank you for your reply. I have checked on my tool_data_table_conf.xml.sample and tool_data_table_conf.xml files and they look to be correctly formatted with <tables> tags at their beginnings and ends.
However, I noticed that this file is already populated, should that be the case with a fresh newly installed Tool Shed?
Can you clarify what you mean here with your statement "this file is already populated"? Are you referring to a file in the tool shed or a file in Galaxy?
My issue doesn't occur when I'm importing a tool from the Tool Shed to Galaxy, but when I'm uploading a tool that I've downloaded from the Galaxy Tool Shed to my Tool Shed.
Are you still referring to the same repository from the main tool shed that is discussed at the start of this thread below? How did you download the repository from the Galaxy tool shed ( I assume you are talking about the main Galaxy tool shed, but please confirm ). Did you download it as a tarball? Can you clarify your statement "when I'm uploading a tool"? Do you mean that you are attempting to upload the downloaded repository tarball, or something else?
The last of the errors reported after I attempt an upload being: Module galaxy.util.shed_util:336 in check_tool_input_params
if options.tool_data_table or options.missing_tool_data_table_name: AttributeError: 'str' object has no attribute 'tool_data_table'
I'll need all of the answers above along with the entire stack trace to be able to help you here. Greg Von Kuster
Many Thanks, Adam.
-----Original Message----- From: Greg Von Kuster [mailto:greg@bx.psu.edu] Sent: 04 December 2012 16:40 To: Adam Carr (NBI) Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Main toolshed broken??
Hi Adam,
I believe this is related to the invalid xml definition in your repository's tool_data_table_conf.xml.sample file which I discussed in a previous reply.
Greg Von Kuster
On Dec 4, 2012, at 8:08 AM, Adam Carr (NBI) wrote:
Hi,
I hadn't caught this as I posted my query to the list, I'm having trouble uploading to a brand new repository. Could my issue described here: http://dev.list.galaxyproject.org/Tool-Shed-Upload-Files-To-Repository-Crash..., be related?
Many Thanks, Adam.
--- Adam Carr Linux Support & Developmnent E adam.carr@nbi.ac.uk T +44 1603 450161 W jic.ac.uk ifr.ac.uk tgac.ac.uk tsl.ac.uk
NBI Partnership Ltd Norwich Research Park Norwich NR4 7UH
The NBI Partnership Ltd provides non-scientific services to the Institute of Food Research, the John Innes Centre, The Genome Analysis Centre and The Sainsbury Laboratory
-----Original Message-----
Hi list,
Trying to upload, delete, update files from a repository I own in the toolshed I keep getting Server Error..
This is the repo: http://fcaramia@.../repos/fcaramia/methylation_analysis_bismark
Is anyone having the same issues?? I could just delete the repository but no option for that is given..
Thanks,
Franco
___________________________________________________________ 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, 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 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?
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 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?
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?
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?
___________________________________________________________ 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:
participants (3)
-
Adam Carr (NBI) -
Dave Bouvier -
Greg Von Kuster