Re: [galaxy-dev] Main toolshed broken??
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:g...@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-td4657324.html, be related? Many Thanks, Adam. --- Adam Carr Linux Support Developmnent E adam.c...@nbi.ac.ukmailto:adam.c...@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: http://lists.bx.psu.edu/ ___ 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/
Re: [galaxy-dev] Main toolshed broken??
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=ecc93bc8f0382e9echangeset_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.edumailto: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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Main toolshed broken??
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=ecc93bc8f0382e9echangeset_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=7a78893ba4596583app_iter *=* self*.*application*(*environ*,* start_response*)*| Module paste.debug.prints:*98* in |__call__| | http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583environ*,* self*.*app*)*| Module paste.wsgilib:*539* in |intercept_output| | http://galaxy-tools.nbi.ac.uk:9009/upload/upload?repository_id=7a78893ba4596583app_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=7a78893ba4596583body *=* 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=7a78893ba4596583set_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=7a78893ba4596583error_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=7a78893ba4596583updating_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=7a78893ba4596583invalid_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
Re: [galaxy-dev] Main toolshed broken??
Hi Franco, The server error is thrown when your file named tool_data_table_conf.xml.sample is parsed. The content of this file is the following. !-- Locations of indexes in the bisulphite conversion -- table name=bismark_indexes comment_char=# columnsvalue, dbkey, name, path/columns file path=tool-data/bismark_indices.loc / /table !-- Locations of bed files for bisulphite analysis -- table name=bismark_bed_files comment_char=# columnsvalue, name, path/columns file path=tool-data/bismark_bed_files.loc / /table This is an invalid xml file because it requires a containing tables tag set since multiple table tag sets are defined. I've improved the current server error behavior by displaying an appropriate error message for this problem, but the fix will not make it out to the main Galaxy tool shed until the next Galaxy release, currently scheduled for about December 20. In the meantime, I believe you should see better behavior if you upload a new version of this file to your repository that looks something like this: tables !-- Locations of indexes in the bisulphite conversion -- table name=bismark_indexes comment_char=# columnsvalue, dbkey, name, path/columns file path=tool-data/bismark_indices.loc / /table !-- Locations of bed files for bisulphite analysis -- table name=bismark_bed_files comment_char=# columnsvalue, name, path/columns file path=tool-data/bismark_bed_files.loc / /table /tables Thanks, Greg Von Kuster On Dec 3, 2012, at 6:40 PM, Franco Caramia wrote: 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://fcara...@toolshed.g2.bx.psu.edu/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 This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt. ___ 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/ ___ 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/
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-td4657324.html, be related? Many Thanks, Adam. --- Adam Carr Linux Support Developmnent E adam.c...@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: http://lists.bx.psu.edu/ ___ 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/
[galaxy-dev] Main toolshed broken??
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://fcara...@toolshed.g2.bx.psu.edu/repos/fcaramia/methylation_analysis_b ismark Is anyone having the same issues?? I could just delete the repository but no option for that is given.. Thanks, Franco This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt. ___ 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/
