Re: [galaxy-dev] Toolshed Collaboration Issues
Hi Lance, I worked for me the last time. I usually create a repository under the IUC account and add me as contributor. No problem so far. Cheers, Bjoern I'm having some difficulty collaborating on a tool development in the toolshed. It seems to happen on the production toolshed as well as the testtoolshed. When I try to grant another user the ability to update a repository (or when the other person tries to add me) we get the following error: URL: http://testtoolshed.g2.bx.psu.edu/repository/manage_repository?id=f49c56ded06bdcd9 File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py', line 106 in __call__ environ, self.app) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py', line 543 in intercept_output app_iter = application(environ, replacement_start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/__init__.py', line 98 in decorator return func( self, trans, *args, **kwargs ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/webapps/tool_shed/controllers/repository.py', line 2124 in manage_repository user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/security/__init__.py', line 60 in decode_id return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( ! ) ) File '/usr/lib/python2.7/encodings/hex_codec.py', line 42 in hex_decode output = binascii.a2b_hex(input) TypeError: Non-hexadecimal digit found Can anyone else successfully grant a user update permission to a repository? I've submitted an issue on Trello (https://trello.com/c/XYkqW3Lr). ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Toolshed Collaboration Issues
Perhaps it has something to do with a specific account? The user 'nilesh' tried to add me to his rseqc repository (http://toolshed.g2.bx.psu.edu/view/nilesh/rseqc ) and got a Server Error. I then created the rseqc_dev3 repository (http://testtoolshed.g2.bx.psu.edu/view/lparsons/rseqc_dev3 )on the testtoolshed and tried to add him (nilesh) and got the error indicated below. Any help in tracking this down would be appreciated. Björn Grüning wrote: Hi Lance, I worked for me the last time. I usually create a repository under the IUC account and add me as contributor. No problem so far. Cheers, Bjoern I'm having some difficulty collaborating on a tool development in the toolshed. It seems to happen on the production toolshed as well as the testtoolshed. When I try to grant another user the ability to update a repository (or when the other person tries to add me) we get the following error: URL: http://testtoolshed.g2.bx.psu.edu/repository/manage_repository?id=f49c56ded06bdcd9 File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py', line 106 in __call__ environ, self.app) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py', line 543 in intercept_output app_iter = application(environ, replacement_start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/__init__.py', line 98 in decorator return func( self, trans, *args, **kwargs ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/webapps/tool_shed/controllers/repository.py', line 2124 in manage_repository user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/security/__init__.py', line 60 in decode_id return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( ! ) ) File '/usr/lib/python2.7/encodings/hex_codec.py', line 42 in hex_decode output = binascii.a2b_hex(input) TypeError: Non-hexadecimal digit found Can anyone else successfully grant a user update permission to a repository? I've submitted an issue on Trello (https://trello.com/c/XYkqW3Lr). -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Toolshed Collaboration Issues
Hi, I added you successfully to: http://testtoolshed.g2.bx.psu.edu/view/bgruening/precommit_test please keep in mind that you need to remove the 'select one' button before you click submit, that is not intuitive but a known bug. Cheers, Bjoern Perhaps it has something to do with a specific account? The user 'nilesh' tried to add me to his rseqc repository (http://toolshed.g2.bx.psu.edu/view/nilesh/rseqc ) and got a Server Error. I then created the rseqc_dev3 repository (http://testtoolshed.g2.bx.psu.edu/view/lparsons/rseqc_dev3 ) on the testtoolshed and tried to add him (nilesh) and got the error indicated below. Any help in tracking this down would be appreciated. Björn Grüning wrote: Hi Lance, I worked for me the last time. I usually create a repository under the IUC account and add me as contributor. No problem so far. Cheers, Bjoern I'm having some difficulty collaborating on a tool development in the toolshed. It seems to happen on the production toolshed as well as the testtoolshed. When I try to grant another user the ability to update a repository (or when the other person tries to add me) we get the following error: URL: http://testtoolshed.g2.bx.psu.edu/repository/manage_repository?id=f49c56ded06bdcd9 File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py', line 106 in __call__ environ, self.app) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py', line 543 in intercept_output app_iter = application(environ, replacement_start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/__init__.py', line 98 in decorator return func( self, trans, *args, **kwargs ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/webapps/tool_shed/controllers/repository.py', line 2124 in manage_repository user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/security/__init__.py', line 60 in decode_id return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( ! ) ) File '/usr/lib/python2.7/encodings/hex_codec.py', line 42 in hex_decode output = binascii.a2b_hex(input) TypeError: Non-hexadecimal digit found Can anyone else successfully grant a user update permission to a repository? I've submitted an issue on Trello (https://trello.com/c/XYkqW3Lr). -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
