Error granting permissions on new Tool Shed repository
Hi Greg, Dave, While logged into the Test Tool Shed as 'iuc', I just created a new (empty) repository: http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26 See background discussion on this thread: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/015890.html As 'iuc', I then tried to grant write access to myself ('peterjc') and Bjoern ('bgruening') as we are both IUC members and working on the Galaxy BLAST+ project: https://github.com/peterjc/galaxy_blast The default dummy entry "Select One" entry was still being displayed. I clicked 'Grant Access' and got this error: Internal Server Error Galaxy was unable to sucessfully complete your request URL: http://testtoolshed.g2.bx.psu.edu/repository/manage_repository?id=2f85dfc573... Module galaxy.web.framework.middleware.error:149 in __call__
app_iter = self.application(environ, sr_checker) Module paste.debug.prints:106 in __call__ environ, self.app) Module paste.wsgilib:543 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:84 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request body = method( trans, **kwargs ) Module galaxy.web.framework:98 in decorator return func( self, trans, *args, **kwargs ) Module galaxy.webapps.tool_shed.controllers.repository:2072 in manage_repository user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) ) Module galaxy.web.security:60 in decode_id return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( "!" ) ) Module encodings.hex_codec:42 in hex_decode output = binascii.a2b_hex(input) TypeError: Non-hexadecimal digit found extra data
full traceback text version This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. -- I tried again but explicitly removed the dummy entry "Select One" and it seemed to have worked. I am running Firefox v22.0 on Mac OS X. Regards, Peter
Hi Peter, This is a known issue ( not a Tool Shed issue, but a Galaxy issue ) related to the Select list that gets automatically populated with the "Select one" option. You have to actually click the x" on this option to eliminate it. Again, this feature is inherited from Galaxy, so it's not specific to the tool shed. I haven't had time to track it down and fix it since I'm under water with just the tool shed. Greg Von Kuster On Aug 7, 2013, at 11:12 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi Greg, Dave,
While logged into the Test Tool Shed as 'iuc', I just created a new (empty) repository: http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26
See background discussion on this thread: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/015890.html
As 'iuc', I then tried to grant write access to myself ('peterjc') and Bjoern ('bgruening') as we are both IUC members and working on the Galaxy BLAST+ project: https://github.com/peterjc/galaxy_blast
The default dummy entry "Select One" entry was still being displayed. I clicked 'Grant Access' and got this error:
Internal Server Error Galaxy was unable to sucessfully complete your request
URL: http://testtoolshed.g2.bx.psu.edu/repository/manage_repository?id=2f85dfc573... Module galaxy.web.framework.middleware.error:149 in __call__
app_iter = self.application(environ, sr_checker) Module paste.debug.prints:106 in __call__ environ, self.app) Module paste.wsgilib:543 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:84 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request body = method( trans, **kwargs ) Module galaxy.web.framework:98 in decorator return func( self, trans, *args, **kwargs ) Module galaxy.webapps.tool_shed.controllers.repository:2072 in manage_repository user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) ) Module galaxy.web.security:60 in decode_id return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( "!" ) ) Module encodings.hex_codec:42 in hex_decode output = binascii.a2b_hex(input) TypeError: Non-hexadecimal digit found extra data
full traceback
text version
This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem.
--
I tried again but explicitly removed the dummy entry "Select One" and it seemed to have worked.
I am running Firefox v22.0 on Mac OS X.
Regards,
Peter ___________________________________________________________ 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/
I've made a note on the Trello issue Ross filed for this, https://trello.com/c/SqrjrnNg/986 On Wed, Aug 7, 2013 at 4:16 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Peter,
This is a known issue ( not a Tool Shed issue, but a Galaxy issue ) related to the Select list that gets automatically populated with the "Select one" option. You have to actually click the x" on this option to eliminate it. Again, this feature is inherited from Galaxy, so it's not specific to the tool shed. I haven't had time to track it down and fix it since I'm under water with just the tool shed.
Greg Von Kuster
On Aug 7, 2013, at 11:12 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi Greg, Dave,
While logged into the Test Tool Shed as 'iuc', I just created a new (empty) repository: http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26
See background discussion on this thread: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/015890.html
As 'iuc', I then tried to grant write access to myself ('peterjc') and Bjoern ('bgruening') as we are both IUC members and working on the Galaxy BLAST+ project: https://github.com/peterjc/galaxy_blast
The default dummy entry "Select One" entry was still being displayed. I clicked 'Grant Access' and got this error:
Internal Server Error Galaxy was unable to sucessfully complete your request
URL: http://testtoolshed.g2.bx.psu.edu/repository/manage_repository?id=2f85dfc573... Module galaxy.web.framework.middleware.error:149 in __call__
app_iter = self.application(environ, sr_checker) Module paste.debug.prints:106 in __call__ environ, self.app) Module paste.wsgilib:543 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:84 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request body = method( trans, **kwargs ) Module galaxy.web.framework:98 in decorator return func( self, trans, *args, **kwargs ) Module galaxy.webapps.tool_shed.controllers.repository:2072 in manage_repository user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) ) Module galaxy.web.security:60 in decode_id return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( "!" ) ) Module encodings.hex_codec:42 in hex_decode output = binascii.a2b_hex(input) TypeError: Non-hexadecimal digit found extra data
full traceback
text version
This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem.
--
I tried again but explicitly removed the dummy entry "Select One" and it seemed to have worked.
I am running Firefox v22.0 on Mac OS X.
Regards,
Peter
Thanks Peter, I've added some comments as well, and relabeld the Trello card as trivial bug: Using Galaxy select lists fail unless the "Select one" option removed first. since this is not a tool shed issue, but a Selectlist issue in the Galaxy formbuilder framework. The tool shed simply inherits this problem from there. https://trello.com/c/SqrjrnNg/986-trivial-bug-toolshed-adding-a-user-using-t... Greg Von Kuster On Aug 21, 2013, at 9:21 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
I've made a note on the Trello issue Ross filed for this, https://trello.com/c/SqrjrnNg/986
On Wed, Aug 7, 2013 at 4:16 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Peter,
This is a known issue ( not a Tool Shed issue, but a Galaxy issue ) related to the Select list that gets automatically populated with the "Select one" option. You have to actually click the x" on this option to eliminate it. Again, this feature is inherited from Galaxy, so it's not specific to the tool shed. I haven't had time to track it down and fix it since I'm under water with just the tool shed.
Greg Von Kuster
On Aug 7, 2013, at 11:12 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi Greg, Dave,
While logged into the Test Tool Shed as 'iuc', I just created a new (empty) repository: http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26
See background discussion on this thread: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/015890.html
As 'iuc', I then tried to grant write access to myself ('peterjc') and Bjoern ('bgruening') as we are both IUC members and working on the Galaxy BLAST+ project: https://github.com/peterjc/galaxy_blast
The default dummy entry "Select One" entry was still being displayed. I clicked 'Grant Access' and got this error:
Internal Server Error Galaxy was unable to sucessfully complete your request
URL: http://testtoolshed.g2.bx.psu.edu/repository/manage_repository?id=2f85dfc573... Module galaxy.web.framework.middleware.error:149 in __call__
app_iter = self.application(environ, sr_checker) Module paste.debug.prints:106 in __call__ environ, self.app) Module paste.wsgilib:543 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:84 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request body = method( trans, **kwargs ) Module galaxy.web.framework:98 in decorator return func( self, trans, *args, **kwargs ) Module galaxy.webapps.tool_shed.controllers.repository:2072 in manage_repository user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) ) Module galaxy.web.security:60 in decode_id return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( "!" ) ) Module encodings.hex_codec:42 in hex_decode output = binascii.a2b_hex(input) TypeError: Non-hexadecimal digit found extra data
full traceback
text version
This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem.
--
I tried again but explicitly removed the dummy entry "Select One" and it seemed to have worked.
I am running Firefox v22.0 on Mac OS X.
Regards,
Peter
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/
participants (2)
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Greg Von Kuster -
Peter Cock