Hi, On our prod server that we udated to 16.01, I get this error when trying to access the list of saved histories... Do you see what's happening? Anthony URL: https://galaxy.genouest.org/history/list File '/opt/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 151 in __call__ app_iter = self.application(environ, sr_checker) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__ return self.application(environ, start_response) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in __call__ return self.application(environ, start_response) File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 126 in __call__ return self.handle_request( environ, start_response ) File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 184 in handle_request body = method( trans, **kwargs ) File '/opt/galaxy-dist/lib/galaxy/web/framework/decorators.py', line 66 in decorator return func( self, trans, *args, **kwargs ) File '/opt/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/history.py', line 325 in list return self.stored_list_grid( trans, status=status, message=message, **kwargs ) File '/opt/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 309 in __call__ kwargs=kwargs ) File '/opt/galaxy-dist/lib/galaxy/web/framework/webapp.py', line 811 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/opt/galaxy-dist/lib/galaxy/web/framework/webapp.py', line 825 in fill_template_mako return template.render( **data ) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/template.py', line 445 in render return runtime._render(self, self.callable_, args, data) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/runtime.py', line 829 in _render **_kwargs_for_callable(callable_, data)) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/runtime.py', line 864 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/runtime.py', line 890 in _exec_template callable_(context, *args, **kwargs) File '/opt/galaxy-dist/database/compiled_templates/base.mako.py', line 61 in render_body __M_writer(unicode(next.body())) File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 79 in render_body __M_writer(unicode(self.load())) File '/opt/galaxy-dist/database/compiled_templates/history/grid.mako.py', line 53 in render_load __M_writer(unicode(parent.load( embedded=embedded, insert=insert ))) File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 107 in render_load __M_writer(unicode( h.dumps( self.get_grid_config( embedded=embedded, insert=insert ) ) )) File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 293 in render_get_grid_config value = column.get_value( trans, grid, item ) File '/opt/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 374 in get_value return escape(value) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 1: ordinal not in range(128)
Can you set your locale to something US UTF8 and restart your Galaxy. I guess this is happening because of some dates do are not in UTF-8. Am 07.03.2016 um 16:03 schrieb Anthony Bretaudeau:
Hi, On our prod server that we udated to 16.01, I get this error when trying to access the list of saved histories... Do you see what's happening? Anthony
URL: https://galaxy.genouest.org/history/list File '/opt/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 151 in __call__ app_iter = self.application(environ, sr_checker) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__ return self.application(environ, start_response) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in __call__ return self.application(environ, start_response) File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 126 in __call__ return self.handle_request( environ, start_response ) File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 184 in handle_request body = method( trans, **kwargs ) File '/opt/galaxy-dist/lib/galaxy/web/framework/decorators.py', line 66 in decorator return func( self, trans, *args, **kwargs ) File '/opt/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/history.py', line 325 in list return self.stored_list_grid( trans, status=status, message=message, **kwargs ) File '/opt/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 309 in __call__ kwargs=kwargs ) File '/opt/galaxy-dist/lib/galaxy/web/framework/webapp.py', line 811 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/opt/galaxy-dist/lib/galaxy/web/framework/webapp.py', line 825 in fill_template_mako return template.render( **data ) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/template.py', line 445 in render return runtime._render(self, self.callable_, args, data) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/runtime.py', line 829 in _render **_kwargs_for_callable(callable_, data)) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/runtime.py', line 864 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/runtime.py', line 890 in _exec_template callable_(context, *args, **kwargs) File '/opt/galaxy-dist/database/compiled_templates/base.mako.py', line 61 in render_body __M_writer(unicode(next.body())) File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 79 in render_body __M_writer(unicode(self.load())) File '/opt/galaxy-dist/database/compiled_templates/history/grid.mako.py', line 53 in render_load __M_writer(unicode(parent.load( embedded=embedded, insert=insert ))) File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 107 in render_load __M_writer(unicode( h.dumps( self.get_grid_config( embedded=embedded, insert=insert ) ) )) File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 293 in render_get_grid_config value = column.get_value( trans, grid, item ) File '/opt/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 374 in get_value return escape(value) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 1: ordinal not in range(128)
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Also it is sometimes necessary to remove outdated compiled mako. By default this is in database/compiled_templates/ On 7 March 2016 at 16:07, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Can you set your locale to something US UTF8 and restart your Galaxy.
I guess this is happening because of some dates do are not in UTF-8.
Am 07.03.2016 um 16:03 schrieb Anthony Bretaudeau:
Hi, On our prod server that we udated to 16.01, I get this error when trying to access the list of saved histories... Do you see what's happening? Anthony
URL: https://galaxy.genouest.org/history/list File '/opt/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 151 in __call__ app_iter = self.application(environ, sr_checker) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__ return self.application(environ, start_response) File
'/opt/galaxy-dist/.venv/lib/python2.7/site-packages/paste/httpexceptions.py',
line 640 in __call__ return self.application(environ, start_response) File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 126 in __call__ return self.handle_request( environ, start_response ) File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 184 in handle_request body = method( trans, **kwargs ) File '/opt/galaxy-dist/lib/galaxy/web/framework/decorators.py', line 66 in decorator return func( self, trans, *args, **kwargs ) File '/opt/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/history.py', line 325 in list return self.stored_list_grid( trans, status=status, message=message, **kwargs ) File '/opt/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 309 in __call__ kwargs=kwargs ) File '/opt/galaxy-dist/lib/galaxy/web/framework/webapp.py', line 811 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/opt/galaxy-dist/lib/galaxy/web/framework/webapp.py', line 825 in fill_template_mako return template.render( **data ) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/template.py', line 445 in render return runtime._render(self, self.callable_, args, data) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/runtime.py', line 829 in _render **_kwargs_for_callable(callable_, data)) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/runtime.py', line 864 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/runtime.py', line 890 in _exec_template callable_(context, *args, **kwargs) File '/opt/galaxy-dist/database/compiled_templates/base.mako.py', line 61 in render_body __M_writer(unicode(next.body())) File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 79 in render_body __M_writer(unicode(self.load())) File '/opt/galaxy-dist/database/compiled_templates/history/grid.mako.py', line 53 in render_load __M_writer(unicode(parent.load( embedded=embedded, insert=insert ))) File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 107 in render_load __M_writer(unicode( h.dumps( self.get_grid_config( embedded=embedded, insert=insert ) ) )) File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 293 in render_get_grid_config value = column.get_value( trans, grid, item ) File '/opt/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 374 in get_value return escape(value) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 1: ordinal not in range(128)
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Before changing things, what's the output of 'locale'? You'll need to specify the .UTF-8 variant of that, though it need not be en_US. Python's datetime functions use the configured locale, which when it isn't the UTF-8 variant, outputs incompatible encodings. On Mon, Mar 7, 2016 at 10:09 AM, Marius van den Beek <m.vandenbeek@gmail.com
wrote:
Also it is sometimes necessary to remove outdated compiled mako. By default this is in database/compiled_templates/
On 7 March 2016 at 16:07, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Can you set your locale to something US UTF8 and restart your Galaxy.
I guess this is happening because of some dates do are not in UTF-8.
Am 07.03.2016 um 16:03 schrieb Anthony Bretaudeau:
Hi, On our prod server that we udated to 16.01, I get this error when trying to access the list of saved histories... Do you see what's happening? Anthony
URL: https://galaxy.genouest.org/history/list File '/opt/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 151 in __call__ app_iter = self.application(environ, sr_checker) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__ return self.application(environ, start_response) File
'/opt/galaxy-dist/.venv/lib/python2.7/site-packages/paste/httpexceptions.py',
line 640 in __call__ return self.application(environ, start_response) File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 126 in __call__ return self.handle_request( environ, start_response ) File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 184 in handle_request body = method( trans, **kwargs ) File '/opt/galaxy-dist/lib/galaxy/web/framework/decorators.py', line 66 in decorator return func( self, trans, *args, **kwargs ) File '/opt/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/history.py', line 325 in list return self.stored_list_grid( trans, status=status, message=message, **kwargs ) File '/opt/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 309 in __call__ kwargs=kwargs ) File '/opt/galaxy-dist/lib/galaxy/web/framework/webapp.py', line 811 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/opt/galaxy-dist/lib/galaxy/web/framework/webapp.py', line 825 in fill_template_mako return template.render( **data ) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/template.py', line 445 in render return runtime._render(self, self.callable_, args, data) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/runtime.py', line 829 in _render **_kwargs_for_callable(callable_, data)) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/runtime.py', line 864 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/runtime.py', line 890 in _exec_template callable_(context, *args, **kwargs) File '/opt/galaxy-dist/database/compiled_templates/base.mako.py', line 61 in render_body __M_writer(unicode(next.body())) File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 79 in render_body __M_writer(unicode(self.load())) File '/opt/galaxy-dist/database/compiled_templates/history/grid.mako.py', line 53 in render_load __M_writer(unicode(parent.load( embedded=embedded, insert=insert ))) File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 107 in render_load __M_writer(unicode( h.dumps( self.get_grid_config( embedded=embedded, insert=insert ) ) )) File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 293 in render_get_grid_config value = column.get_value( trans, grid, item ) File '/opt/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 374 in get_value return escape(value) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 1: ordinal not in range(128)
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Ok, glad it's working for you now, but just swapping to English isn't the long term solution I'd want to recommend :) I had started some work on this a little while ago with Bjoern in https://github.com/dannon/galaxy/commit/f9c3890135758a37c78aa18fe8b100be5895..., but I wasn't particularly happy with that brute-force approach. I'll follow up on this, though, and make sure other locales also display correctly in these grids -- I might go ahead and apply this for the time being. On Mon, Mar 7, 2016 at 10:18 AM, Anthony Bretaudeau < anthony.bretaudeau@inria.fr> wrote:
Thanks all for your (very efficient) help! I added this to the env, and now it works:
export LC_ALL=en_US.UTF-8 export LANG=en_US.UTF-8 export LANGUAGE=en_US.UTF-8
It was fr_FR.UTF-8 before
Anthony
On 07/03/2016 16:15, Dannon Baker wrote:
Before changing things, what's the output of 'locale'?
You'll need to specify the .UTF-8 variant of that, though it need not be en_US. Python's datetime functions use the configured locale, which when it isn't the UTF-8 variant, outputs incompatible encodings.
On Mon, Mar 7, 2016 at 10:09 AM, Marius van den Beek < m.vandenbeek@gmail.com> wrote:
Also it is sometimes necessary to remove outdated compiled mako. By default this is in database/compiled_templates/
On 7 March 2016 at 16:07, Björn Grüning < <bjoern.gruening@gmail.com> bjoern.gruening@gmail.com> wrote:
Can you set your locale to something US UTF8 and restart your Galaxy.
I guess this is happening because of some dates do are not in UTF-8.
Hi, On our prod server that we udated to 16.01, I get this error when
Am 07.03.2016 um 16:03 schrieb Anthony Bretaudeau: trying
to access the list of saved histories... Do you see what's happening? Anthony
URL: https://galaxy.genouest.org/history/list File '/opt/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 151 in __call__ app_iter = self.application(environ, sr_checker) File
'/opt/galaxy-dist/.venv/lib/python2.7/site-packages/paste/recursive.py',
line 85 in __call__ return self.application(environ, start_response) File
'/opt/galaxy-dist/.venv/lib/python2.7/site-packages/paste/httpexceptions.py',
line 640 in __call__ return self.application(environ, start_response) File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 126 in __call__ return self.handle_request( environ, start_response ) File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 184 in handle_request body = method( trans, **kwargs ) File '/opt/galaxy-dist/lib/galaxy/web/framework/decorators.py', line 66 in decorator return func( self, trans, *args, **kwargs ) File '/opt/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/history.py', line 325 in list return self.stored_list_grid( trans, status=status, message=message, **kwargs ) File '/opt/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 309 in __call__ kwargs=kwargs ) File '/opt/galaxy-dist/lib/galaxy/web/framework/webapp.py', line 811 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/opt/galaxy-dist/lib/galaxy/web/framework/webapp.py', line 825 in fill_template_mako return template.render( **data ) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/template.py', line 445 in render return runtime._render(self, self.callable_, args, data) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/runtime.py', line 829 in _render **_kwargs_for_callable(callable_, data)) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/runtime.py', line 864 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/opt/galaxy-dist/.venv/lib/python2.7/site-packages/mako/runtime.py', line 890 in _exec_template callable_(context, *args, **kwargs) File '/opt/galaxy-dist/database/compiled_templates/base.mako.py', line 61 in render_body __M_writer(unicode(next.body())) File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 79 in render_body __M_writer(unicode(self.load())) File '/opt/galaxy-dist/database/compiled_templates/history/grid.mako.py', line 53 in render_load __M_writer(unicode(parent.load( embedded=embedded, insert=insert ))) File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 107 in render_load __M_writer(unicode( h.dumps( self.get_grid_config( embedded=embedded, insert=insert ) ) )) File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 293 in render_get_grid_config value = column.get_value( trans, grid, item ) File '/opt/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 374 in get_value return escape(value) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 1: ordinal not in range(128)
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (4)
-
Anthony Bretaudeau -
Björn Grüning -
Dannon Baker -
Marius van den Beek