Question: UnicodeDecodeError: 'utf8' codec can't decode
gravatar for christophe.habib
3.8 years ago by
christophe.habib340 wrote:

Hello everybody,

I am using SVDetect in Galaxy, unfortunately I have this error when I use it in galaxy :

Module galaxy.web.framework.middleware.error:149 in __call__
>>  app_iter = self.application(environ, sr_checker)
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.webapps.galaxy.controllers.history:575 in view
>>  show_deleted=show_deleted, show_hidden=show_hidden, use_panels=use_panels )
Module galaxy.web.framework:1224 in fill_template_mako
>>  return template.render( **data )
Module mako.template:296 in render
>>  return runtime._render(self, self.callable_, args, data)
Module mako.runtime:660 in _render
>>  **_kwargs_for_callable(callable_, data))
Module mako.runtime:692 in _render_context
>>  _exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
Module mako.runtime:718 in _exec_template
>>  callable_(context, *args, **kwargs)
Module _base_mako:66 in render_body
>>  __M_writer(unicode(next.body()))
Module history_view_mako:78 in render_body
>>  __M_writer(unicode(center_panel()))
Module history_view_mako:73 in center_panel
>>  return render_center_panel(context)
Module history_view_mako:189 in render_center_panel
>>  __M_writer(unicode(h.to_json_string( hdas )))
Module json:231 in dumps
>>  return _default_encoder.encode(obj)
Module json.encoder:200 in encode
>>  chunks = self.iterencode(o, _one_shot=True)
Module json.encoder:263 in iterencode
>>  return _iterencode(o, 0)
UnicodeDecodeError: 'utf8' codec can't decode byte 0xe9 in position 20: invalid continuation byte

I found this similar post about codec error (for ASCII in this post) : but there is no explanation at all on the solution.

I have really no idea about the origin of this problem.. Did you already see this kind of error and found a solution?

Thank you for your help.



svdetect utf8 codec • 2.6k views
ADD COMMENTlink modified 3.8 years ago by carlfeberhard390 • written 3.8 years ago by christophe.habib340

Are you by any chance using some very rare characters in your history name/dataset names?

If not please specify what are you doing when the error happens, what Galaxy you are using and where is the error displayed.

ADD REPLYlink written 3.8 years ago by Martin Čech ♦♦ 4.9k
gravatar for carlfeberhard
3.8 years ago by
United States
carlfeberhard390 wrote:

This looks to be a latin-1 to UTF8 conversion error on our part. As mentioned here: it may well be an e-acute character. 

To work around this error for now, you may want to remove the e-acute character from your datasets. Most likely it is in the name and you can use the 'edit attributes' button on each dataset to edit it. If it still occurs you may want to look at your annotations and tags for the datasets.

Sorry for the trouble and let us know if we can provide more information.

ADD COMMENTlink written 3.8 years ago by carlfeberhard390
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