Colleen Doherty wrote:
> Hi,
>  I get the following error when trying to upload data to Galaxy
> AttributeError: 'NoneType' object has no attribute 'lower'
> 
> Same error for many different types of files (fastq, sam, bam) some of
> which uploaded last week.
> 
> What I've tried:
> Deleting browser cache
> Deleting cookie
> Deleting database/compiled_templates
> Deleting eggs/
> 
> 
> Please let me know what else I should try / what I am doing wrong.
> More info below.
> Thank you!

Hi Colleen,

I don't think the error below is the true cause of the upload problem -
this is indicating that the file's extension is unset and we are not
properly handling displaying a dataset when this is the case.  I've
fixed this in changeset 6054:e28ebc25b2e7.

But there's presumably a failure further up since the extension is
unset.  Is the uploaded dataset red?  If so, is there an error displayed
when you click on the dataset's "bug" icon?  If not, were there any
other errors logged in the Galaxy server output when you uploaded the
file?

Thanks,
--nate

> 
> 
> 
> 
> 
> 
> 
> 
> 
> More information: TRACEBACK:
> 
> URL: http://127.0.0.1:8080/datasets/59c76a119581e190/display/?preview=True
> File 
> '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
> line 364 in respond
>   app_iter = self.application(environ, detect_start_response)
> File 
> '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py',
> line 98 in __call__
>   environ, self.app)
> File 
> '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py',
> line 539 in intercept_output
>   app_iter = application(environ, replacement_start_response)
> File 
> '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
> line 80 in __call__
>   return self.application(environ, start_response)
> File 
> '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
> line 632 in __call__
>   return self.application(environ, start_response)
> File 
> '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/lib/galaxy/web/framework/base.py',
> line 145 in __call__
>   body = method( trans, **kwargs )
> File 
> '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/lib/galaxy/web/controllers/dataset.py',
> line 361 in display
>   mime = trans.app.datatypes_registry.get_mimetype_by_extension(
> data.extension.lower() )
> AttributeError: 'NoneType' object has no attribute 'lower'
> 
> 
> 
> Extra Data
> CGI Variables
> CONTENT_LENGTH        '0'
> HTTP_ACCEPT   
> 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
> HTTP_ACCEPT_CHARSET   'ISO-8859-1,utf-8;q=0.7,*;q=0.7'
> HTTP_ACCEPT_ENCODING  'gzip, deflate'
> HTTP_ACCEPT_LANGUAGE  'en-us,en;q=0.5'
> HTTP_CONNECTION       'keep-alive'
> HTTP_COOKIE   
> 'galaxysession=c6ca0ddb55be603a2c2796e41769bc2412b1c87332f54f840b1876eab065f3113e1ca20ff6a4ab5c'
> HTTP_HOST     '127.0.0.1:8080'
> HTTP_REFERER  'http://127.0.0.1:8080/history'
> HTTP_USER_AGENT       'Mozilla/5.0 (X11; Linux x86_64; rv:6.0.2)
> Gecko/20100101 Firefox/6.0.2'
> PATH_INFO     '/datasets/59c76a119581e190/display/'
> QUERY_STRING  'preview=True'
> REMOTE_ADDR   '127.0.0.1'
> REQUEST_METHOD        'GET'
> SERVER_NAME   '127.0.0.1'
> SERVER_PORT   '8080'
> SERVER_PROTOCOL       'HTTP/1.1'
> Extra Data
> WSGI Variables
> application   <paste.debug.prints.PrintDebugMiddleware object at 0x7834350>
> paste.cookies         (<SimpleCookie:
> galaxysession='c6ca0ddb55be603a2c2796e41769bc2412b1c87332f54f840b1876eab065f3113e1ca20ff6a4ab5c'>,
> 'galaxysession=c6ca0ddb55be603a2c2796e41769bc2412b1c87332f54f840b1876eab065f3113e1ca20ff6a4ab5c')
> paste.evalexception   <weberror.evalexception.middleware.EvalException
> object at 0x6dd11d0>
> paste.evalexception.debug_count       1316648566
> paste.expected_exceptions     [<class 'paste.httpexceptions.HTTPException'>]
> paste.httpexceptions  <paste.httpexceptions.HTTPExceptionHandler
> object at 0x7823090>
> paste.httpserver.thread_pool  <paste.httpserver.ThreadPool object at 
> 0x2b66f90>
> paste.printdebug_listeners    [<cStringIO.StringO object at 0x6e24fb8>,
> <open file '<stderr>', mode 'w' at 0x7fb208c901e0>]
> paste.recursive.forward       <paste.recursive.Forwarder from />
> paste.recursive.include       <paste.recursive.Includer from />
> paste.recursive.include_app_iter      <paste.recursive.IncluderAppIter from />
> paste.recursive.script_name   ''
> paste.remove_printdebug       <function remove_printdebug at 0x6e23a28>
> paste.throw_errors    True
> weberror.evalexception
>       <weberror.evalexception.middleware.EvalException object at 0x6dd11d0>
> weberror.evalexception.debug_count    1316648566
> webob._parsed_query_vars      (MultiDict([('preview', 'True')]), 
> 'preview=True')
> wsgi process  'Multithreaded'
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