Re: [galaxy-dev] Stalled data set imports, where should I be looking?

Ry4an Brase wrote:

I tried importing a new single (big) fasta file and it's in a similar state. It shows up as queued in the admin interface, but isn't actually running - system load is zero.

I did get this error after clicking submit when importing, but since it looked 'view-level' I discounted it. The 'message' field was empty.

Error Traceback:
View as:   Interactive  |  Text  |  XML (full)
⇝ TypeError: 'NoneType' object is not iterable
URL: http://galaxy.msi.umn.edu/library_common/upload_library_dataset
Module weberror.evalexception.middleware:364 in respond          view
>>  app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__          view
>>  environ, self.app)
Module paste.wsgilib:539 in intercept_output          view
>>  app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__          view
>>  return self.application(environ, start_response)
Module galaxy.web.framework.middleware.remoteuser:107 in __call__          view
>>  return self.app( environ, start_response )
Module paste.httpexceptions:632 in __call__          view
>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:145 in __call__          view
>>  body = method( trans, **kwargs )
Module galaxy.web.controllers.library_common:978 in upload_library_dataset          view
>>  **kwd )
Module galaxy.web.controllers.library_common:1158 in upload_dataset          view
>>  message=util.sanitize_text( message ),
Module galaxy.util:138 in sanitize_text          view
>>  for c in text:
TypeError: 'NoneType' object is not iterable

could that be resulting in the stuff half-imported?

Sure could, this is an interface error but it's masking a deeper problem. There's an error occurring somewhere higher up, but 'message' is somehow set to None, and then in trying to display the error to you, it fails to sanitize the message text since it's not a string.

Are you importing via a server directory or filesystem paths?

--nate

Thanks,