Hi Dannon

You're right. I updated the code and it's fixed now.

Thanks a lot for your help
Ulf

On 08/12/14 14:43, Dannon Baker wrote:
> Actually, this *is* already handled better than it looks like in your stack
> trace.
>
> Dan changed the handling here in revision 14522:38f8adbf6a47:
> https://bitbucket.org/galaxy/galaxy-central/commits/38f8adbf6a47 and you
> should no longer have this issue to the forthcoming release.
>
> -Dannon
>
> On Mon, Dec 8, 2014 at 9:26 AM, Dannon Baker <dannon.ba...@gmail.com> wrote:
>
>> Hey Ulf,
>>
>> Thanks for reporting this; the error handling should definitely be better
>> here -- I'll get a fix out shortly.
>>
>> -Dannon
>>
>> On Mon, Dec 8, 2014 at 7:23 AM, Ulf Schaefer <ulf.schae...@phe.gov.uk>
>> wrote:
>>
>>> Dear Galaxy Dev
>>>
>>> One of our users has managed to lock himself out of his Custom Builds.
>>> An 'Internal Server Error' appears and this shows up in the web process
>>> log:
>>>
>>> ---
>>>
>>> Error - <type 'exceptions.IOError'>: [Errno 2] No such file or
>>> directory: '/phengs/galaxy/database/files/000/127/dataset_127764.dat'
>>> URL: http://158.119.147.85/user/dbkeys
>>> File
>>>
>>> '/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
>>> line 149 in __call__
>>>     app_iter = self.application(environ, sr_checker)
>>> File
>>>
>>> '/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py',
>>> line 84 in __call__
>>>     return self.application(environ, start_response)
>>> File
>>>
>>> '/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py',
>>> line 633 in __call__
>>>     return self.application(environ, start_response)
>>> File
>>>
>>> '/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/lib/galaxy/web/framework/base.py',
>>> line 132 in __call__
>>>     return self.handle_request( environ, start_response )
>>> File
>>>
>>> '/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/lib/galaxy/web/framework/base.py',
>>> line 190 in handle_request
>>>     body = method( trans, **kwargs )
>>> File
>>>
>>> '/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/lib/galaxy/web/framework/__init__.py',
>>> line 98 in decorator
>>>     return func( self, trans, *args, **kwargs )
>>> File
>>>
>>> '/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/user.py',
>>> line 1680 in dbkeys
>>>     chrom_count = int( open( chrom_count_dataset.file_name ).readline() )
>>> IOError: [Errno 2] No such file or directory:
>>> '/phengs/galaxy/database/files/000/127/dataset_127764.dat'
>>>
>>>
>>> CGI Variables
>>> -------------
>>>     CONTENT_LENGTH: '0'
>>>     HTTP_ACCEPT:
>>>
>>> 'text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8'
>>>     HTTP_ACCEPT_ENCODING: 'gzip'
>>>     HTTP_ACCEPT_LANGUAGE: 'en-GB,en;q=0.8,en-US;q=0.6,de;q=0.4'
>>>     HTTP_CONNECTION: 'Keep-Alive'
>>>     HTTP_COOKIE:
>>>
>>> 'galaxysession=c6ca0ddb55be603a1e24419432331618f5a7191d55ca4813cd28cd8c84abb88b122c85b9044b10ba'
>>>     HTTP_HOST: '158.119.147.85'
>>>     HTTP_REFERER: 'http://158.119.147.85/root'
>>>     HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36
>>> (KHTML, like Gecko) Chrome/39.0.2171.71 Safari/537.36'
>>>     HTTP_VIA: '1.1 TMGCOL001'
>>>     HTTP_X_FORWARDED_FOR: '158.119.150.18'
>>>     HTTP_X_FORWARDED_HOST: '158.119.147.85'
>>>     HTTP_X_FORWARDED_SERVER: 'bioinformatics-galaxy.phe.org.uk'
>>>     ORGINAL_HTTP_HOST: 'localhost:8084'
>>>     ORGINAL_REMOTE_ADDR: '127.0.0.1'
>>>     PATH_INFO: '/user/dbkeys'
>>>     REMOTE_ADDR: '158.119.150.18'
>>>     REQUEST_METHOD: 'GET'
>>>     SERVER_NAME: '0.0.0.0'
>>>     SERVER_PORT: '8084'
>>>     SERVER_PROTOCOL: 'HTTP/1.1'
>>>
>>>
>>> WSGI Variables
>>> --------------
>>>     application: <paste.recursive.RecursiveMiddleware object at 0x8fe2c90>
>>>     is_api_request: False
>>>     paste.cookies: (<SimpleCookie:
>>>
>>> galaxysession='c6ca0ddb55be603a1e24419432331618f5a7191d55ca4813cd28cd8c84abb88b122c85b9044b10ba'>,
>>>
>>> 'galaxysession=c6ca0ddb55be603a1e24419432331618f5a7191d55ca4813cd28cd8c84abb88b122c85b9044b10ba')
>>>     paste.expected_exceptions: [<class
>>> 'paste.httpexceptions.HTTPException'>]
>>>     paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler
>>> object at 0x8fe2510>
>>>     paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
>>> 0x9332210>
>>>     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.throw_errors: True
>>>     request_id: '965c3b007ecc11e4b771005056983c1e'
>>>     webob._parsed_query_vars: (MultiDict([]), '')
>>>     wsgi process: 'Multithreaded'
>>>
>>> ---
>>>
>>> The file it is looking for (dataset_127764.dat) is indeed not there and
>>> I suspect that once it contained a genome of a custom build that this
>>> user had added. How it was removed I cannot tell.
>>>
>>> I don't need to get this particular genome back, but I need to stop
>>> Galaxy from looking for it, so that the user can get back into the
>>> interface. Does anyone know how I can wipe all Custom Builds for a given
>>> user?
>>>
>>> Thanks a lot for your help
>>> Best regards
>>> Ulf
>>>
>>> --
>>> Ulf Schaefer, PhD
>>> Bioinformatics Scientist
>>> Bioinformatics Unit - Infectious Disease Informatics
>>> Public Health England
>>> 61 Colindale Ave
>>> London NW9 5EQ
>>> ulf.schae...@phe.gov.uk
>>> Tel: 020 832 77296
>>> http://www.gov.uk/phe
>>> Protecting and improving the nation’s health
>>>
>>> **************************************************************************
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>>> both. If you are not the intended recipient, you must not disclose, copy,
>>> distribute or retain this message or any part of it. This footnote also
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>>
>>
>

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any part of it. This footnote also confirms that this EMail has been swept for 
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