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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