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.Schaefer@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.schaefer@phe.gov.uk Tel: 020 832 77296 http://www.gov.uk/phe Protecting and improving the nation’s health
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