Re: [galaxy-dev] custom builds
I will admit I don't understand how the mapper problem is related or why it would occur in monitor_step or custom builds, but I do know there is an important bug fix in release 15.05 from Dannon (https://github.com/galaxyproject/galaxy/pull/198) that multiple people have reported fixing the problem with mapper initialization. It might be worth upgrading or applying the diffs manually to your instance. -John On Wed, May 13, 2015 at 1:48 PM, Shrum, Donald C wrote: > Hi all, > > > > I have a public galaxy server here at FSU that is running behind an apache > proxy and on our cluster file system so that jobs can be submitted to our > hpc cluster. > > > > I have a user that receives an ‘Internal Server Error’ when going to ‘Custom > Builds’ This error seems to only occur for the one user and from what I can > see it may be the case that there is a single mapper is causing the problem. > (Sys-admin here, not a bioinformatics person :) > > > > The errors I pulled from the logs are below. Is it possible there is some > mapper causing the problem? If so is there a way I can remove it? > > > > Any help would be appreciated and thanks, > > Don Shrum > > FSU Research Computing Center > > > > InvalidRequestError: One or more mappers failed to initialize - can't > proceed with initialization of other mappers. Original exception was: Class > 'kombu.transport.sqlalchemy.Message' is not mapped > > galaxy.jobs.handler ERROR 2015-05-13 13:44:25,150 Exception in monitor_step > > > > > > WSGI Variables > > -- > > application: > > is_api_request: False > > original_wsgi.url_scheme: 'http' > > paste.cookies: ( __utma='51326654.2116930099.1431360039.1431360039.1431360039.1' > __utmz='51326654.1431360039.1.1.utmcsr=directory.fsu.edu|utmccn=(referral)|utmcmd=referral|utmcct=/' > _ga='GA1.2.2116930099.1431360039' > galaxysession='c6ca0ddb55be603abe1a0bf853fb54302d17fe1509e1ff998221f8b85399eb4a8bcf9d852c6fb740'>, > '__utma=51326654.2116930099.1431360039.1431360039.1431360039.1; > __utmz=51326654.1431360039.1.1.utmcsr=directory.fsu.edu|utmccn=(referral)|utmcmd=referral|utmcct=/; > _ga=GA1.2.2116930099.1431360039; > galaxysession=c6ca0ddb55be603abe1a0bf853fb54302d17fe1509e1ff998221f8b85399eb4a8bcf9d852c6fb740') > > paste.expected_exceptions: [] > > paste.httpexceptions: 0x867ff10> > > paste.httpserver.thread_pool: 0x8a21f50> > > paste.recursive.forward: > > paste.recursive.include: > > paste.recursive.include_app_iter: > > paste.recursive.script_name: '' > > paste.throw_errors: True > > request_id: '57170782f99611e4af7a00219ba29ca2' > > webob._parsed_query_vars: (MultiDict([]), '') > > wsgi process: 'Multithreaded' > > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] custom builds
Hi all, I have a public galaxy server here at FSU that is running behind an apache proxy and on our cluster file system so that jobs can be submitted to our hpc cluster. I have a user that receives an 'Internal Server Error' when going to 'Custom Builds' This error seems to only occur for the one user and from what I can see it may be the case that there is a single mapper is causing the problem. (Sys-admin here, not a bioinformatics person :) The errors I pulled from the logs are below. Is it possible there is some mapper causing the problem? If so is there a way I can remove it? Any help would be appreciated and thanks, Don Shrum FSU Research Computing Center InvalidRequestError: One or more mappers failed to initialize - can't proceed with initialization of other mappers. Original exception was: Class 'kombu.transport.sqlalchemy.Message' is not mapped galaxy.jobs.handler ERROR 2015-05-13 13:44:25,150 Exception in monitor_step WSGI Variables -- application: is_api_request: False original_wsgi.url_scheme: 'http' paste.cookies: (, '__utma=51326654.2116930099.1431360039.1431360039.1431360039.1; __utmz=51326654.1431360039.1.1.utmcsr=directory.fsu.edu|utmccn=(referral)|utmcmd=referral|utmcct=/; _ga=GA1.2.2116930099.1431360039; galaxysession=c6ca0ddb55be603abe1a0bf853fb54302d17fe1509e1ff998221f8b85399eb4a8bcf9d852c6fb740') paste.expected_exceptions: [] paste.httpexceptions: paste.httpserver.thread_pool: paste.recursive.forward: paste.recursive.include: paste.recursive.include_app_iter: paste.recursive.script_name: '' paste.throw_errors: True request_id: '57170782f99611e4af7a00219ba29ca2' webob._parsed_query_vars: (MultiDict([]), '') wsgi process: 'Multithreaded' ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Custom Builds not accessible for user
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 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 >> 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 - : [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: >>> is_api_request: False >>> paste.cookies: (>> >>> galaxysession='c6ca0ddb55be603a1e24419432331618f5a7191d55ca4813cd28cd8c84abb88b122c85b9044b10ba'>, >>> >>> 'galaxysession=c6ca0ddb55be603a1e24419432331618f5a7191d55ca4813cd28cd8c84abb88b122c85b9044b10ba') >>> paste.expected_exceptions: [>> 'paste.httpexceptions.HTTPException'>] >>> paste.httpexceptions: >> object at 0x8fe2510> >>> paste.httpserver.thread_pool: >> 0x9332210> >>> paste.recursive.forward: >>> paste.recursive.include: >>> paste.recursive.include_app_iter: >> 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? >>> >
Re: [galaxy-dev] Custom Builds not accessible for user
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 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 > 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 - : [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: >>is_api_request: False >>paste.cookies: (> >> galaxysession='c6ca0ddb55be603a1e24419432331618f5a7191d55ca4813cd28cd8c84abb88b122c85b9044b10ba'>, >> >> 'galaxysession=c6ca0ddb55be603a1e24419432331618f5a7191d55ca4813cd28cd8c84abb88b122c85b9044b10ba') >>paste.expected_exceptions: [> 'paste.httpexceptions.HTTPException'>] >>paste.httpexceptions: > object at 0x8fe2510> >>paste.httpserver.thread_pool: > 0x9332210> >>paste.recursive.forward: >>paste.recursive.include: >>paste.recursive.include_app_iter: > 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 i
Re: [galaxy-dev] Custom Builds not accessible for user
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 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 - : [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: >is_api_request: False >paste.cookies: ( > galaxysession='c6ca0ddb55be603a1e24419432331618f5a7191d55ca4813cd28cd8c84abb88b122c85b9044b10ba'>, > > 'galaxysession=c6ca0ddb55be603a1e24419432331618f5a7191d55ca4813cd28cd8c84abb88b122c85b9044b10ba') >paste.expected_exceptions: [ 'paste.httpexceptions.HTTPException'>] >paste.httpexceptions: object at 0x8fe2510> >paste.httpserver.thread_pool: 0x9332210> >paste.recursive.forward: >paste.recursive.include: >paste.recursive.include_app_iter: 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 > > ** > The information contained in the EMail and any attachments is confidential > and intended solely and for the attention and use of the named > addressee(s). It may not be disclosed to any other person without the > express authority of Public Health England, or the intended recipient, or > both. If you are not the intended recipient, you must not disclose, copy, > distribute or r
[galaxy-dev] Custom Builds not accessible for user
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 - : [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: is_api_request: False paste.cookies: (, 'galaxysession=c6ca0ddb55be603a1e24419432331618f5a7191d55ca4813cd28cd8c84abb88b122c85b9044b10ba') paste.expected_exceptions: [] paste.httpexceptions: paste.httpserver.thread_pool: paste.recursive.forward: paste.recursive.include: paste.recursive.include_app_iter: 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 ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or 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 confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE ** ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Ga
