nglims error: "sequencing results" menu
Hi, I get an internal server error when clicking "sequencing results" under the lab menu. I'm hoping for an easy fix :) This is in my server log file (and I'm removing some data and IP addresses found in the log): 10.xx.xx.xx - - [09/Jul/2013:15:45:21 -0400] "GET /chapman/nglims/list_sqn_results HTTP/1.1" 500 - " http://mydomain/chapman/nglims" "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/27.0.1453.116 Safari/537.36" Error - <class 'sqlalchemy.exc.ArgumentError'>: SQL expression object or string expected. URL: http://mydomain/chapman/nglims/list_sqn_results File '/home/galaxy/bin/chapman-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/home/galaxy/bin/chapman-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/galaxy/bin/chapman-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/galaxy/bin/chapman-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/home/galaxy/bin/chapman-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/home/galaxy/bin/chapman-dist/lib/galaxy/web/framework/__init__.py', line 98 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxy/bin/chapman-dist/lib/galaxy/webapps/galaxy/controllers/nglims.py', line 312 in list_sqn_results return grid(trans, **kwd) File '/home/galaxy/bin/chapman-dist/lib/galaxy/web/framework/helpers/grids.py', line 78 in __call__ query = self.apply_query_filter( trans, query, **kwargs ) File '/home/galaxy/bin/chapman-dist/lib/galaxy/webapps/galaxy/controllers/nglims.py', line 2577 in apply_query_filter ["sqn_run_results.request_id DESC", "lane ASC", "sample_id DESC"]) File '<string>', line 1 in <lambda> File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 50 in generate File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 1239 in order_by File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 204 in _adapt_col_list File 'build/bdist.linux-x86_64/egg/sqlalchemy/sql/expression.py', line 1409 in _literal_as_text ArgumentError: SQL expression object or string expected. CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' HTTP_ACCEPT_ENCODING: 'gzip,deflate,sdch' HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.8' HTTP_CONNECTION: 'Keep-Alive' HTTP_COOKIE: xxxxxxxxxxxxxxxxxxxxx WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x9e68750> is_api_request: False paste.cookies: (<SimpleCookie: __utma='56454061.1423238699.1342718372.1353518961.1353970254.7' __utmz='56454061.1353970254.7.5.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=(not%20provided)' fsr.s.session.11.2.0='{' galaxysession='c6ca0ddb55be603a9c0efb539e40d0336dececb67b847917dbf9a94fc6cf855c6779ace204504c35' s_cc='true' s_ppv='100' s_ria='%7CSilverlight%205.1' s_sq='%5B%5BB%5D%5D' s_vi=''>, 'galaxysession=c6ca0ddb55be603a9c0efb539e40d0336dececb67b847917dbf9a94fc6cf855c6779ace204504c35; __utma=56454061.1423238699.1342718372.1353518961.1353970254.7; __utmz=56454061.1353970254.7.5.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=(not%20provided); fsr.s.session.11.2.0={"v":1,"rid":"d445cf6-83333627-36f4-dc7a-687e3","ru":" https://www.google.com/","r":"www.google.com ","st":"","cp":{"GovDelivery":"N"},"to":3,"c":" http://www.cdc.gov/nchs/health_policy/ADL_tables.htm","pv":1,"lc":{"d0":{"v":1,"s":false}},"cd":0,"f":1373396348260}; s_cc=true; s_ria=%7CSilverlight%205.1; s_sq=%...[CE]; s_ppv=100') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x9e68710> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x27d5e10> paste.recursive.forward: <paste.recursive.Forwarder from /chapman> paste.recursive.include: <paste.recursive.Includer from /chapman> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /chapman> paste.recursive.script_name: '/chapman' paste.throw_errors: True request_id: '1720335ce8d011e296e1b8ac6f45c6b6' webob._parsed_query_vars: (MultiDict([]), '') wsgi process: 'Multithreaded' ------------------------------------------------------------
Basically the same thing happens on a few different menus actually including most recently "Review tool migration stages" so I don't think it's a nglims thing anymore. On Tue, Jul 9, 2013 at 3:54 PM, Lee Katz <lskatz@gmail.com> wrote:
Hi, I get an internal server error when clicking "sequencing results" under the lab menu. I'm hoping for an easy fix :)
This is in my server log file (and I'm removing some data and IP addresses found in the log):
10.xx.xx.xx - - [09/Jul/2013:15:45:21 -0400] "GET /chapman/nglims/list_sqn_results HTTP/1.1" 500 - " http://mydomain/chapman/nglims" "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/27.0.1453.116 Safari/537.36" Error - <class 'sqlalchemy.exc.ArgumentError'>: SQL expression object or string expected. URL: http://mydomain/chapman/nglims/list_sqn_results File '/home/galaxy/bin/chapman-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/home/galaxy/bin/chapman-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/galaxy/bin/chapman-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/galaxy/bin/chapman-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/home/galaxy/bin/chapman-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/home/galaxy/bin/chapman-dist/lib/galaxy/web/framework/__init__.py', line 98 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxy/bin/chapman-dist/lib/galaxy/webapps/galaxy/controllers/nglims.py', line 312 in list_sqn_results return grid(trans, **kwd) File '/home/galaxy/bin/chapman-dist/lib/galaxy/web/framework/helpers/grids.py', line 78 in __call__ query = self.apply_query_filter( trans, query, **kwargs ) File '/home/galaxy/bin/chapman-dist/lib/galaxy/webapps/galaxy/controllers/nglims.py', line 2577 in apply_query_filter ["sqn_run_results.request_id DESC", "lane ASC", "sample_id DESC"]) File '<string>', line 1 in <lambda> File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 50 in generate File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 1239 in order_by File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 204 in _adapt_col_list File 'build/bdist.linux-x86_64/egg/sqlalchemy/sql/expression.py', line 1409 in _literal_as_text ArgumentError: SQL expression object or string expected.
CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' HTTP_ACCEPT_ENCODING: 'gzip,deflate,sdch' HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.8' HTTP_CONNECTION: 'Keep-Alive' HTTP_COOKIE: xxxxxxxxxxxxxxxxxxxxx
WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x9e68750> is_api_request: False paste.cookies: (<SimpleCookie: __utma='56454061.1423238699.1342718372.1353518961.1353970254.7' __utmz='56454061.1353970254.7.5.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=(not%20provided)' fsr.s.session.11.2.0='{' galaxysession='c6ca0ddb55be603a9c0efb539e40d0336dececb67b847917dbf9a94fc6cf855c6779ace204504c35' s_cc='true' s_ppv='100' s_ria='%7CSilverlight%205.1' s_sq='%5B%5BB%5D%5D' s_vi=''>, 'galaxysession=c6ca0ddb55be603a9c0efb539e40d0336dececb67b847917dbf9a94fc6cf855c6779ace204504c35; __utma=56454061.1423238699.1342718372.1353518961.1353970254.7; __utmz=56454061.1353970254.7.5.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=(not%20provided); fsr.s.session.11.2.0={"v":1,"rid":"d445cf6-83333627-36f4-dc7a-687e3","ru":" https://www.google.com/","r":"www.google.com ","st":"","cp":{"GovDelivery":"N"},"to":3,"c":" http://www.cdc.gov/nchs/health_policy/ADL_tables.htm","pv":1,"lc":{"d0":{"v":1,"s":false}},"cd":0,"f":1373396348260}; s_cc=true; s_ria=%7CSilverlight%205.1; s_sq=%...[CE]; s_ppv=100') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x9e68710> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x27d5e10> paste.recursive.forward: <paste.recursive.Forwarder from /chapman> paste.recursive.include: <paste.recursive.Includer from /chapman> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /chapman> paste.recursive.script_name: '/chapman' paste.throw_errors: True request_id: '1720335ce8d011e296e1b8ac6f45c6b6' webob._parsed_query_vars: (MultiDict([]), '') wsgi process: 'Multithreaded' ------------------------------------------------------------
-- Lee Katz, Ph.D.
Lee;
Hi, I get an internal server error when clicking "sequencing results" under the lab menu. I'm hoping for an easy fix :)
Basically the same thing happens on a few different menus actually including most recently "Review tool migration stages" so I don't think it's a nglims thing anymore.
Thanks for the report. This looks like an issue where SQLAlchemy changed the syntax for multiclause order_by and filter_by queries. That's why you're seeing it in other parts of Galaxy as well: a few may have slipped through the cracks. I fixed the nglims ones and pushed to bitbucket, so if you grab the latest it should be working now: https://bitbucket.org/chapmanb/galaxy-central/commits/395ade9a9bda518c63daa0... Thanks again for the report, Brad
participants (2)
-
Brad Chapman -
Lee Katz