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 <lsk...@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.
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