Hi Syed,

Here's the dump from my log file:

2009/07/17 12:07:53 BioMart.Web:449:INFO> Restoring existing session d2e13b828c9c73a18e2b0d1808c66e8c
2009/07/17 12:07:53 BioMart.QueryRunner:169:WARN> NO ATTRIBUTES
2009/07/17 12:07:53 BioMart.QueryRunner:179:WARN> NO FILTERS
2009/07/17 12:07:53 BioMart.Dataset.TableSet:900:INFO> COUNT SQL: SELECT COUNT(*) FROM htgt_mart.kermits__emi_clone__main main
2009/07/17 12:07:53 BioMart.QueryRunner:169:WARN> NO ATTRIBUTES
2009/07/17 12:07:53 BioMart.QueryRunner:174:WARN> FILTER TABLE: kermits status_code main 2009/07/17 12:07:53 BioMart.QueryRunner:174:WARN> FILTER TABLE: kermits centre main 2009/07/17 12:07:53 BioMart.Dataset.TableSet:900:INFO> COUNT SQL: SELECT COUNT(DISTINCT main.id_102_key) FROM htgt_mart.kermits__emi_event__main main WHERE (main.status_code
= 'GC') AND (main.centre = 'WTSI')
2009/07/17 12:07:53 martview:142:ERROR> ERROR: caught BioMart::Exception: non-BioMart die(): Can't use an undefined value as an ARRAY reference at /software/team87/biomart/bio
mart-0_7-prod/lib/BioMart/Dataset/TableSet.pm line 911.

Stacktrace:
Exception::Class::Base::new /software/team87/biomart/biomart-0_7- prod/cgi-bin/martview:125 ModPerl ::ROOT ::ModPerl ::Registry ::software_team87_biomart_biomart_2d0_7_2dprod_cgi_2dbin_martview ::handler /software/team87/HTGT/perl/lib/site_perl/5.8.8/x86_64-linux- threa
d-multi/ModPerl/RegistryCooker.pm:204
(eval) /software/team87/HTGT/perl/lib/site_perl/5.8.8/x86_64-linux- thread-multi/ModPerl/RegistryCooker.pm:204 ModPerl::RegistryCooker::run /software/team87/HTGT/perl/lib/ site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:170 ModPerl::RegistryCooker::default_handler /software/team87/HTGT/ perl/lib/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/Registry.pm: 31
  ModPerl::Registry::handler  -e:0
  (eval)  -e:0
2009/07/17 12:07:53 BioMart.Web:264:INFO> START PROCESSING TEMPLATE error.tt 2009/07/17 12:07:53 BioMart.Web:271:INFO> !!!! 0.03 to get process template error.tt and print to string

Cheers,

Daz

On 17 Jul 2009, at 11:30, Syed Haider wrote:

Hi Darren,

when you hit the count button, please see what goes in the error_log. you would need to switch on the logging to INFO from FATAL in conf/log4perl.conf and reconfigure/restart.

Cheers
Syed


Darren Oakley wrote:
Hi All,
Sorry to disturb, but I'm getting an error which I just can't figure out when doing a count on one of our Marts...
Here's the URL for the search:
http://www.sanger.ac.uk/htgt/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=kermits.default.attributes.sponsor |kermits.default.attributes.marker_symbol| kermits .default .attributes.status&FILTERS=kermits.default.filters.status_code."GC"| kermits.default.filters.centre."WTSI"&VISIBLEPANEL=resultspanel The search works fine and returns results, but when I try to get a count from this search (I'd like to know the number of genes with this criteria), the mart throws the following error (both in MartView and through the APIs): Query ERROR: caught BioMart::Exception: non-BioMart die(): Can't use an undefined value as an ARRAY reference at /software/team87/ biomart/biomart-0_7-prod/lib/BioMart/Dataset/TableSet.pm line 911. To get the count, I'm hitting it via the rest api with the following xml:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="1" count="1" datasetConfigVersion="0.6">
 <Dataset name="kermits" interface="default">
   <Filter name="status_code" value="GC"/>
   <Filter name="centre" value="WTSI"/>
 </Dataset>
</Query>
Any idea what could be the issue here?
Thanks,
Daz
P.S. Forgot to let you all know - our new (preview) Mouse portal at the Sanger is now running off Biomart: http://www.sanger.ac.uk/mouseportal/ (well, several biomarts really...) It's still in development, and things can be flaky every now and then, so be gentle! ;)



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