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! ;)
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.