Hi Darren,
What does that SQL do when you run it direct on the server - it looks fine
but seems like $ret = ${$sth->fetchrow_arrayref}[0]; is giving the error
i.e. no rows are coming back
Cheers
Damian
On Fri, Jul 17, 2009 at 4:10 AM, Darren Oakley <[email protected]> wrote:
> 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 ResearchLimited,
> a charity registered in England with number 1021457 and acompany registered
> in England with number 2742969, whose registeredoffice is 215 Euston Road,
> London, NW1 2BE.
>
