[BioMart Users] BioMart not working

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[BioMart Users] BioMart not working

Rebecca Ewing
Hi

Our BioMart is not working properly. It is up and running but will not get any results. It is not producing any error messages when I hit the results button but if I try to export the results I get the following:

ERROR: caught BioMart::Exception::Query: You need to define virtual schema name in order to create a Query object

If you repeatedly get directed to this error page, there may be a problem with your current session parameters. To clear your session and start with a clean slate, please click the New button below.

Stacktrace:
Exception::Class::Base::throw /www/test/biomart-perl/lib/BioMart/Query.pm:93
BioMart::Query::_new /www/test/biomart-perl/lib/BioMart/RootI.pm:64
BioMart::RootI::new /www/test/biomart-perl/lib/BioMart/Web.pm:1968
BioMart::Web::handle_request /www/test/biomart-perl/cgi-bin/martview:107
(eval) /www/test/biomart-perl/cgi-bin/martview:106
ModPerl::ROOT::ModPerl::Registry::www_test_biomart_2dperl_cgi_2dbin_martview::handler /usr/lib/perl5/ModPerl/RegistryCooker.pm:204
(eval) /usr/lib/perl5/ModPerl/RegistryCooker.pm:204
ModPerl::RegistryCooker::run /usr/lib/perl5/ModPerl/RegistryCooker.pm:170
ModPerl::RegistryCooker::default_handler /usr/lib/perl5/ModPerl/Registry.pm:31
ModPerl::Registry::handler -e:0
(eval) -e:0


Does anyone have any idea what the problem may be.

Thanks

Rebecca

-- 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.

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Re: [BioMart Users] BioMart not working

Syed Haider
Rebecca,

could you please provide a bit more information. Where is your Biomart
running ? is it accessible from outside sanger ?

Best,
Syed

On 07/10/2011 10:41, Rebecca Ewing wrote:

> Hi
>
> Our BioMart is not working properly. It is up and running but will not get any results. It is not producing any error messages when I hit the results button but if I try to export the results I get the following:
>
>
> ERROR: caught BioMart::Exception::Query: You need to define virtual schema name in order to create a Query object
>
> If you repeatedly get directed to this error page, there may be a problem with your current session parameters. To clear your session and start with a clean slate, please click the New button below.
>
> Stacktrace:
> Exception::Class::Base::throw /www/test/biomart-perl/lib/BioMart/Query.pm:93
> BioMart::Query::_new /www/test/biomart-perl/lib/BioMart/RootI.pm:64
> BioMart::RootI::new /www/test/biomart-perl/lib/BioMart/Web.pm:1968
> BioMart::Web::handle_request /www/test/biomart-perl/cgi-bin/martview:107
> (eval) /www/test/biomart-perl/cgi-bin/martview:106
> ModPerl::ROOT::ModPerl::Registry::www_test_biomart_2dperl_cgi_2dbin_martview::handler /usr/lib/perl5/ModPerl/RegistryCooker.pm:204
> (eval) /usr/lib/perl5/ModPerl/RegistryCooker.pm:204
> ModPerl::RegistryCooker::run /usr/lib/perl5/ModPerl/RegistryCooker.pm:170
> ModPerl::RegistryCooker::default_handler /usr/lib/perl5/ModPerl/Registry.pm:31
> ModPerl::Registry::handler -e:0
> (eval) -e:0
>
> Does anyone have any idea what the problem may be.
>
> Thanks
>
> Rebecca
>
> -- 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.
>
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Re: [BioMart Users] BioMart not working

Rebecca Ewing
Hi Syed

It is on a vm and is visible outside the sanger:

http://www.sanger.ac.uk/genetics/CGP/cosmic/biomart/martview/

Thanks

Rebecca

On 7 Oct 2011, at 12:35, Syed Haider wrote:

> Rebecca,
>
> could you please provide a bit more information. Where is your Biomart running ? is it accessible from outside sanger ?
>
> Best,
> Syed
>
> On 07/10/2011 10:41, Rebecca Ewing wrote:
>> Hi
>>
>> Our BioMart is not working properly. It is up and running but will not get any results. It is not producing any error messages when I hit the results button but if I try to export the results I get the following:
>>
>>
>> ERROR: caught BioMart::Exception::Query: You need to define virtual schema name in order to create a Query object
>>
>> If you repeatedly get directed to this error page, there may be a problem with your current session parameters. To clear your session and start with a clean slate, please click the New button below.
>>
>> Stacktrace:
>> Exception::Class::Base::throw /www/test/biomart-perl/lib/BioMart/Query.pm:93
>> BioMart::Query::_new /www/test/biomart-perl/lib/BioMart/RootI.pm:64
>> BioMart::RootI::new /www/test/biomart-perl/lib/BioMart/Web.pm:1968
>> BioMart::Web::handle_request /www/test/biomart-perl/cgi-bin/martview:107
>> (eval) /www/test/biomart-perl/cgi-bin/martview:106
>> ModPerl::ROOT::ModPerl::Registry::www_test_biomart_2dperl_cgi_2dbin_martview::handler /usr/lib/perl5/ModPerl/RegistryCooker.pm:204
>> (eval) /usr/lib/perl5/ModPerl/RegistryCooker.pm:204
>> ModPerl::RegistryCooker::run /usr/lib/perl5/ModPerl/RegistryCooker.pm:170
>> ModPerl::RegistryCooker::default_handler /usr/lib/perl5/ModPerl/Registry.pm:31
>> ModPerl::Registry::handler -e:0
>> (eval) -e:0
>>
>> Does anyone have any idea what the problem may be.
>>
>> Thanks
>>
>> Rebecca
>>
>> -- 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.
>>



--
 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.
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Re: [BioMart Users] BioMart not working

Syed Haider-2
Hi Rebecca,

thats odd, i can get results from webservice but martview is not working
inspite attribtues being selected. Could you please delete the logs
files under biomart-perl/logs/ and restart the server ?

Best,
Syed

On 07/10/2011 13:02, Rebecca Ewing wrote:

> Hi Syed
>
> It is on a vm and is visible outside the sanger:
>
> http://www.sanger.ac.uk/genetics/CGP/cosmic/biomart/martview/
>
> Thanks
>
> Rebecca
>
> On 7 Oct 2011, at 12:35, Syed Haider wrote:
>
>> Rebecca,
>>
>> could you please provide a bit more information. Where is your Biomart running ? is it accessible from outside sanger ?
>>
>> Best,
>> Syed
>>
>> On 07/10/2011 10:41, Rebecca Ewing wrote:
>>> Hi
>>>
>>> Our BioMart is not working properly. It is up and running but will not get any results. It is not producing any error messages when I hit the results button but if I try to export the results I get the following:
>>>
>>>
>>> ERROR: caught BioMart::Exception::Query: You need to define virtual schema name in order to create a Query object
>>>
>>> If you repeatedly get directed to this error page, there may be a problem with your current session parameters. To clear your session and start with a clean slate, please click the New button below.
>>>
>>> Stacktrace:
>>> Exception::Class::Base::throw /www/test/biomart-perl/lib/BioMart/Query.pm:93
>>> BioMart::Query::_new /www/test/biomart-perl/lib/BioMart/RootI.pm:64
>>> BioMart::RootI::new /www/test/biomart-perl/lib/BioMart/Web.pm:1968
>>> BioMart::Web::handle_request /www/test/biomart-perl/cgi-bin/martview:107
>>> (eval) /www/test/biomart-perl/cgi-bin/martview:106
>>> ModPerl::ROOT::ModPerl::Registry::www_test_biomart_2dperl_cgi_2dbin_martview::handler /usr/lib/perl5/ModPerl/RegistryCooker.pm:204
>>> (eval) /usr/lib/perl5/ModPerl/RegistryCooker.pm:204
>>> ModPerl::RegistryCooker::run /usr/lib/perl5/ModPerl/RegistryCooker.pm:170
>>> ModPerl::RegistryCooker::default_handler /usr/lib/perl5/ModPerl/Registry.pm:31
>>> ModPerl::Registry::handler -e:0
>>> (eval) -e:0
>>>
>>> Does anyone have any idea what the problem may be.
>>>
>>> Thanks
>>>
>>> Rebecca
>>>
>>> -- 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.
>>>
>
>
>
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