[BioMart Users] Bug in BioMart 0.7 when search term contains the string 'only'

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[BioMart Users] Bug in BioMart 0.7 when search term contains the string 'only'

HARSHBARGER Jayson
Hello BioMart devs and users,

It took me some time to realize this but if a user uses the text 'only' in any filter BioMart will show an error (copied below).  I've verified that this is not specific to my installation.  In my case I have a field where some entries contain the text 'only' (example 'XXX_only').  The only work around I've discovered is to replace the 'only' text with a wildcard (example: 'XXX_onl%').  I realize 0.7 is is an old version but there are still many installations out there so I felt I should point this out.  Forgive me if this is already known.

Jayson Harshbarger

ERROR: caught BioMart::Exception: non-BioMart die(): Can't locate object method "setExcluded" via package "BioMart::Configuration::ValueFilter" at /ensemblweb/wwwmart/www_71/biomart-perl/lib/BioMart/Query.pm line 1371.

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 theNew button below.

Stacktrace:
Exception::Class::Base::new /ensemblweb/wwwmart/www_71/biomart-perl/cgi-bin/martview:105
ModPerl::ROOT::ModPerl::Registry::ensemblweb_wwwmart_www_71_biomart_2dperl_cgi_2dbin_martview::handler /localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204
(eval) /localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204
ModPerl::RegistryCooker::run /localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:170
ModPerl::RegistryCooker::default_handler /localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ModPerl/Registry.pm:31
ModPerl::Registry::handler -e:0
(eval) -e:0


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Re: [BioMart Users] Bug in BioMart 0.7 when search term contains the string 'only'

Arek Kasprzyk
Hi Jayson,
thanks for reporting this. I am sure your workaround will be useful for a lot of people


a


On 29 May 2013 06:48, Jayson Harshbarger <[hidden email]> wrote:
Hello BioMart devs and users,

It took me some time to realize this but if a user uses the text 'only' in any filter BioMart will show an error (copied below).  I've verified that this is not specific to my installation.  In my case I have a field where some entries contain the text 'only' (example 'XXX_only').  The only work around I've discovered is to replace the 'only' text with a wildcard (example: 'XXX_onl%').  I realize 0.7 is is an old version but there are still many installations out there so I felt I should point this out.  Forgive me if this is already known.

Jayson Harshbarger

ERROR: caught BioMart::Exception: non-BioMart die(): Can't locate object method "setExcluded" via package "BioMart::Configuration::ValueFilter" at /ensemblweb/wwwmart/www_71/biomart-perl/lib/BioMart/Query.pm line 1371.

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 theNew button below.

Stacktrace:
Exception::Class::Base::new /ensemblweb/wwwmart/www_71/biomart-perl/cgi-bin/martview:105
ModPerl::ROOT::ModPerl::Registry::ensemblweb_wwwmart_www_71_biomart_2dperl_cgi_2dbin_martview::handler /localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204
(eval) /localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204
ModPerl::RegistryCooker::run /localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:170
ModPerl::RegistryCooker::default_handler /localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ModPerl/Registry.pm:31
ModPerl::Registry::handler -e:0
(eval) -e:0


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Re: [BioMart Users] Bug in BioMart 0.7 when search term contains the string 'only'

Bob MacCallum
Just to follow up that on the surface this smells like an SQL
injection issue but thankfully it is not.

https://github.com/i-dcc/biomart-server/blob/master/lib/BioMart/Query.pm#L1302-L1314

On Wed, May 29, 2013 at 9:31 AM, Arek Kasprzyk <[hidden email]> wrote:

> Hi Jayson,
> thanks for reporting this. I am sure your workaround will be useful for a
> lot of people
>
>
> a
>
>
> On 29 May 2013 06:48, Jayson Harshbarger <[hidden email]> wrote:
>>
>> Hello BioMart devs and users,
>>
>> It took me some time to realize this but if a user uses the text 'only' in
>> any filter BioMart will show an error (copied below).  I've verified that
>> this is not specific to my installation.  In my case I have a field where
>> some entries contain the text 'only' (example 'XXX_only').  The only work
>> around I've discovered is to replace the 'only' text with a wildcard
>> (example: 'XXX_onl%').  I realize 0.7 is is an old version but there are
>> still many installations out there so I felt I should point this out.
>> Forgive me if this is already known.
>>
>> Jayson Harshbarger
>>
>> ERROR: caught BioMart::Exception: non-BioMart die(): Can't locate object
>> method "setExcluded" via package "BioMart::Configuration::ValueFilter" at
>> /ensemblweb/wwwmart/www_71/biomart-perl/lib/BioMart/Query.pm line 1371.
>>
>> 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 theNew button below.
>>
>> Stacktrace:
>> Exception::Class::Base::new
>> /ensemblweb/wwwmart/www_71/biomart-perl/cgi-bin/martview:105
>>
>> ModPerl::ROOT::ModPerl::Registry::ensemblweb_wwwmart_www_71_biomart_2dperl_cgi_2dbin_martview::handler
>> /localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204
>> (eval)
>> /localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204
>> ModPerl::RegistryCooker::run
>> /localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:170
>> ModPerl::RegistryCooker::default_handler
>> /localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ModPerl/Registry.pm:31
>> ModPerl::Registry::handler -e:0
>> (eval) -e:0
>>
>>
>> _______________________________________________
>> Users mailing list
>> [hidden email]
>> https://lists.biomart.org/mailman/listinfo/users
>
>
>
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
_______________________________________________
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