validation errors

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validation errors

jorge zamora
Hi,

In 'ensembl genes' mart we have a 'validation error' that comes up when
a user tries to select in SEQUENCES attributes upstream AND downstream
sequences. Current we only allow to select upstream OR downstream (just
only one of them).

Now we're considering to allow the users to select both attributes
upstream AND downstream. I've tried to identify the place where we
impose that restriction in the configuration but I haven't found it, not
even the place where 'validation error' message is stored:

Validation Error: For this sequence option choose upstream OR downstream
gene flanking sequence, NOT both, as makes no sense to simply
concatenate them together.

any idea about how to find the restriction in order to disable it?


Many thanks,
Jorge

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Re: validation errors

Syed Haider
Hi Jorge,

please see:

biomart-perl/lib/BioMart/Dataset/GenomicSequence.pm

sub _modFlanks {....}

Hope this helps,
Syed




On 25/10/2010 09:30, jorge zamora wrote:
> NOT both
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Re: validation errors

Damian Smedley
In reply to this post by jorge zamora
Hi Jorge,

This restriction is only in place where users have selected an option that is just flanking sequence i.e. gene/transcript flanks or gene/transcript coding region flanks. If both upstream and downstream was selected you would end up with a concatenated DNA string which makes no sense - hence the warning.

The code lets you select upstream and downstream flanks when there is something sensible in between them like a coding region.

So my advice would be not to change it. The GUI should really be more dynamic to display the options as one or the other where necessary but that should wait for the next release i think.

Cheers
Damian


On Mon, Oct 25, 2010 at 10:30 AM, jorge zamora <[hidden email]> wrote:
Hi,

In 'ensembl genes' mart we have a 'validation error' that comes up when
a user tries to select in SEQUENCES attributes upstream AND downstream
sequences. Current we only allow to select upstream OR downstream (just
only one of them).

Now we're considering to allow the users to select both attributes
upstream AND downstream. I've tried to identify the place where we
impose that restriction in the configuration but I haven't found it, not
even the place where 'validation error' message is stored:

Validation Error: For this sequence option choose upstream OR downstream
gene flanking sequence, NOT both, as makes no sense to simply
concatenate them together.

any idea about how to find the restriction in order to disable it?


Many thanks,
Jorge


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Re: validation errors

Syed Haider
ditto,  this is the best way forward IMHO.

Syed

On 26/10/2010 16:52, Damian Smedley wrote:

> Hi Jorge,
>
> This restriction is only in place where users have selected an option that is just flanking sequence i.e. gene/transcript flanks or gene/transcript coding region flanks. If both upstream and downstream was selected you would end up with a concatenated DNA string which makes no sense - hence the warning.
>
> The code lets you select upstream and downstream flanks when there is something sensible in between them like a coding region.
>
> So my advice would be not to change it. The GUI should really be more dynamic to display the options as one or the other where necessary but that should wait for the next release i think.
>
> Cheers
> Damian
>
>
> On Mon, Oct 25, 2010 at 10:30 AM, jorge zamora<[hidden email]<mailto:[hidden email]>>  wrote:
> Hi,
>
> In 'ensembl genes' mart we have a 'validation error' that comes up when
> a user tries to select in SEQUENCES attributes upstream AND downstream
> sequences. Current we only allow to select upstream OR downstream (just
> only one of them).
>
> Now we're considering to allow the users to select both attributes
> upstream AND downstream. I've tried to identify the place where we
> impose that restriction in the configuration but I haven't found it, not
> even the place where 'validation error' message is stored:
>
> Validation Error: For this sequence option choose upstream OR downstream
> gene flanking sequence, NOT both, as makes no sense to simply
> concatenate them together.
>
> any idea about how to find the restriction in order to disable it?
>
>
> Many thanks,
> Jorge
>
>
>