Attributes from multiple attribute pages are not allowed

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Attributes from multiple attribute pages are not allowed

Kiran Mukhyala
I am getting the error: "Attributes from multiple attribute pages are
not allowed" when trying to use the built-in DAS server of BioMart 0.7.

My local mart is configured similar to Ensembl mart and so the filters
and attributes for the importable/exportable pairs ensembl_das_chr and
ensembl_das_gene are identical to Ensembl.

das_gene request works:
myserver/biomart/das/default__hsapiens_gene_ensembl__ensembl_das_gene/features?segment=....
 
but das_chr request
(myserver/biomart/das/default__hsapiens_gene_ensembl__ensembl_das_chr/features?segment=....)

doesn't work, and shows this error:
"Attributes from multiple attribute pages are not allowed"

The attributes listed in the ensembl_das_chr exportable are:
ensembl_gene_id,start_position,end_position,strand,ensembl_transcript_id,transcript_start,transcript_end,ensembl_exon_id,exon_chrom_start,exon_chrom_end

which does include attributes from multiple pages. If the I remove the
attributes from the structure page, I don't get an error.

I did see the post
(http://www.mail-archive.com/mart-dev@.../msg02381.html) saying
this feature (supporting exportable with attributes from multiple pages)
is not supported in BioMart 0.7.

How did Ensembl get around this? See :
http://www.biomart.org/biomart/das/default__hsapiens_gene_ensembl__ensembl_das_chr/features?segment=13:31787617,31871805

Thanks,

-Kiran










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Re: Attributes from multiple attribute pages are not allowed

Syed Haider
Hi Kiran,

Attribtues from multiple AttributePages are not allowed to be queried
together. However, you can move (create a pointer) to the attribute that
you need from the offending page and leave them with other das
attributes within the same page.

Hope this helps,
Syed

On 10/11/2010 21:09, Kiran Mukhyala wrote:

> I am getting the error: "Attributes from multiple attribute pages are
> not allowed" when trying to use the built-in DAS server of BioMart 0.7.
>
> My local mart is configured similar to Ensembl mart and so the filters
> and attributes for the importable/exportable pairs ensembl_das_chr and
> ensembl_das_gene are identical to Ensembl.
>
> das_gene request works:
> myserver/biomart/das/default__hsapiens_gene_ensembl__ensembl_das_gene/features?segment=....
>
> but das_chr request
> (myserver/biomart/das/default__hsapiens_gene_ensembl__ensembl_das_chr/features?segment=....)
>
> doesn't work, and shows this error:
> "Attributes from multiple attribute pages are not allowed"
>
> The attributes listed in the ensembl_das_chr exportable are:
> ensembl_gene_id,start_position,end_position,strand,ensembl_transcript_id,transcript_start,transcript_end,ensembl_exon_id,exon_chrom_start,exon_chrom_end
>
> which does include attributes from multiple pages. If the I remove the
> attributes from the structure page, I don't get an error.
>
> I did see the post
> (http://www.mail-archive.com/mart-dev@.../msg02381.html) saying
> this feature (supporting exportable with attributes from multiple pages)
> is not supported in BioMart 0.7.
>
> How did Ensembl get around this? See :
> http://www.biomart.org/biomart/das/default__hsapiens_gene_ensembl__ensembl_das_chr/features?segment=13:31787617,31871805
>
> Thanks,
>
> -Kiran
>
>
>
>
>
>
>
>
>
>
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Re: Attributes from multiple attribute pages are not allowed

Kiran Mukhyala
Pointer Attributes! solved the problem.

Thanks for your help,

-Kiran


On Wed, 2010-11-10 at 13:51 +0000, Syed Haider wrote:

> Hi Kiran,
>
> Attribtues from multiple AttributePages are not allowed to be queried
> together. However, you can move (create a pointer) to the attribute that
> you need from the offending page and leave them with other das
> attributes within the same page.
>
> Hope this helps,
> Syed
>
> On 10/11/2010 21:09, Kiran Mukhyala wrote:
> > I am getting the error: "Attributes from multiple attribute pages are
> > not allowed" when trying to use the built-in DAS server of BioMart 0.7.
> >
> > My local mart is configured similar to Ensembl mart and so the filters
> > and attributes for the importable/exportable pairs ensembl_das_chr and
> > ensembl_das_gene are identical to Ensembl.
> >
> > das_gene request works:
> > myserver/biomart/das/default__hsapiens_gene_ensembl__ensembl_das_gene/features?segment=....
> >
> > but das_chr request
> > (myserver/biomart/das/default__hsapiens_gene_ensembl__ensembl_das_chr/features?segment=....)
> >
> > doesn't work, and shows this error:
> > "Attributes from multiple attribute pages are not allowed"
> >
> > The attributes listed in the ensembl_das_chr exportable are:
> > ensembl_gene_id,start_position,end_position,strand,ensembl_transcript_id,transcript_start,transcript_end,ensembl_exon_id,exon_chrom_start,exon_chrom_end
> >
> > which does include attributes from multiple pages. If the I remove the
> > attributes from the structure page, I don't get an error.
> >
> > I did see the post
> > (http://www.mail-archive.com/mart-dev@.../msg02381.html) saying
> > this feature (supporting exportable with attributes from multiple pages)
> > is not supported in BioMart 0.7.
> >
> > How did Ensembl get around this? See :
> > http://www.biomart.org/biomart/das/default__hsapiens_gene_ensembl__ensembl_das_chr/features?segment=13:31787617,31871805
> >
> > Thanks,
> >
> > -Kiran
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >

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specify dataset for a new filter

Kiran Mukhyala

I have added a new filter based on a newly added dimension table to my
mart.
The query generated is using the table name of the form content_type__dm
instead of the form dataset__content_type__dm and so throws the error:
table does not exist.
How do I specify the dataset name with my new filter?

Thanks,

-Kiran

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Re: specify dataset for a new filter

Syed Haider
Hi Kiran,

please make sure that an attribute with same name as of filter exists in
the configuration and then do File->Export (MartEditor). Once done,
reconfigure (perl bin/configure.pl..... --clean) and restart apache. It
should be fixed.

Best,
Syed

On 12/11/2010 22:29, Kiran Mukhyala wrote:

>
> I have added a new filter based on a newly added dimension table to my
> mart.
> The query generated is using the table name of the form content_type__dm
> instead of the form dataset__content_type__dm and so throws the error:
> table does not exist.
> How do I specify the dataset name with my new filter?
>
> Thanks,
>
> -Kiran
>
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Re: specify dataset for a new filter

Kiran Mukhyala
Hi Syed,

I've already tried that but it didn't help.

I just realized that I haven't really added a new filter but added a new
option to an exiting filter of type id_list. The existing options in
this filter work fine. The internal_name of the new option and attribute
are identical.

Thanks,

-Kiran

On Fri, 2010-11-12 at 23:21 +0000, Syed Haider wrote:

> Hi Kiran,
>
> please make sure that an attribute with same name as of filter exists in
> the configuration and then do File->Export (MartEditor). Once done,
> reconfigure (perl bin/configure.pl..... --clean) and restart apache. It
> should be fixed.
>
> Best,
> Syed
>
> On 12/11/2010 22:29, Kiran Mukhyala wrote:
> >
> > I have added a new filter based on a newly added dimension table to my
> > mart.
> > The query generated is using the table name of the form content_type__dm
> > instead of the form dataset__content_type__dm and so throws the error:
> > table does not exist.
> > How do I specify the dataset name with my new filter?
> >
> > Thanks,
> >
> > -Kiran
> >

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Re: specify dataset for a new filter

nndegwa
Hi Kiran,
I have bumped into a similar problem before - not sure my fix is the
recomended solution but it seemed to work.
What i did was that in the 'tableConstraint' attribute of the filter,
instead of the 'content__dm', i replaced that with the full name of the
dimension table i.e. 'dataset__content__dm' then did as Syeid just
advised. Give it a try and see it works, then check that the returned
values on a query are indeed coming from that dimension table. Any
comments Syeid?
Nelson

Kiran Mukhyala wrote:

> Hi Syed,
>
> I've already tried that but it didn't help.
>
> I just realized that I haven't really added a new filter but added a new
> option to an exiting filter of type id_list. The existing options in
> this filter work fine. The internal_name of the new option and attribute
> are identical.
>
> Thanks,
>
> -Kiran
>
> On Fri, 2010-11-12 at 23:21 +0000, Syed Haider wrote:
>  
>> Hi Kiran,
>>
>> please make sure that an attribute with same name as of filter exists in
>> the configuration and then do File->Export (MartEditor). Once done,
>> reconfigure (perl bin/configure.pl..... --clean) and restart apache. It
>> should be fixed.
>>
>> Best,
>> Syed
>>
>> On 12/11/2010 22:29, Kiran Mukhyala wrote:
>>    
>>> I have added a new filter based on a newly added dimension table to my
>>> mart.
>>> The query generated is using the table name of the form content_type__dm
>>> instead of the form dataset__content_type__dm and so throws the error:
>>> table does not exist.
>>> How do I specify the dataset name with my new filter?
>>>
>>> Thanks,
>>>
>>> -Kiran
>>>
>>>      

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Re: specify dataset for a new filter

Kiran Mukhyala
That's exactly how I got it to work but its probably not the right
solution.

Thanks,
-Kiran

On Sat, 2010-11-13 at 09:39 +0000, Nelson Ndegwa wrote:

> Hi Kiran,
> I have bumped into a similar problem before - not sure my fix is the
> recomended solution but it seemed to work.
> What i did was that in the 'tableConstraint' attribute of the filter,
> instead of the 'content__dm', i replaced that with the full name of the
> dimension table i.e. 'dataset__content__dm' then did as Syeid just
> advised. Give it a try and see it works, then check that the returned
> values on a query are indeed coming from that dimension table. Any
> comments Syeid?
> Nelson
>
> Kiran Mukhyala wrote:
> > Hi Syed,
> >
> > I've already tried that but it didn't help.
> >
> > I just realized that I haven't really added a new filter but added a new
> > option to an exiting filter of type id_list. The existing options in
> > this filter work fine. The internal_name of the new option and attribute
> > are identical.
> >
> > Thanks,
> >
> > -Kiran
> >
> > On Fri, 2010-11-12 at 23:21 +0000, Syed Haider wrote:
> >  
> >> Hi Kiran,
> >>
> >> please make sure that an attribute with same name as of filter exists in
> >> the configuration and then do File->Export (MartEditor). Once done,
> >> reconfigure (perl bin/configure.pl..... --clean) and restart apache. It
> >> should be fixed.
> >>
> >> Best,
> >> Syed
> >>
> >> On 12/11/2010 22:29, Kiran Mukhyala wrote:
> >>    
> >>> I have added a new filter based on a newly added dimension table to my
> >>> mart.
> >>> The query generated is using the table name of the form content_type__dm
> >>> instead of the form dataset__content_type__dm and so throws the error:
> >>> table does not exist.
> >>> How do I specify the dataset name with my new filter?
> >>>
> >>> Thanks,
> >>>
> >>> -Kiran
> >>>
> >>>      
>