On 21 Jun 2006, at 18:21, Caroline Johnston wrote:
Hi,
I'm having problems getting placeholder attributes to work (see error
message below).
I've got a 'mirna' dataset which has a mature_name attribute from its
mature dimension.
I've also got seperate datasets for the predicted miRNA targets for
each
species. These are just single tables which have mature_name as an
attribute.
I've defined an exportable mature_name on mirna and importable
mature_name
on each of the targets datasets. This seems to be working: I can now
select mirna as a second dataset in biomart_web. I can use the filters
from the second dataset, so I can do something like 'give me all the
target ensembl ids in this species which map to mature miRNAs derived
from
human miRNAs'. And I seem to be getting the right results.
What I want to be able to do is something like: 'Give me the target
ensembl ids and the associated miRNA database link in this species
which
map to mature miRNA derived from human miRNAs'.
In other words, I want my result set to contain attributes from the
target
dataset and the mirna dataset. I tried to create placeholder
attributes,
like mirna.db_link in the target dataset, and they appear as selectable
attributes on the output page, but if I try to select any of them I get
the error below. Just selecting target attributes still works fine.
Any idea what I've missed? Is there a way of viewing the query it's
trying
to run?
Thanks,
Cass.
Hi Cass,
just to add that ... the easiest way to combine attributes from two
visible
datasets is simply to replicate data in dimension tables. It makes it
easier
for the user to interact with the data and the query performance is
better.
Ensembl mart uses this approach a lot for things like snps in gene
dataset
or homologies. We typically only use explicit joining of two datasets
when
one of them is remote, all other use cases are dealt with by introducing
extra dimension tables
a.
<---------------- Error --------------------------->
SQL FAILED - LIKELY XML MISCONFIGURATION ERROR--------------------
EXCEPTION -------------------- DATE: 21-JUN-2006 MSG: returning undef
...
missing filters from your importable? STACK
BioMart::Configuration::FilterList::_toSQL
/srv/biomart-web/biomart-plib/BioMart/Configuration/FilterList.pm:159
STACK BioMart::Configuration::BaseFilter::toSQL
/srv/biomart-web/biomart-plib/BioMart/Configuration/BaseFilter.pm:290
STACK BioMart::Dataset::TableSet::_generateSQL
/srv/biomart-web/biomart-plib/BioMart/Dataset/TableSet.pm:681 STACK
BioMart::Dataset::TableSet::_fillAttributeTableWith
/srv/biomart-web/biomart-plib/BioMart/Dataset/TableSet.pm:245 STACK
BioMart::Dataset::TableSet::_getResultTable
/srv/biomart-web/biomart-plib/BioMart/Dataset/TableSet.pm:152 STACK
BioMart::DatasetI::getResultTable
/srv/biomart-web/biomart-plib/BioMart/DatasetI.pm:573 STACK
BioMart::QueryPlanner::_processPath
/srv/biomart-web/biomart-plib/BioMart/QueryPlanner.pm:232 STACK
BioMart::QueryPlanner::_processPath
/srv/biomart-web/biomart-plib/BioMart/QueryPlanner.pm:346 STACK
BioMart::QueryPlanner::_processPath
/srv/biomart-web/biomart-plib/BioMart/QueryPlanner.pm:346 STACK
BioMart::QueryPlanner::getResultTable
/srv/biomart-web/biomart-plib/BioMart/QueryPlanner.pm:165 STACK (eval)
/srv/biomart-web/perl/multi/martview:2993 STACK martview::print_results
/srv/biomart-web/perl/multi/martview:2992 STACK
Apache::ROOT::perl::biomart::martview::handler
/srv/biomart-web/perl/multi/martview:227 STACK (eval)
/usr/lib/perl5/site_perl/5.8.7/i586-linux-thread-multi/Apache/
Registry.pm:149
STACK Apache::Registry::handler
/usr/lib/perl5/site_perl/5.8.7/i586-linux-thread-multi/Apache/
Registry.pm:149
STACK (eval) /dev/null:0 STACK toplevel /dev/null:0
------------------------------------------- at
/srv/biomart-web/biomart-plib/BioMart/Dataset/TableSet.pm line 681
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Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
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