possible biomart bug

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possible biomart bug

Gabriel Berriz
Hi.  The following queries result in the server-side errors shown:

<Query completionStamp="1" virtualSchemaName="default" uniqueRows="1" requestId="biomart-client">
  <Dataset interface="default" name="dmelanogaster_gene_ensembl">
    <Attribute name="merops"/>
  </Dataset>
</Query>

Query ERROR: caught BioMart::Exception::Database: Error during query execution: Unknown column 'ensembl_mart_59.dmelanogaster_gene_ensembl__ox_MEROPS__dm.translation_id_1068_key' in 'where clause'


<Query completionStamp="1" virtualSchemaName="default" uniqueRows="1" requestId="biomart-client">
  <Dataset interface="default" name="dmelanogaster_gene_ensembl">
    <Attribute name="pdb"/>
  </Dataset>
</Query>

Query ERROR: caught BioMart::Exception::Database: Error during query execution: Unknown column 'ensembl_mart_59.dmelanogaster_gene_ensembl__ox_PDB__dm.translation_id_1068_key' in 'where clause' (drosophila_melanogaster/pdb)


Other similar queries work fine.  E.g.:

<Query completionStamp="1" virtualSchemaName="default" uniqueRows="1" requestId="biomart-client">
  <Dataset interface="default" name="dmelanogaster_gene_ensembl">
    <Attribute name="embl"/>
  </Dataset>
</Query>


Similar errors arise if one attempts the same query through the web interface.  E.g., for MEROPS:

Serious Error: Error during query execution: Unknown column 'ensembl_mart_59.dmelanogaster_gene_ensembl__ox_MEROPS__dm.translation_id_1068_key' in 'where clause'
ERROR: caught BioMart::Exception::Database: Error during query execution: Unknown column 'ensembl_mart_59.dmelanogaster_gene_ensembl__ox_MEROPS__dm.translation_id_1068_key' in 'where clause'
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 /ensemblweb/wwwmart/www_59/biomart-perl/lib/BioMart/Dataset/TableSet.pm:241
BioMart::Dataset::TableSet::_fillAttributeTableWith /ensemblweb/wwwmart/www_59/biomart-perl/lib/BioMart/Dataset/TableSet.pm:124
BioMart::Dataset::TableSet::_getResultTable /ensemblweb/wwwmart/www_59/biomart-perl/lib/BioMart/DatasetI.pm:1170
BioMart::DatasetI::getResultTable /ensemblweb/wwwmart/www_59/biomart-perl/lib/BioMart/QueryRunner.pm:472
BioMart::QueryRunner::_processPath /ensemblweb/wwwmart/www_59/biomart-perl/lib/BioMart/QueryRunner.pm:374
BioMart::QueryRunner::_getResultTable /ensemblweb/wwwmart/www_59/biomart-perl/lib/BioMart/QueryRunner.pm:194
BioMart::QueryRunner::execute /ensemblweb/wwwmart/www_59/biomart-perl/lib/BioMart/Web.pm:2461
(eval) /ensemblweb/wwwmart/www_59/biomart-perl/lib/BioMart/Web.pm:2213
BioMart::Web::handle_request /ensemblweb/wwwmart/www_59/biomart-perl/cgi-bin/martview:100
(eval) /ensemblweb/wwwmart/www_59/biomart-perl/cgi-bin/martview:99
ModPerl::ROOT::ModPerl::Registry::ensemblweb_wwwmart_www_59_biomart_2dperl_cgi_2dbin_martview::handler /localsw/ensembl_web/apache/lib/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204
(eval) /localsw/ensembl_web/apache/lib/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204
ModPerl::RegistryCooker::run /localsw/ensembl_web/apache/lib/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:170
ModPerl::RegistryCooker::default_handler /localsw/ensembl_web/apache/lib/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/Registry.pm:31
ModPerl::Registry::handler -e:0
(eval) -e:0


Thanks!
Gabriel



=============================================================
Gabriel F. Berriz, PhD
Senior Bioinformatics Developer
Roth Lab
Biological Chemistry and Molecular Pharmacology -- Harvard Medical School
250 Longwood Avenue
Seeley G. Mudd Building 322B
Boston, MA 02115-5701
Telephone: 617.432.3555
Fax: 617.432.3557





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Fwd: [mart-dev] possible biomart bug

Junjun Zhang
Forward to Ensembl team that is responsible for the Ensembl marts.



Begin forwarded message:

From: Gabriel Berriz <[hidden email]>
Date: September 3, 2010 3:03:27 PM EDT
Cc: Kenny Chua <[hidden email]>
Subject: [mart-dev] possible biomart bug

Hi.  The following queries result in the server-side errors shown:

<Query completionStamp="1" virtualSchemaName="default" uniqueRows="1" requestId="biomart-client">
  <Dataset interface="default" name="dmelanogaster_gene_ensembl">
    <Attribute name="merops"/>
  </Dataset>
</Query>

Query ERROR: caught BioMart::Exception::Database: Error during query execution: Unknown column 'ensembl_mart_59.dmelanogaster_gene_ensembl__ox_MEROPS__dm.translation_id_1068_key' in 'where clause'


<Query completionStamp="1" virtualSchemaName="default" uniqueRows="1" requestId="biomart-client">
  <Dataset interface="default" name="dmelanogaster_gene_ensembl">
    <Attribute name="pdb"/>
  </Dataset>
</Query>

Query ERROR: caught BioMart::Exception::Database: Error during query execution: Unknown column 'ensembl_mart_59.dmelanogaster_gene_ensembl__ox_PDB__dm.translation_id_1068_key' in 'where clause' (drosophila_melanogaster/pdb)


Other similar queries work fine.  E.g.:

<Query completionStamp="1" virtualSchemaName="default" uniqueRows="1" requestId="biomart-client">
  <Dataset interface="default" name="dmelanogaster_gene_ensembl">
    <Attribute name="embl"/>
  </Dataset>
</Query>


Similar errors arise if one attempts the same query through the web interface.  E.g., for MEROPS:

Serious Error: Error during query execution: Unknown column 'ensembl_mart_59.dmelanogaster_gene_ensembl__ox_MEROPS__dm.translation_id_1068_key' in 'where clause'
ERROR: caught BioMart::Exception::Database: Error during query execution: Unknown column 'ensembl_mart_59.dmelanogaster_gene_ensembl__ox_MEROPS__dm.translation_id_1068_key' in 'where clause'
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 /ensemblweb/wwwmart/www_59/biomart-perl/lib/BioMart/Dataset/TableSet.pm:241
BioMart::Dataset::TableSet::_fillAttributeTableWith /ensemblweb/wwwmart/www_59/biomart-perl/lib/BioMart/Dataset/TableSet.pm:124
BioMart::Dataset::TableSet::_getResultTable /ensemblweb/wwwmart/www_59/biomart-perl/lib/BioMart/DatasetI.pm:1170
BioMart::DatasetI::getResultTable /ensemblweb/wwwmart/www_59/biomart-perl/lib/BioMart/QueryRunner.pm:472
BioMart::QueryRunner::_processPath /ensemblweb/wwwmart/www_59/biomart-perl/lib/BioMart/QueryRunner.pm:374
BioMart::QueryRunner::_getResultTable /ensemblweb/wwwmart/www_59/biomart-perl/lib/BioMart/QueryRunner.pm:194
BioMart::QueryRunner::execute /ensemblweb/wwwmart/www_59/biomart-perl/lib/BioMart/Web.pm:2461
(eval) /ensemblweb/wwwmart/www_59/biomart-perl/lib/BioMart/Web.pm:2213
BioMart::Web::handle_request /ensemblweb/wwwmart/www_59/biomart-perl/cgi-bin/martview:100
(eval) /ensemblweb/wwwmart/www_59/biomart-perl/cgi-bin/martview:99
ModPerl::ROOT::ModPerl::Registry::ensemblweb_wwwmart_www_59_biomart_2dperl_cgi_2dbin_martview::handler /localsw/ensembl_web/apache/lib/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204
(eval) /localsw/ensembl_web/apache/lib/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204
ModPerl::RegistryCooker::run /localsw/ensembl_web/apache/lib/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:170
ModPerl::RegistryCooker::default_handler /localsw/ensembl_web/apache/lib/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/Registry.pm:31
ModPerl::Registry::handler -e:0
(eval) -e:0


Thanks!
Gabriel



=============================================================
Gabriel F. Berriz, PhD
Senior Bioinformatics Developer
Roth Lab
Biological Chemistry and Molecular Pharmacology -- Harvard Medical School
250 Longwood Avenue
Seeley G. Mudd Building 322B
Boston, MA 02115-5701
Telephone: 617.432.3555
Fax: 617.432.3557