[ensembl-dev] DBEntry fetch_all() call dies

Nicole Washington nlwashington at lbl.gov
Fri Mar 1 21:58:07 GMT 2013


Hi ENSEMBL API dev team,

I've done a simple call to fetch all DBEntries via a DBEntryAdaptor object:

my $species='homo_sapiens';
my $dbentry_adaptor =$registry->get_adaptor($species, 'Core', 'DBEntry' );
print STDOUT Dumper($dbentry_adaptor->fetch_all());

And I get the following error output, dying at the line of the fetch_all call.

-------------------- EXCEPTION --------------------
MSG: abstract method _tables not defined by implementing subclass of BaseAdaptor
STACK Bio::EnsEMBL::DBSQL::BaseAdaptor::_tables /Users/Nicole/src/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm:819
STACK Bio::EnsEMBL::DBSQL::BaseAdaptor::_generate_sql /Users/Nicole/src/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm:455
STACK Bio::EnsEMBL::DBSQL::BaseAdaptor::generic_fetch /Users/Nicole/src/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm:409
STACK Bio::EnsEMBL::DBSQL::BaseAdaptor::fetch_all /Users/Nicole/src/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm:710
STACK toplevel get_all_ensembl_genes.pl:117
Date (localtime)    = Fri Mar  1 13:48:54 2013
Ensembl API version = 70

Are there any patches available?

Nicole



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