sub run {
my ($self) = @_;
my $dbas = {};
my $compara_name = $self->param_required('species');
$log->info("Processing compara $compara_name");
# TODO
my $compara_dba = $self->get_DBAdaptor("compara");
$log->info("Connecting to info database");
my $dba =
Bio::EnsEMBL::MetaData::DBSQL::MetaDataDBAdaptor->new(
-USER =>,
$self->param('info_user'),
-PASS =>,
$self->param('info_pass'),
-HOST =>,
$self->param('info_host'),
-PORT =>,
$self->param('info_port'),
-DBNAME =>,
$self->param('info_dbname')
);
my $gdba = $dba->get_GenomeInfoAdaptor();
my $cdba = $dba->get_GenomeComparaInfoAdaptor();
# set the release to use when storing genomes
my $rdba = $dba->get_DataReleaseInfoAdaptor();
my $release;
if ( defined $self->param('eg_release') ) {
$release =
$rdba->fetch_by_ensembl_genomes_release(
$self->param('eg_release') );
}
else {
$release =
$rdba->fetch_by_ensembl_release( $self->param('release') );
}
$gdba->data_release($release);
#$cdba->data_release($release);
my $upd = $self->param('force_update') || 0;
my $opts = { -INFO_ADAPTOR => $gdba,
-ANNOTATION_ANALYZER =>
Bio::EnsEMBL::MetaData::AnnotationAnalyzer->new(),
-COMPARA => 0,
-CONTIGS => 0,
-FORCE_UPDATE => $upd,
-VARIATION => 0 };
$log->info("Processing $compara_name");
my $processor =
Bio::EnsEMBL::MetaData::MetaDataProcessor->new(%$opts);
my $compara_infos = $processor->process_compara( $compara_dba, {} );
for my $compara_info (@$compara_infos) {
my $nom = $compara_info->method() . "/" . $compara_info->set_name();
if ( defined $compara_info->dbID() ) {
$log->info( "Updating compara info for " . $nom );
$cdba->update($compara_info);
}
else {
$log->info( "Storing compara info for " . $nom );
$cdba->store($compara_info);
}
}
$log->info("Completed processing compara $compara_name");
return;
} ## end sub run
Code:
