Commit 92310f88 authored by Steve Trevanion's avatar Steve Trevanion
Browse files

whitespace, remove old Glovar method!

parent 1fcf4a7e
......@@ -394,7 +394,6 @@ sub create_commandline_options {
$param_hash{$param} = $first;
}
}
}
# replace values
......@@ -684,10 +683,8 @@ sub get_database {
"${prefix}host",
"${prefix}port",
"${prefix}user",
# "${prefix}pass", not required since might be empty
"${prefix}dbname",
);
my %adaptors = (
core => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
ensembl => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
......@@ -780,60 +777,6 @@ sub get_dbconnection {
}
=head2 get_glovar_database
Example : my $dba = $support->get_glovar_database;
Description : Connects to the Glovar database.
Return type : Bio::EnsEMBL::ExternalData::Glovar::DBAdaptor
Exceptions : thrown if no connection to a core db exists
Caller : general
=cut
sub get_glovar_database {
my $self = shift;
$self->check_required_params(qw(
glovarhost
glovarport
glovaruser
glovarpass
glovardbname
oracle_home
ld_library_path
glovar_snp_consequence_exp
));
# check for core dbadaptor
my $core_db = $self->dba;
unless ($core_db && (ref($core_db) =~ /Bio::.*::DBSQL::DBAdaptor/)) {
$self->log_error("You have to connect to a core db before you can get a glovar dbadaptor.\n");
exit;
}
# setup Oracle environment
$ENV{'ORACLE_HOME'} = $self->param('oracle_home');
$ENV{'LD_LIBRARY_PATH'} = $self->param('ld_library_path');
# connect to Glovar db
$self->dynamic_use('Bio::EnsEMBL::ExternalData::Glovar::DBAdaptor');
my $dba = Bio::EnsEMBL::ExternalData::Glovar::DBAdaptor->new(
-host => $self->param("glovarhost"),
-port => $self->param("glovarport"),
-user => $self->param("glovaruser"),
-pass => $self->param("glovarpass"),
-dbname => $self->param("glovardbname"),
-group => 'glovar',
);
# setup adaptor inter-relationships
$dba->dnadb($core_db);
$self->dynamic_use('Bio::EnsEMBL::ExternalData::Glovar::GlovarSNPAdaptor');
my $glovar_snp_adaptor = $dba->get_GlovarSNPAdaptor;
$glovar_snp_adaptor->consequence_exp($self->param('glovar_snp_consequence_exp'));
$core_db->add_ExternalFeatureAdaptor($glovar_snp_adaptor);
return $dba;
}
=head2 dba
......@@ -867,8 +810,7 @@ sub dba {
sub dynamic_use {
my ($self, $classname) = @_;
my ($parent_namespace, $module) = $classname =~/^(.*::)(.*)$/ ?
($1,$2) : ('::', $classname);
my ($parent_namespace, $module) = $classname =~/^(.*::)(.*)$/ ? ($1,$2) : ('::', $classname);
no strict 'refs';
# return if module has already been imported
......@@ -1272,9 +1214,7 @@ sub log_error {
sub log_verbose {
my ($self, $txt, $indent) = @_;
return(0) unless $self->param('verbose');
$self->log($txt, $indent);
return(1);
}
......@@ -1295,11 +1235,9 @@ sub log_verbose {
sub log_stamped {
my ($self, $txt, $indent) = @_;
# append timestamp and memory usage to log text
$txt =~ s/(\n*)$//;
$txt .= " ".$self->date_and_mem.$1;
$self->log($txt, $indent);
return(1);
}
......
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