Commit dbd2c8e1 authored by Andy Yates's avatar Andy Yates
Browse files

Changes to allow ontology databases called ensemblgenome_ontology_60 in order...

Changes to allow ontology databases called ensemblgenome_ontology_60 in order to differentiate ourselves from the ensembl_ontology database
parent 969ac5a7
...@@ -1404,6 +1404,7 @@ sub load_registry_from_db { ...@@ -1404,6 +1404,7 @@ sub load_registry_from_db {
} }
my $go_version = 0; my $go_version = 0;
my $ontology_db_name = '';
my $ontology_version = 0; my $ontology_version = 0;
$user ||= "ensro"; $user ||= "ensro";
...@@ -1455,8 +1456,9 @@ sub load_registry_from_db { ...@@ -1455,8 +1456,9 @@ sub load_registry_from_db {
if ( $1 eq $software_version ) { if ( $1 eq $software_version ) {
$go_version = $1; $go_version = $1;
} }
} elsif ( $db =~ /^(ensembl_ontology)_(\d+)/ ) { } elsif ( $db =~ /^(ensembl\w*_ontology)_(\d+)/ ) {
if ( $2 eq $software_version ) { if ( $2 eq $software_version ) {
$ontology_db_name = $db;
$ontology_version = $2; $ontology_version = $2;
} }
} elsif ( $db =~ /^([a-z]+_[a-z0-9]+_[a-z]+(?:_\d+)?)_(\d+)_(\w+)/ ) } elsif ( $db =~ /^([a-z]+_[a-z0-9]+_[a-z]+(?:_\d+)?)_(\d+)_(\w+)/ )
...@@ -1919,9 +1921,6 @@ sub load_registry_from_db { ...@@ -1919,9 +1921,6 @@ sub load_registry_from_db {
if ( $ontology_version != 0 ) { if ( $ontology_version != 0 ) {
require Bio::EnsEMBL::DBSQL::OntologyDBAdaptor; require Bio::EnsEMBL::DBSQL::OntologyDBAdaptor;
my $ontology_db =
sprintf( "ensembl_ontology_%d", $ontology_version );
my $dba = Bio::EnsEMBL::DBSQL::OntologyDBAdaptor->new( my $dba = Bio::EnsEMBL::DBSQL::OntologyDBAdaptor->new(
'-species' => 'multi'.$species_suffix, '-species' => 'multi'.$species_suffix,
'-group' => 'ontology', '-group' => 'ontology',
...@@ -1929,11 +1928,11 @@ sub load_registry_from_db { ...@@ -1929,11 +1928,11 @@ sub load_registry_from_db {
'-port' => $port, '-port' => $port,
'-user' => $user, '-user' => $user,
'-pass' => $pass, '-pass' => $pass,
'-dbname' => $ontology_db, '-dbname' => $ontology_db_name
); );
if ($verbose) { if ($verbose) {
printf( "%s loaded\n", $ontology_db ); printf( "%s loaded\n", $ontology_db_name );
} }
} elsif ($verbose) { } elsif ($verbose) {
print("No ontology database found\n"); print("No ontology database found\n");
...@@ -2363,7 +2362,7 @@ sub version_check { ...@@ -2363,7 +2362,7 @@ sub version_check {
$database_version = $1; $database_version = $1;
} elsif ( $dba->dbc()->dbname() =~ /ensembl_help_(\d+)/ ) { } elsif ( $dba->dbc()->dbname() =~ /ensembl_help_(\d+)/ ) {
$database_version = $1; $database_version = $1;
} elsif ( $dba->dbc()->dbname() =~ /ensembl_ontology_(\d+)/ ) { } elsif ( $dba->dbc()->dbname() =~ /ensembl\w*_ontology_(\d+)/ ) {
$database_version = $1; $database_version = $1;
} else { } else {
warn( warn(
......
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