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Commit bf83037a authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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Added hooks for ontology adaptors.

parent c3adfd6e
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Showing with 139 additions and 71 deletions
modules/Bio/EnsEMBL/Registry.pm
View file @ bf83037a
......@@ -131,8 +131,8 @@ use vars qw(%registry_register);
my $API_VERSION = 54;
# This is a map from group names to Ensembl DB adaptors.
#Used by load_all and reset_DBAdaptor
# This is a map from group names to Ensembl DB adaptors. Used by
# load_all() and reset_DBAdaptor().
my %group2adaptor =
(
'blast' => 'Bio::EnsEMBL::External::BlastAdaptor',
......@@ -1322,7 +1322,8 @@ sub load_registry_from_db {
@args
);
my $go_version = 0;
my $go_version = 0;
my $ontology_version = 0;
$user ||= "ensro";
if ( !defined($port) ) {
......@@ -1373,8 +1374,12 @@ sub load_registry_from_db {
if ( $1 eq $software_version ) {
$go_version = $1;
}
} elsif ( $db =~ /^(ensembl_ontology)_(\d+)/ ) {
if ( $2 eq $software_version ) {
$ontology_version = $2;
}
} elsif (
$db =~ /^([a-z]+_[a-z]+_[a-z]+(?:_\d+)?)_(\d+)_(\d+[a-z]*)/)
$db =~ /^([a-z]+_[a-z]+_[a-z]+(?:_\d+)?)_(\d+)_(\d+[a-z]*)/ )
{
if ( $2 eq $software_version ) {
$temp{$1} = $2 . "_" . $3;
......@@ -1746,6 +1751,31 @@ sub load_registry_from_db {
print("No GO database found\n");
}
# Ontology
if ( $ontology_version != 0 ) {
require Bio::EnsEMBL::DBSQL::OntologyDBAdaptor;
my $ontology_db =
sprintf( "ensembl_ontology_%d", $ontology_version );
my $dba = Bio::EnsEMBL::DBSQL::OntologyDBAdaptor->new(
'-species' => 'multi',
'-group' => 'ontology',
'-host' => $host,
'-port' => $port,
'-user' => $user,
'-pass' => $pass,
'-dbname' => $ontology_db,
);
if ($verbose) {
printf( "%s loaded\n", $ontology_db );
}
} elsif ($verbose) {
print("No ontology database found\n");
}
# Hard coded aliases for the different species
my @aliases = ( 'chimp', 'PanTro1', 'Pan', 'P_troglodytes' );
......@@ -2036,6 +2066,10 @@ sub load_registry_from_db {
-alias => \@aliases
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => 'multi',
-alias => ['ontology'] );
# Register aliases as found in adaptor meta tables.
$self->find_and_add_aliases( '-handle' => $dbh );
$dbh->disconnect();
......@@ -2044,12 +2078,17 @@ sub load_registry_from_db {
=head2 find_and_add_aliases
Arg [DBH] : (optional) DBI handle
A connected DBI database handle. Used instead
of the database handles stored in the DBAdaptor
objects. Bypasses the use of MetaContainer.
Arg [ADAPTOR] : (optional) Bio::EnsEMBL::DBSQL::DBAdaptor
The adaptor to use to retrieve aliases from.
Arg [GROUP] : (optional) string
The group you want to find aliases for. If not given
assumes all types.
The group you want to find aliases for. If not
given assumes all types.
Arg [HANDLE] : (optional) DBI database handle
A connected database handle to use instead of the
......@@ -2127,7 +2166,6 @@ sub find_and_add_aliases {
if ( defined( $dba->dbc() ) ) {
$dba->dbc()->disconnect_if_idle();
}
}
foreach my $alias (@aliases) {
......@@ -2297,50 +2335,73 @@ sub no_version_check {
=cut
sub version_check{
my ($self, $dba) = @_;
sub version_check {
my ( $self, $dba ) = @_;
# Check the datbase and versions match
# give warning if they do not.
my $check = no_version_check();
if( (defined($ENV{HOME}) and (-e $ENV{HOME}."/.ensemblapi_no_version_check"))
or (defined($check) and ($check != 0))){
if ( (
defined( $ENV{HOME} )
and ( -e $ENV{HOME} . "/.ensemblapi_no_version_check" ) )
or ( defined($check) and ( $check != 0 ) ) )
{
return 1;
}
my $mca = $self->get_adaptor($dba->species(),$dba->group(),"MetaContainer");
my $mca =
$self->get_adaptor( $dba->species(), $dba->group(),
"MetaContainer" );
my $database_version = 0;
if(defined($mca)){
if ( defined($mca) ) {
$database_version = $mca->get_schema_version();
}
if($database_version == 0){
if ( $database_version == 0 ) {
# Try to work out the version
if($dba->dbc->dbname() =~ /^_test_db_/){
if ( $dba->dbc()->dbname() =~ /^_test_db_/ ) {
return 1;
}
if($dba->dbc->dbname() =~ /(\d+)_\S+$/){
if ( $dba->dbc()->dbname() =~ /(\d+)_\S+$/ ) {
$database_version = $1;
}
elsif($dba->dbc->dbname() =~ /ensembl_compara_(\d+)/){
} elsif ( $dba->dbc()->dbname() =~ /ensembl_compara_(\d+)/ ) {
$database_version = $1;
}
elsif($dba->dbc->dbname() =~ /ensembl_go_(\d+)/){
} elsif ( $dba->dbc()->dbname() =~ /ensembl_go_(\d+)/ ) {
$database_version = $1;
}
elsif($dba->dbc->dbname() =~ /ensembl_help_(\d+)/){
} elsif ( $dba->dbc()->dbname() =~ /ensembl_help_(\d+)/ ) {
$database_version = $1;
} elsif ( $dba->dbc()->dbname() =~ /ensembl_ontology_(\d+)/ ) {
$database_version = $1;
} else {
warn(
sprintf(
"No database version for database %s "
. ". You must be using a pre version 34 database "
. "with version 34 or later code.\n"
. "You need to update your database "
. "or use the appropriate Ensembl software release "
. "to ensure your script does not crash\n",
$dba->dbc()->dbname() ) );
}
else{
warn("No database version for database ".$dba->dbc->dbname().". You must be using a pre version 34 database with version 34 or later code. You need to update your database or use the appropriate ensembl software release to ensure your script does not crash\n");
}
}
if($database_version != $API_VERSION){
warn("For ".$dba->dbc->dbname()." there is a difference in the software release (".$API_VERSION.") and the database release (".$database_version."). You should change one of these to ensure your script does not crash.\n");
} ## end if ( $database_version...
if ( $database_version != $API_VERSION ) {
warn(
sprintf(
"For %s there is a difference in the software release (%s) "
. "and the database release (%s). "
. "You should update one of these to ensure that your script "
. "does not crash.\n",
$dba->dbc()->dbname(),
$API_VERSION, $database_version
) );
return 0;
}
else {
return 1;
}
}
return 1; # Ok
} ## end sub version_check
=head2 get_species_and_object_type
......
modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm
View file @ bf83037a
......@@ -125,6 +125,12 @@ sub gen_load{
}
$config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_funcgen;
}
elsif ( $dba->isa('Bio::Ensembl::DBSQL::OntologyTermAdaptor') ) {
if ( !defined( $dba->group() ) ) {
$dba->group('ontology');
}
$config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_ontology;
}
elsif($dba->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')){
#vega uses the core DBAdaptor so test if vega is in the dbname
if(!defined($dba->group())){
......@@ -192,37 +198,37 @@ sub gen_load{
sub find_unique_species{
my ($species, $group) = @_;
sub find_unique_species {
my ( $species, $group ) = @_;
$reg->add_alias($species,$species);
$reg->add_alias( $species, $species );
my $i = 0;
my $free =0;
while(!$free){
if($i == 0){
if(!defined($reg->get_DBAdaptor($species, $group))){
$free =1;
$i ="";
my $i = 0;
my $free = 0;
while ( !$free ) {
if ( $i == 0 ) {
if ( !defined( $reg->get_DBAdaptor( $species, $group ) ) ) {
$free = 1;
$i = "";
} else {
$i = 1;
}
else{
$i = 1;
}
}
else{
$reg->add_alias($species.$i,$species.$i); #set needed self alias
if(!defined($reg->get_DBAdaptor($species.$i, $group))){
$free =1;
}
else{
$i++;
} else {
# set needed self alias
$reg->add_alias( $species . $i, $species . $i );
if ( !defined( $reg->get_DBAdaptor( $species . $i, $group ) ) ) {
$free = 1;
} else {
$i++;
}
}
}
$species .= $i;
return ($species);
}
} ## end sub find_unique_species
......@@ -231,9 +237,9 @@ sub load_adaptors {
my %pairs = %{ $dba->get_available_adaptors() };
foreach my $key ( keys %pairs ) {
Bio::EnsEMBL::Registry->add_adaptor( $dba->species, $dba->group,
$key, $pairs{$key} );
while ( my ( $key, $value ) = each(%pairs) ) {
Bio::EnsEMBL::Registry->add_adaptor( $dba->species(), $dba->group(),
$key, $value );
}
}
......@@ -241,9 +247,8 @@ sub load_and_attach_dnadb_to_core {
my ($dba) = @_;
load_adaptors($dba);
$reg->add_DNAAdaptor( $dba->species, $dba->group,
$dba->species, "core" );
$reg->add_DNAAdaptor( $dba->species(), $dba->group(), $dba->species(),
'core' );
}
......@@ -256,6 +261,7 @@ sub load_SNP { load_adaptors(@_) }
sub load_variation { load_and_attach_dnadb_to_core(@_) }
sub load_funcgen { load_and_attach_dnadb_to_core(@_) }
sub load_haplotype { load_adaptors(@_) }
sub load_ontology { load_adaptors(@_) }
# these that need to attach to the core to get the sequense data
......@@ -265,20 +271,21 @@ sub load_otherfeatures { load_and_attach_dnadb_to_core(@_) }
sub load_vega { load_and_attach_dnadb_to_core(@_) }
sub add_alias{
my ($class, @args) = @_;
my ($species, $aliases) = rearrange([qw(SPECIES ALIAS)],@args);
sub add_alias {
my ( $class, @args ) = @_;
#make sure it exists itself
Bio::EnsEMBL::Registry->add_alias($species,$species);
my ( $species, $aliases ) = rearrange( [qw(SPECIES ALIAS)], @args );
if($aliases){
foreach my $ali (@$aliases){
Bio::EnsEMBL::Registry->add_alias($species,$ali);
# Make sure it exists itself
Bio::EnsEMBL::Registry->add_alias( $species, $species );
if ( defined($aliases) ) {
foreach my $ali (@$aliases) {
Bio::EnsEMBL::Registry->add_alias( $species, $ali );
}
}
}
#
# overwrite/load new types. Done this way to enable no changes to CVS for
# external users. External users should add there own "GROUPS" in the file
......
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