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Commit 2a9af710 authored by Andy Yates's avatar Andy Yates
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[ENSCORESW-284]. Fixing registry lookups for compara gene trees. Also... 

[ENSCORESW-284]. Fixing registry lookups for compara gene trees. Also refactored it slightly; we will rip this out soon as we need a clearer separation.
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modules/Bio/EnsEMBL/Registry.pm
+ 99
− 67
View file @ 2a9af710
......@@ -2728,87 +2728,119 @@ my %stable_id_stmts = (
);
my %compara_stable_id_stmts = (
genetree => 'SELECT 1 FROM %1$s.gene_tree_root WHERE stable_id =?',
);
sub get_species_and_object_type {
my ($self, $stable_id, $known_type, $known_species, $known_db_type, $force_long_lookup) = @_;
#get the stable_id lookup database adaptor
my $stable_ids_dba = $self->get_DBAdaptor("multi", "stable_ids", 1);
if ($stable_ids_dba && ! $force_long_lookup) {
my $statement = 'SELECT name, object_type, db_type FROM stable_id_lookup join species using(species_id) WHERE stable_id = ?';
if ($known_species) {
$statement .= ' AND name = ?';
}
if ($known_db_type) {
$statement .= ' AND db_type = ?';
}
if ($known_type) {
$statement .= ' AND object_type = ?';
}
my $sth = $stable_ids_dba->dbc()->prepare($statement);
$sth->bind_param(1, $stable_id, SQL_VARCHAR);
my $param_count = 1;
if ($known_species) {
$known_species = $self->get_alias($known_species);
$param_count++;
$sth->bind_param($param_count, $known_species, SQL_VARCHAR);
}
if ($known_db_type) {
$param_count++;
$sth->bind_param($param_count, $known_db_type, SQL_VARCHAR);
}
if ($known_type) {
$param_count++;
$sth->bind_param($param_count, $known_type, SQL_VARCHAR);
}
$sth->execute();
my ($species, $type, $db_type) = $sth->fetchrow_array();
$sth->finish();
return ($species ,$type, $db_type);
} else {
if (defined $known_type && !exists $stable_id_stmts{lc $known_type}) {
return;
return $self->_lookup_db_get_species_and_object_type($stable_id, $known_type, $known_species, $known_db_type);
}
else {
if(defined $known_type) {
my $lc_known_type = lc $known_type;
if(!exists $stable_id_stmts{$lc_known_type} && ! exists $compara_stable_id_stmts{$lc_known_type}) {
return;
}
}
$known_db_type = 'core' if ! $known_db_type;
my %get_adaptors_args = ('-GROUP' => $known_db_type);
$get_adaptors_args{'-species'} = $known_species if $known_species;
my @types = defined $known_type ? ($known_type) : ('Gene', 'Transcript', 'Translation', 'Exon', 'Operon', 'OperonTranscript');
if(! $known_db_type) {
$known_db_type = 'core';
my @dbas =
sort { $a->dbc->host cmp $b->dbc->host || $a->dbc->port <=> $b->dbc->port }
@{$self->get_all_DBAdaptors(%get_adaptors_args)};
foreach my $dba (@dbas) {
my @results;
my $dba_adaptor_type = $group2adaptor{$dba->group()};
if($dba_adaptor_type eq 'Bio::EnsEMBL::DBSQL::DBAdaptor') {
@results = $self->_core_get_species_and_object_type($stable_id, $known_type, $known_species, $known_db_type, $dba);
}
my %get_adaptors_args;
$get_adaptors_args{'-group'} = $known_db_type;
if ($known_species) {
$get_adaptors_args{'-species'} = $known_species;
elsif($dba_adaptor_type eq 'Bio::EnsEMBL::Compara::DBSQL::DBAdaptor') {
@results = $self->_compara_get_species_and_object_type($stable_id, $known_type, $known_species, $known_db_type, $dba);
}
return @results if scalar(@results) > 0;
} ## end foreach my $dba ( sort { $a...})
}
return;
} ## end sub get_species_and_object_type
my @dbas = sort { $a->dbc->host cmp $b->dbc->host || $a->dbc->port <=> $b->dbc->port }
@{$self->get_all_DBAdaptors(%get_adaptors_args)};
foreach my $dba (@dbas) {
foreach my $type (@types) {
my $statement = sprintf $stable_id_stmts{lc $type}, $dba->dbc->dbname;
my $sth = $dba->dbc()->prepare($statement);
$sth->bind_param(1, $stable_id, SQL_VARCHAR);
$sth->execute;
my $species = $sth->fetchall_arrayref->[0][0];
$sth->finish;
return ($species, $type, $known_db_type) if defined $species;
}
} ## end foreach my $dba ( sort { $a...})
sub _lookup_db_get_species_and_object_type {
my ($self, $stable_id, $known_type, $known_species, $known_db_type) = @_;
my $stable_ids_dba = $self->get_DBAdaptor("multi", "stable_ids", 1);
my $statement = 'SELECT name, object_type, db_type FROM stable_id_lookup join species using(species_id) WHERE stable_id = ?';
if ($known_species) {
$statement .= ' AND name = ?';
}
if ($known_db_type) {
$statement .= ' AND db_type = ?';
}
if ($known_type) {
$statement .= ' AND object_type = ?';
}
my $sth = $stable_ids_dba->dbc()->prepare($statement);
$sth->bind_param(1, $stable_id, SQL_VARCHAR);
my $param_count = 1;
if ($known_species) {
$known_species = $self->get_alias($known_species);
$param_count++;
$sth->bind_param($param_count, $known_species, SQL_VARCHAR);
}
if ($known_db_type) {
$param_count++;
$sth->bind_param($param_count, $known_db_type, SQL_VARCHAR);
}
if ($known_type) {
$param_count++;
$sth->bind_param($param_count, $known_type, SQL_VARCHAR);
}
$sth->execute();
my ($species, $type, $db_type) = $sth->fetchrow_array();
$sth->finish();
return ($species ,$type, $db_type);
} ## end sub _lookup_db_get_species_and_object_type
# Loop over a known set of object types for a core DB until we find a hit
sub _core_get_species_and_object_type {
my ($self, $stable_id, $known_type, $known_species, $known_db_type, $dba) = @_;
my @types = defined $known_type ? ($known_type) : ('Gene', 'Transcript', 'Translation', 'Exon', 'Operon', 'OperonTranscript');
foreach my $type (@types) {
my $statement = sprintf $stable_id_stmts{lc $type}, $dba->dbc->dbname;
my $sth = $dba->dbc()->prepare($statement);
$sth->bind_param(1, $stable_id, SQL_VARCHAR);
$sth->execute;
my $species = $sth->fetchall_arrayref->[0][0];
$sth->finish;
return ($species, $type, $known_db_type) if defined $species;
}
return;
}
# Loop over a known set of object types for a compara DB until we find a hit
sub _compara_get_species_and_object_type {
my ($self, $stable_id, $known_type, $known_species, $known_db_type, $dba) = @_;
my @types = defined $known_type ? ($known_type) : ('GeneTree');
foreach my $type (@types) {
my $statement = sprintf $compara_stable_id_stmts{lc $type}, $dba->dbc->dbname;
my $sth = $dba->dbc()->prepare($statement);
$sth->bind_param(1, $stable_id, SQL_VARCHAR);
$sth->execute;
my $found = $sth->fetchall_arrayref->[0][0];
$sth->finish;
return ($known_species, $type, $known_db_type) if defined $found;
}
return;
} ## end sub get_species_and_object_type
}
1;
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