Raw content of Bio::EnsEMBL::ExternalData::Mole::DBSQL::EntryAdaptor
<![CDATA[package Bio::EnsEMBL::ExternalData::Mole::DBSQL::EntryAdaptor;
use strict;
use Bio::EnsEMBL::ExternalData::Mole::Entry;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::ExternalData::Mole::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning stack_trace_dump );
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use vars '@ISA';
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
sub _tables {
my $self = shift;
return (['entry' , 'e']);
}
sub _columns {
my $self = shift;
return ( 'e.entry_id', 'e.accession_version',
'e.name', 'e.topology', 'e.molecule_type',
'e.data_class', 'e.tax_division',
'e.sequence_length');
}
sub fetch_by_dbID {
my $self = shift;
my $entryid = shift;
my $constraint = "e.entry_id = '$entryid'";
my ($entry_obj) = @{ $self->generic_fetch($constraint) };
return $entry_obj;
}
sub full_fetch_by_dbID {
my ($self, $objectid) = @_;
my $constraint = "e.entry_id = '$objectid'";
my ($entry_object) = @{$self->generic_fetch($constraint)};
my $description_obj = $self->db()->get_DescriptionAdaptor->fetch_by_entry_id($entry_object->dbID);
$entry_object->description_obj($description_obj);
my $sequence_obj = $self->db()->get_SequenceAdaptor->fetch_by_entry_id($entry_object->dbID);
$entry_object->sequence_obj($sequence_obj);
my $accession_obj = $self->db()->get_AccessionAdaptor->fetch_by_entry_id($entry_object->dbID);
$entry_object->accession_obj($accession_obj);
my $taxonomy_obj = $self->db()->get_TaxonomyAdaptor->fetch_by_entry_id($entry_object->dbID);
$entry_object->taxonomy_obj($taxonomy_obj);
my $dbxrefs = $self->db()->get_DBXrefAdaptor->fetch_all_by_entry_id($entry_object->dbID);
$entry_object->{'dbxref_objs'} = $dbxrefs;
my $comments = $self->db()->get_CommentAdaptor->fetch_all_by_entry_id($entry_object->dbID);
$entry_object->{'comment_objs'} = $comments;
return $entry_object;
}
sub fetch_all_by_ncbi_taxID {
my $self = shift;
my $ncbi_taxonomy_id = shift;
my $sth = $self->prepare(
"SELECT t.entry_id ".
"FROM taxonomy t ".
"WHERE t.ncbi_tax_id = ?");
$sth->bind_param(1, $ncbi_taxonomy_id, SQL_INTEGER);
$sth->execute();
my @entries;
while ( my $id = $sth->fetchrow()) {
push @entries, $self->db()->get_EntryAdaptor->full_fetch_by_dbID($id);
}
return \@entries;
}
sub fetch_all_by_description_tag {
my $self = shift;
my $description_tag = shift;
my $sth = $self->prepare(
"SELECT d.entry_id ".
"FROM description d ".
"WHERE d.description like ?");
$sth->bind_param(1, $description_tag, SQL_VARCHAR);
$sth->execute();
my @entries;
while ( my $id = $sth->fetchrow()) {
push @entries, $self->db()->get_EntryAdaptor->full_fetch_by_dbID($id);
}
return \@entries;
}
sub fetch_by_primary_id {
my $self = shift;
my $primary_id = shift;
my $sth = $self->prepare(
"SELECT e.entry_id ".
"FROM entry e, dbxref dbxrf ".
"WHERE e.entry_id=dbxrf.entry_id ".
"AND dbxrf.primary_id=? ".
"AND dbxrf.secondary_id=\'source\'");
$sth->bind_param(1, $primary_id, SQL_VARCHAR);
$sth->execute;
my ($entry_id) = $sth->fetchrow();
$sth->finish();
return undef if (!defined $entry_id);
my $entry = $self->fetch_by_dbID($entry_id);
return $entry;
}
sub fetch_by_accession {
my $self = shift;
my $acc = shift;
my $sth = $self->prepare(
"SELECT a.entry_id ".
"FROM accession a ".
"WHERE a.accession = ?");
$sth->bind_param(1, $acc, SQL_VARCHAR);
$sth->execute;
my ($entry_id) = $sth->fetchrow();
$sth->finish();
return undef if (!defined $entry_id);
my $entry = $self->fetch_by_dbID($entry_id);
return $entry;
}
sub fetch_by_accession_version {
my $self = shift;
my $acc = shift;
my $constraint = "e.accession_version = '$acc'";
my ($entry_obj) = @{ $self->generic_fetch($constraint) };
return $entry_obj;
}
sub fetch_by_name {
my $self = shift;
my $name = shift;
my $constraint = "e.name = '$name'";
my ($entry_obj) = @{ $self->generic_fetch($constraint) };
return $entry_obj;
}
sub fetch_by_topology {
my $self = shift;
my $topology = shift;
my $constraint = "e.topology = '$topology'";
my ($entry_obj) = @{ $self->generic_fetch($constraint) };
return $entry_obj;
}
sub fetch_by_molecule_type {
my $self = shift;
my $molecule_type = shift;
my $constraint = "e.molecule_type = '$molecule_type'";
my ($entry_obj) = @{ $self->generic_fetch($constraint) };
return $entry_obj;
}
sub fetch_by_data_class {
my $self = shift;
my $data_class = shift;
my $constraint = "e.data_class = '$data_class'";
my ($entry_obj) = @{ $self->generic_fetch($constraint) };
return $entry_obj;
}
sub fetch_by_tax_division {
my $self = shift;
my $tax_division = shift;
my $constraint = "e.tax_division = '$tax_division'";
my ($entry_obj) = @{ $self->generic_fetch($constraint) };
return $entry_obj;
}
sub fetch_by_sequence_length {
my $self = shift;
my $sequence_length = shift;
my $constraint = "e.sequence_length = '$sequence_length'";
my ($entry_obj) = @{ $self->generic_fetch($constraint) };
return $entry_obj;
}
sub fetch_all_for_est_update {
my ($self, $taxdivision) = @_;
my $sth = $self->prepare(
"SELECT e.entry_id ".
"FROM entry e ".
"WHERE e.tax_division = ? ".
"AND e.data_class = 'EST'");
$sth->bind_param(1, $taxdivision, SQL_CHAR);
$sth->execute();
my @entries;
while ( my $id = $sth->fetchrow()) {
push @entries, $self->db()->get_EntryAdaptor->fetch_entry_seq_and_comment_by_dbID($id);
}
return \@entries;
}
sub fetch_entry_seq_and_comment_by_dbID {
my ($self, $objectid) = @_;
my $constraint = "e.entry_id = '$objectid'";
my ($entry_object) = @{$self->generic_fetch($constraint)};
my $sequence_obj = $self->db()->get_SequenceAdaptor->fetch_by_entry_id($entry_object->dbID);
$entry_object->sequence_obj($sequence_obj);
my $comments = $self->db()->get_CommentAdaptor->fetch_all_by_entry_id($entry_object->dbID);
$entry_object->comment_objs($comments);
return $entry_object;
}
sub fetch_all_by_dbID_list {
my ($self,$id_list_ref) = @_;
if(!defined($id_list_ref) || ref($id_list_ref) ne 'ARRAY') {
throw("entry id list reference argument is required");
}
return [] if(!@$id_list_ref);
my @out;
#construct a constraint like 't1.table1_id = 123'
my @tabs = $self->_tables;
my ($name, $syn) = @{$tabs[0]};
# mysql is faster and we ensure that we do not exceed the max query size by
# splitting large queries into smaller queries of 200 ids
my $max_size = 200;
my @id_list = @$id_list_ref;
while(@id_list) {
my @ids;
if(@id_list > $max_size) {
@ids = splice(@id_list, 0, $max_size);
} else {
@ids = splice(@id_list, 0);
}
my $id_str;
if(@ids > 1) {
$id_str = " IN (" . join(',', @ids). ")";
} else {
$id_str = " = " . $ids[0];
}
my $constraint = "${syn}.${name}_id $id_str";
push @out, @{$self->generic_fetch($constraint)};
}
return \@out;
}
sub _objs_from_sth {
my ($self, $sth) = @_;
my @out;
my ( $entry_id, $accession_version, $name,
$topology, $molecule_type, $data_class,
$tax_division, $sequence_length );
$sth->bind_columns( \$entry_id, \$accession_version, \$name,
\$topology, \$molecule_type, \$data_class,
\$tax_division, \$sequence_length);
while($sth->fetch()) {
my $acc_obj = $self->db->get_AccessionAdaptor->fetch_by_entry_id($entry_id);
my $dbxref_objs = $self->db->get_DBXrefAdaptor->fetch_all_by_entry_id($entry_id);
my $desc_obj = $self->db->get_DescriptionAdaptor->fetch_by_entry_id($entry_id);
my $seq_obj = $self->db->get_SequenceAdaptor->fetch_by_entry_id($entry_id);
my $taxonomy_obj = $self->db->get_TaxonomyAdaptor->fetch_by_entry_id($entry_id);
push @out, Bio::EnsEMBL::ExternalData::Mole::Entry->new(
-dbID => $entry_id,
-accession_version => $accession_version,
-name => $name,
-topology => $topology,
-molecule_type => $molecule_type,
-data_class => $data_class,
-tax_division => $tax_division,
-sequence_length => $sequence_length,
-accession_obj => $acc_obj,
-dbxref_objs => $dbxref_objs,
-description_obj => $desc_obj,
-sequence_obj => $seq_obj,
-taxonomy_obj => $taxonomy_obj,
);
}
return \@out;
}
1;
]]>