Raw content of Bio::EnsEMBL::Funcgen::DBSQL::ExperimentalChipAdaptor
<![CDATA[#
# Ensembl module for Bio::EnsEMBL::Funcgen::DBSQL::ExperimentalChipAdaptor
#
# You may distribute this module under the same terms as Perl itself
=head1 NAME
Bio::EnsEMBL::Funcgen::DBSQL::ExperimentalChipAdaptor - A database adaptor for fetching and
storing Funcgen ExperimentalChip objects.
=head1 SYNOPSIS
my $ec_a = $db->get_ExperimentalChipAdaptor();
my @ecs = @{$ec_a->fetch_all_by_Experiment($exp)};
=head1 DESCRIPTION
The ExperimentalChipAdaptor is a database adaptor for storing and retrieving
Funcgen ExperimentalChip objects.
=head1 AUTHOR
This module was created by Nathan Johnson.
This module is part of the Ensembl project: /
=head1 CONTACT
Post comments or questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=head1 METHODS
=cut
use strict;
use warnings;
package Bio::EnsEMBL::Funcgen::DBSQL::ExperimentalChipAdaptor;
use Bio::EnsEMBL::Utils::Exception qw( warning throw );
use Bio::EnsEMBL::Funcgen::ExperimentalChip;
use Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor;
use vars qw(@ISA);
#May need to our this?
@ISA = qw(Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor);
=head2 fetch_all_by_experiment_dbID
Arg [1] : int - dbID of Experiment
Example : my @ecs = @{$ec_a->fetch_all_by_experiment_dbID($ac_dbid);
Description: Does what it says on the tin
Returntype : Listref of Bio::EnsEMBL::Funcgen::ExperimentalChip
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub fetch_all_by_experiment_dbID {
my $self = shift;
my $e_dbid = shift;
my ($ec_id, @results);
throw("Must specify an experiemntal dbID") if(! $e_dbid);
my $sth = $self->prepare("
SELECT ec.experimental_chip_id
FROM experimental_chip ec, experiment e
WHERE ec.experiment_id = $e_dbid
");
#can we do a generic fetch here?
$sth->execute();
while ($ec_id = $sth->fetchrow()){
#warn("got ec id $ec_id\n");
push @results, $self->fetch_by_dbID($ec_id);
}
return \@results;
}
=head2 fetch_all_by_Experiment
Arg [1] : Bio::EnsEMBL::Funcgen::Experiment
Example : my @ecs = @{$ec_a->fetch_all_by_Experiment($exp)};
Description: Does what it says on the tin
Returntype : Listref of Bio::EnsEMBL::Funcgen::ExperimentalChips
Exceptions : throws if valid stored Experiment not passed
Caller : General
Status : at risk
=cut
sub fetch_all_by_Experiment(){
my ($self, $exp) = @_;
if(! ($exp && $exp->isa('Bio::EnsEMBL::Funcgen::Experiment') && $exp->dbID())){
throw('Must provide a valid stored Bio::EnsEMBL::Funcgen::Experiment');
}
$self->generic_fetch("ec.experiment_id=".$exp->dbID());
}
=head2 fetch_all_by_ArrayChip
Arg [1] : Bio::EnsEMBL::Funcgen::ArrayChip
Example : my @ecs = @{$ec_a->fetch_all_by_ArrayChip($achip)};
Description: Retrieves all ExperimentChips which have the corresponding ArrayChip design
Returntype : Listref of Bio::EnsEMBL::Funcgen::ExperimentalChips
Exceptions : throws if valid stored ArrayChip not passed
Caller : General
Status : at risk
=cut
sub fetch_all_by_ArrayChip{
my ($self, $achip) = @_;
$self->db->is_stored_and_valid('Bio::EnsEMBL::Funcgen::ArrayChip', $achip);
$self->generic_fetch("ec.array_chip_id=".$achip->dbID());
}
=head2 fetch_by_unique_and_experiment_id
Arg [2] : int - unique_id
Arg [1] : int - dbID of Experiment
Example : my $ec = ec_a->fetch_by_unique_and_experiment_id($c_uid, $exp_dbid);
Description: Does what it says on the tin
Returntype : Bio::EnsEMBL::Funcgen::ExperimentalChip
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub fetch_by_unique_and_experiment_id {
my ($self, $c_uid, $e_dbid) = @_;
throw("Must provide and unique_id and and experiment_id") if(! $c_uid || ! $e_dbid);
my $sth = $self->prepare("
SELECT ec.experimental_chip_id
FROM experimental_chip ec
WHERE ec.unique_id ='$c_uid'
AND ec.experiment_id = $e_dbid
");
$sth->execute();
my ($ec_id) = $sth->fetchrow();
return $self->fetch_by_dbID($ec_id) if $ec_id;
}
=head2 fetch_by_unique_id_vendor
Arg [2] : string - unique_id
Arg [1] : string - name of array vendor e.g. NIMBLEGEN
Example : my $ec = $ec_a->fetch_by_unique_id_vendor($c_uid, $vendor);
Description: Fetches a unique ExperimentalChip for a given unique id and vendor
Returntype : Bio::EnsEMBL::Funcgen::ExperimentalChip
Exceptions : None
Caller : General
Status : at Risk
=cut
sub fetch_by_unique_id_vendor {
my ($self, $c_uid, $vendor) = @_;
throw("Must provide and unique_id and and vendor") if(! $c_uid || ! $vendor);
my ($ec_id, $ac_id, @ecids, $avendor);
my $sth = $self->prepare("
SELECT ec.experimental_chip_id, ec.array_chip_id
FROM experimental_chip ec
WHERE ec.unique_id ='$c_uid'
");
$sth->execute();
while (($ec_id, $ac_id) = $sth->fetchrow()){
my $sql = "SELECT a.vendor from array a, array_chip ac where a.array_id=ac.array_id and ac.array_chip_id=$ac_id;";
($avendor) = @{$self->db->dbc->db_handle->selectrow_arrayref($sql)};
push @ecids, $ec_id if (uc($avendor) eq uc($vendor));
}
#This check shouldn't be necessary if this control is illicited on import
#no unique key possible so just for safety until import fully tested.
if(scalar(@ecids) > 1){
throw("Found more than one ExperimentalChip with the same unique_id($c_uid) for $vendor");
}
return $self->fetch_by_dbID($ecids[0]) if $ecids[0];
}
=head2 _tables
Args : None
Example : None
Description: PROTECTED implementation of superclass abstract method.
Returns the names and aliases of the tables to use for queries.
Returntype : List of listrefs of strings
Exceptions : None
Caller : Internal
Status : Medium Risk
=cut
sub _tables {
my $self = shift;
return ['experimental_chip', 'ec'];
}
=head2 _columns
Args : None
Example : None
Description: PROTECTED implementation of superclass abstract method.
Returns a list of columns to use for queries.
Returntype : List of strings
Exceptions : None
Caller : Internal
Status : Medium Risk
=cut
sub _columns {
my $self = shift;
return qw( ec.experimental_chip_id ec.unique_id
ec.experiment_id ec.array_chip_id
ec.feature_type_id ec.cell_type_id
ec.biological_replicate ec.technical_replicate);
}
=head2 _objs_from_sth
Arg [1] : DBI statement handle object
Example : None
Description: PROTECTED implementation of superclass abstract method.
Creates Array objects from an executed DBI statement
handle.
Returntype : Listref of Bio::EnsEMBL::Funcgen::ExperimentalChip objects
Exceptions : None
Caller : Internal
Status : At Risk
=cut
sub _objs_from_sth {
my ($self, $sth) = @_;
my (@result, $ec_id, $c_uid, $exp_id, $ac_id, $ftype_id, $ctype_id, $brep, $trep, $ftype, $ctype);
my $ft_adaptor = $self->db->get_FeatureTypeAdaptor();
my $ct_adaptor = $self->db->get_CellTypeAdaptor();
$sth->bind_columns(\$ec_id, \$c_uid, \$exp_id, \$ac_id, \$ftype_id, \$ctype_id, \$brep, \$trep);
while ( $sth->fetch() ) {
$ftype = (defined $ftype_id) ? $ft_adaptor->fetch_by_dbID($ftype_id) : undef;
$ctype = (defined $ctype_id) ? $ct_adaptor->fetch_by_dbID($ctype_id) : undef;
my $array = Bio::EnsEMBL::Funcgen::ExperimentalChip->new(
-dbID => $ec_id,
-unique_id => $c_uid,
-experiment_id => $exp_id,
-array_chip_id => $ac_id,
-feature_type => $ftype,
-cell_type => $ctype,
-biological_replicate => $brep,
-technical_replicate => $trep,
-adaptor => $self,
);
push @result, $array;
}
return \@result;
}
=head2 store
Args : List of Bio::EnsEMBL::Funcgen::ExperimentalChip objects
Example : $oaa->store($ec1, $ec2, $ec3);
Description: Stores given ExperimentalChip objects in the database. Should only be
called once per array because no checks are made for duplicates.
Sets dbID and adaptor on the objects that it stores.
Returntype : ARRAYREF
Exceptions : Throws if passed non-ExperimentalChip arg or if ExperimentalChip already stored but arg has no dbID
Caller : General
Status : Medium Risk
=cut
sub store {
my $self = shift;
my @args = @_;
my ($sarray);
my $sth = $self->prepare("
INSERT INTO experimental_chip
(unique_id, experiment_id, array_chip_id, feature_type_id,
cell_type_id, biological_replicate, technical_replicate)
VALUES (?, ?, ?, ?, ?, ?, ?)");
foreach my $ec (@args) {
throw('Can only store ExperimentalChip objects') if ( ! $ec->isa('Bio::EnsEMBL::Funcgen::ExperimentalChip') );
if (!( $ec->dbID() && $ec->adaptor() == $self )){
#Some slight jiggery pokery here to get the vendor as the EC does not yet have an adaptor
#cache these?
my $vendor = $self->db->get_ArrayChipAdaptor->fetch_by_dbID($ec->array_chip_id)->get_Array->vendor();
my $s_ec = $self->fetch_by_unique_id_vendor($ec->unique_id(), $vendor);
throw("ExperimentalChip already exists in the database with dbID:".$s_ec->dbID().
"\nTo reuse/update this ExperimentalChip you must retrieve it using the ExperimentalChipAdaptor".
"\nMaybe you want to use the -recover option?") if $s_ec;
my $ftype_id = (defined $ec->feature_type()) ? $ec->feature_type->dbID() : undef;
my $ctype_id = (defined $ec->cell_type()) ? $ec->cell_type->dbID() : undef;
$sth->bind_param(1, $ec->unique_id(), SQL_VARCHAR);
$sth->bind_param(2, $ec->experiment_id(), SQL_VARCHAR);
$sth->bind_param(3, $ec->array_chip_id(), SQL_VARCHAR);
$sth->bind_param(4, $ftype_id, SQL_INTEGER);
$sth->bind_param(5, $ctype_id, SQL_INTEGER);
$sth->bind_param(6, $ec->biological_replicate(), SQL_VARCHAR);
$sth->bind_param(7, $ec->technical_replicate(), SQL_VARCHAR);
$sth->execute();
my $dbID = $sth->{'mysql_insertid'};
$ec->dbID($dbID);
$ec->adaptor($self);
#}
#else{
# $ec = $s_ec;
#my @states = @{$self->db->fetch_all_states('experimental_chip', $ec->dbID())};
# my @states = @{$self->db->get_StatusAdaptor->fetch_all_states($ec)};
# warn("Using previously stored ExperimentalChip (".$ec->unique_id().") with states\t@states\n");
# }
}else{
#assume we want to update the states
warn('You may want to use $exp_chip->adaptor->store_states($exp_chip)');
$self->store_states($ec);
}
}
return \@args;
}
sub update_replicate_types{
my ($self, $echip) = @_;
if(! ($echip && $echip->isa('Bio::EnsEMBL::Funcgen::ExperimentalChip') && $echip->dbID())){
throw('Must provide a valid store Bio::EnsEMBL::Funcgen::ExperimentalChip');
}
my $sql = 'UPDATE experimental_chip set biological_replicate="'.$echip->biological_replicate().
'" where experimental_chip_id='.$echip->dbID();
$self->db->dbc->do($sql);
$sql = 'UPDATE experimental_chip set technical_replicate="'.$echip->technical_replicate().
'" where experimental_chip_id='.$echip->dbID();
$self->db->dbc->do($sql);
if(defined $echip->cell_type()){
$sql = 'UPDATE experimental_chip set cell_type_id="'.$echip->cell_type()->dbID.
'" where experimental_chip_id='.$echip->dbID();
$self->db->dbc->do($sql);
}
if(defined $echip->feature_type()){
$sql = 'UPDATE experimental_chip set feature_type_id="'.$echip->feature_type()->dbID.
'" where experimental_chip_id='.$echip->dbID();
$self->db->dbc->do($sql);
}
return;
}
=head2 list_dbIDs
Args : None
Example : my @array_ids = @{$ec_a->list_dbIDs()};
Description: Gets an array of internal IDs for all ExperimentalChip objects in the
current database.
Returntype : List of ints
Exceptions : None
Caller : ?
Status : Medium Risk
=cut
sub list_dbIDs {
my ($self) = @_;
return $self->_list_dbIDs('experimental_chip');
}
1;
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