# # Ensembl module for Bio::EnsEMBL::Funcgen::DBSQL::ArrayChipAdaptor # =head1 LICENSE Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2019] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. =head1 CONTACT Please email comments or questions to the public Ensembl developers list at . Questions may also be sent to the Ensembl help desk at . =head1 NAME Bio::EnsEMBL::Funcgen::DBSQL::ArrayChipAdaptor - A database adaptor for fetching and storing Funcgen ArrayChip objects. =head1 SYNOPSIS my $ac_adaptor = $db->get_ArrayChipAdaptor(); my @achips = @{$ec_adaptor->fetch_all_by_Array($array)}; =head1 DESCRIPTION The ArrayChipAdaptor is a database adaptor for storing and retrieving Funcgen ArrayChip objects. =cut package Bio::EnsEMBL::Funcgen::DBSQL::ArrayChipAdaptor; use strict; use warnings; use Bio::EnsEMBL::Utils::Exception qw( warning throw ); use Bio::EnsEMBL::Funcgen::ArrayChip; use Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor; use base qw(Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor); =head2 fetch_all_by_array_id Arg [1] : int - dbID of Array Example : my @ccs = @{$ec_a->fetch_all_by_array_dbID($array->dbID()); Description: Does what it says on the tin Returntype : Listref of Bio::EnsEMBL::Funcgen::ArrayChip Exceptions : None Caller : General Status : Medium Risk =cut sub fetch_all_by_array_id { my ($self, $array_id) = @_; throw("Must specify an array dbID") if(! $array_id); $self->bind_param_generic_fetch($array_id, SQL_INTEGER); return $self->generic_fetch('ac.array_id= ?'); } sub fetch_by_name { my ($self, $name) = @_; my $arrays = $self->generic_fetch("ac.name = '$name'"); if(scalar(@$arrays) > 1) { throw("There is more than one array with this name."); } return $arrays->[0]; } =head2 fetch_all_by_Array Arg [1] : Bio::EnsEMBL::Funcgen::Array Example : my @ccs = @{$ec_a->fetch_all_by_Array($array); Description: Returns all ArrayChips which belong to the given Array Returntype : Arrayref of Bio::EnsEMBL::Funcgen::ArrayChip objects Exceptions : Throws if ARg not valid and stored Caller : General Status : At Risk =cut sub fetch_all_by_Array { my ($self, $array) = @_; if(! (ref($array) && $array->isa->('Bio::EnsEMBL::Funcgen::Array') && $array->dbID())){ throw("Must pass a valid stored Bio::EnsEMBL::Funcgen::Array"); } return $self->fetch_all_by_array_id($array->dbID); } =head2 fetch_all_by_ExperimentalChips Arg [1] : arrayref of - Bio::EnsEMBL::Funcgen::ExperimentalChips Example : my @achips = @{$ec_a->fetch_all_by_ExperimentalChips($echips); Description: Gets a non-redundant list of the corresponding ArrayChips Returntype : Listref of Bio::EnsEMBL::Funcgen::ArrayChips Exceptions : Throws if no ExperimentalChips passed or if ExperimentalChips are not stored or valid Caller : General Status : at risk =cut sub fetch_all_by_ExperimentalChips { my ($self, $echips) = @_; my %ac_ids; foreach my $echip(@$echips){ if(! ($echip->isa('Bio::EnsEMBL::Funcgen::ExperimentalChip') && $echip->dbID())){ throw('Must provide an arrayref of valid stored Bio::EnsEMBL::Funcgen::ExperimentalChips'); } $ac_ids{$echip->array_chip_id} = 1; } if(! keys(%ac_ids)){ throw('Must provide an arrayref of valid stored Bio::EnsEMBL::Funcgen::ExperimentalChips'); } return $self->generic_fetch('ac.array_chip_id IN ('.join(', ', keys(%ac_ids)).')'); } =head2 fetch_by_array_design_ids Arg [1] : int - dbID of Array Arg [2] : string - Design ID of ArrayChip Example : my $ac = $ac_adaptpr->fetch_by_array_design_ids($array->dbID, $design_id); Description: Does what it says on the tin Returntype : Bio::EnsEMBL::Funcgen::ArrayChip Exceptions : Throws if args not met. Caller : General Status : Medium Risk =cut sub fetch_by_array_design_ids{ my ($self, $array_id, $design_id) = @_; if( ! ($array_id && $design_id)){ throw('You must pass an Array dbID and a ArrayChip design ID'); } my $constraint = "ac.array_id='$array_id' and ac.design_id='$design_id'"; my ($ac) = @{$self->generic_fetch($constraint)}; #unique key means this always has just one element return $ac; } =head2 _true_tables Args : None Example : None Description: Returns the names and aliases of the tables to use for queries. Returntype : List of listrefs of strings Exceptions : None Caller : Internal Status : At Risk =cut sub _true_tables { return (['array_chip', 'ac']); } =head2 _columns Args : None Example : None Description: PROTECTED implementation of superclass abstract method. Returns a list of columns to use for queries. Returntype : List of strings Exceptions : None Caller : Internal Status : Medium Risk =cut sub _columns { return qw( ac.array_chip_id ac.design_id ac.array_id ac.name ); } =head2 _objs_from_sth Arg [1] : DBI statement handle object Example : None Description: PROTECTED implementation of superclass abstract method. Creates Array objects from an executed DBI statement handle. Returntype : Listref of Bio::EnsEMBL::Funcgen::ArrayChip objects Exceptions : None Caller : Internal Status : At Risk =cut sub _objs_from_sth { my ($self, $sth) = @_; my (@result, $ac_id, $design_id, $array_id, $name); $sth->bind_columns(\$ac_id, \$design_id, \$array_id, \$name); while ( $sth->fetch() ) { my $array = Bio::EnsEMBL::Funcgen::ArrayChip->new( -dbID => $ac_id, -design_id => $design_id, -array_id => $array_id, -name => $name, -adaptor => $self, ); push @result, $array; } return \@result; } =head2 store Args : List of Bio::EnsEMBL::Funcgen::ArrayChip objects Example : $arraychip_adaptor->store($ac1, $ac2, $ac3); Description: Stores given ArrayChip objects in the database. Should only be called once per ArrayChip because no checks are made for duplicates. Returntype : ARRAYREF Exceptions : warns if passed non-ArrayChip arg Caller : General Status : At Risk =cut sub store { my $self = shift; my @args = @_; #my ($stored_ac); #Should we implement a throw here is the caller is not Array? #make private _store? my $sth = $self->prepare(" INSERT INTO array_chip (design_id, array_id, name) VALUES (?, ?, ?)" ); foreach my $ac (@args) { if ( ! $ac->isa('Bio::EnsEMBL::Funcgen::ArrayChip') ) { warning('Can only store ExperimentalChip objects, skipping $ec'); next; } throw("ArrayChip must have an array_id to be stored") if ! $ac->array_id(); #check for array_id here? this is done by not null in sql #check for previously stored array_chips is done in Array via add_ArrayChip if (!( $ac->dbID() && $ac->adaptor() == $self )){ my $s_ac = $self->fetch_by_array_design_ids($ac->array_id(), $ac->design_id()); if(! $s_ac){ $sth->bind_param(1, $ac->design_id(), SQL_VARCHAR); $sth->bind_param(2, $ac->array_id(), SQL_INTEGER); $sth->bind_param(3, $ac->name(), SQL_VARCHAR); $sth->execute(); $ac->dbID($self->last_insert_id); $ac->adaptor($self); }else{ $ac = $s_ac; # my @states = @{$self->db->fetch_all_states('experimental_chip', $ec->dbID())}; # warn("Using previously stored ExperimentalChip (".$ec->unique_id().") with states\t@states\n"); } } } return \@args; } 1;