Raw content of Bio::EnsEMBL::Pipeline::DBSQL::AnalysisAdaptor
<![CDATA[# Perl module for Bio::EnsEMBL::DBSQL::AnalysisAdaptor
#
# Creator: Arne Stabenau <stabenau@ebi.ac.uk>
# Date of creation: 25.01.2001
# Last modified : 25.01.2001 by Arne Stabenau
#
# Copyright EMBL-EBI 2000
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::EnsEMBL::DBSQL::Pipeline::AnalysisAdaptor
=head1 SYNOPSIS
$analysisAdaptor = $db_adaptor->getAnalysisAdaptor;
$analysisAdaptor = $analysisobj->getAnalysisAdaptor;
=head1 DESCRIPTION
Module to encapsulate all db access for persistent class Analysis.
There should be just one per application and database connection.
=head1 CONTACT
Contact Arne Stabenau on implemetation/design detail: stabenau@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::EnsEMBL::Pipeline::DBSQL::AnalysisAdaptor;
use Bio::EnsEMBL::Pipeline::Analysis;
use Bio::EnsEMBL::DBSQL::AnalysisAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(verbose throw warning info);
use vars qw(@ISA);
use strict;
@ISA = qw( Bio::EnsEMBL::DBSQL::AnalysisAdaptor);
=head2 new
Args : Bio::EnsEMBL::DBSQL::DBAdaptor
Example : my $aa = new Bio::EnsEMBL::Pipeline::DBSQL::AnalysisAdaptor();
Description: Creates a new Bio::EnsEMBL::Pipeline::DBSQL::AnalysisAdaptor object and
internally loads and caches all the Analysis objects from the
database.
Returntype : Bio::EnsEMBL::Pipeline::DBSQL::AnalysisAdaptor
Exceptions : none
Caller : Bio::EnsEMBL::DBSQL::DBAdaptor
=cut
sub new {
my ($class, $db) = @_;
my $self = $class->SUPER::new($db);
#load and cache all of the Analysis objects
$self->fetch_all;
return $self;
}
=head2 store
Arg [1] : Bio:EnsEMBL::Analysis $analysis
Example : $analysis_adaptor->store($analysis);
Description: stores $analysis in db. Does not if already equiped with dbID.
Sets created date if not already set. Sets dbID and adaptor
inside $analysis. Returns dbID.
Returntype : int dbID of stored analysis
Exceptions : thrown if analysis argument does not have a logic name
Caller : ?
=cut
sub store {
my $self = shift;
my $analysis = shift;
if( !$analysis || !($analysis->isa('Bio::EnsEMBL::Pipeline::Analysis'))) {
throw("called store on Pipeline::AnalysisAdaptor with a [$analysis]");
}
$analysis->dbID && $analysis->adaptor && ( $analysis->adaptor() == $self ) &&
return $analysis->dbID;
my $dbID;
if( $dbID = $self->exists( $analysis )) {
$analysis->adaptor( $self );
$analysis->dbID( $dbID );
return $dbID;
}
if( !$analysis->logic_name ) {
throw("Must have a logic name on the analysis object");
}
if (!$analysis->input_id_type) {
throw("Must have an input_id_type");
}
if($analysis->created ) {
my $sth = $self->prepare( q{
INSERT IGNORE INTO analysis
SET created = ?,
logic_name = ?,
db = ?,
db_version = ?,
db_file = ?,
program = ?,
program_version = ?,
program_file = ?,
parameters = ?,
module = ?,
module_version = ?,
gff_source = ?,
gff_feature = ? } );
$sth->execute
( $analysis->created,
$analysis->logic_name,
$analysis->db,
$analysis->db_version,
$analysis->db_file,
$analysis->program,
$analysis->program_version,
$analysis->program_file,
$analysis->parameters,
$analysis->module,
$analysis->module_version,
$analysis->gff_source,
$analysis->gff_feature
);
$dbID = $sth->{'mysql_insertid'};
} else {
my $sth = $self->prepare( q{
INSERT IGNORE INTO analysis
SET created = now(),
logic_name = ?,
db = ?,
db_version = ?,
db_file = ?,
program = ?,
program_version = ?,
program_file = ?,
parameters = ?,
module = ?,
module_version = ?,
gff_source = ?,
gff_feature = ? } );
$sth->execute
( $analysis->logic_name,
$analysis->db,
$analysis->db_version,
$analysis->db_file,
$analysis->program,
$analysis->program_version,
$analysis->program_file,
$analysis->parameters,
$analysis->module,
$analysis->module_version,
$analysis->gff_source,
$analysis->gff_feature
);
$dbID = $sth->{'mysql_insertid'};
if( $dbID ) {
$sth = $self->prepare( q{
SELECT created
FROM analysis
WHERE analysis_id = ? } );
$sth->execute( $dbID );
$analysis->created( ($sth->fetchrow_array)[0] );
}
}
$self->{_cache}->{$dbID} = $analysis;
$self->{_logic_name_cache}{lc($analysis->logic_name)} = $analysis;
$analysis->adaptor( $self );
$analysis->dbID( $dbID );
if($analysis->input_id_type){
my $sql = 'insert into input_id_type_analysis(input_id_type, analysis_id) values(?, ?)';
my $sth = $self->prepare($sql);
$sth->execute($analysis->input_id_type, $analysis->dbID);
}
return $dbID;
}
=head2 _objFromHashref
Arg [1] : hashref $rowHash
Description: Private helper function generates an Analysis object from a
mysql row hash reference.
Returntype : Bio::EnsEMBL::Analysis
Exceptions : none
Caller : Bio::EnsEMBL::DBSQL::AnalsisAdaptor::fetch_* methods
=cut
sub _objFromHashref {
my $self = shift;
my $rowHash = shift;
my $analysis = Bio::EnsEMBL::Pipeline::Analysis->new
(
-id => $rowHash->{analysis_id},
-adaptor => $self,
-db => $rowHash->{db},
-db_file => $rowHash->{db_file},
-db_version => $rowHash->{db_version},
-program => $rowHash->{program},
-program_version => $rowHash->{program_version},
-program_file => $rowHash->{program_file},
-gff_source => $rowHash->{gff_source},
-gff_feature => $rowHash->{gff_feature},
-module => $rowHash->{module},
-module_version => $rowHash->{module_version},
-parameters => $rowHash->{parameters},
-created => $rowHash->{created},
-logic_name => $rowHash->{logic_name},
);
my $type = $self->fetch_analysis_input_id_type($analysis);
$analysis->input_id_type($type);
return $analysis;
}
sub fetch_analysis_input_id_type{
my ($self, $analysis) = @_;
my $sql = "select input_id_type from input_id_type_analysis".
" where analysis_id = ?";
my $sth = $self->prepare($sql);
$sth->execute($analysis->dbID);
my ($type) = $sth->fetchrow;
return $type;
}
=head2 db
Arg [1] : (optional) Bio::EnsEMBL::DBSQL::DBAdaptor $db
the database used by this adaptor.
Example : my $db = $analysis_adaptor->db()
Description: Getter/Setter for the database this adaptor uses internally
to fetch and store database objects.
Returntype : Bio::EnsEMBL::DBSQL::DBAdaptor
Exceptions : none
Caller : BaseAdaptor::new, general
=cut
sub db {
my ( $self, $arg ) = @_;
( defined $arg ) &&
($self->{_db} = $arg);
$self->{_db};;
}
sub remove {
my $self = shift;
my $analysis = shift;
if( !$analysis || !($analysis->isa('Bio::EnsEMBL::Pipeline::Analysis'))) {
throw("called store on Pipeline::AnalysisAdaptor with a [$analysis]");
}
my $sql = 'delete from analysis where analysis_id = ?';
my $sth = $self->prepare($sql);
$sth->execute($analysis->dbID);
if($analysis->input_id_type){
my $sql = 'delete from input_id_type_analysis where analysis_id = ?';
my $sth = $self->prepare($sql);
$sth->execute($analysis->dbID);
}
}
sub fetch_by_input_id_type{
my ($self, $input_id_type) = @_;
my $query = q{ SELECT analysis_id
FROM input_id_type_analysis
WHERE input_id_type = ? };
my $sth = $self->prepare($query);
$sth->execute($input_id_type);
my @analysis_ids;
while(my ($id) = $sth->fetchrow){
push(@analysis_ids, $id);
}
my @analyses;
foreach my $id(@analysis_ids){
my $analysis = $self->fetch_by_dbID($id);
push(@analyses, $analysis);
}
return(\@analyses);
}
1;
]]>