modules/Bio/EnsEMBL/Hive/DataflowTarget.pm
=pod
=head1 NAME
Bio::EnsEMBL::Hive::DataflowTarget
=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2021] 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 subscribe to the Hive mailing list: http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users to discuss Hive-related questions or to be notified of our updates
=cut
package Bio::EnsEMBL::Hive::DataflowTarget;
use strict;
use warnings;
use Bio::EnsEMBL::Hive::Utils ('stringify', 'throw');
use Bio::EnsEMBL::Hive::TheApiary;
use base ( 'Bio::EnsEMBL::Hive::Cacheable', 'Bio::EnsEMBL::Hive::Storable' );
sub unikey { # override the default from Cacheable parent
return [ 'source_dataflow_rule', 'on_condition', 'input_id_template', 'to_analysis_url' ];
}
=head1 AUTOLOADED
source_dataflow_rule_id / source_dataflow_rule
=cut
=head2 on_condition
Function: getter/setter method for the on_condition of the dataflow target
=cut
sub on_condition {
my $self = shift @_;
if(@_) {
$self->{'_on_condition'} = shift @_;
}
return $self->{'_on_condition'};
}
=head2 input_id_template
Function: getter/setter method for the input_id_template of the dataflow target
=cut
sub input_id_template {
my $self = shift @_;
if(@_) {
my $input_id_template = shift @_;
$self->{'_input_id_template'} = (ref($input_id_template) ? stringify($input_id_template) : $input_id_template),
}
return $self->{'_input_id_template'};
}
=head2 extend_param_stack
Function: getter/setter method. The boolean value defines whether the newly created jobs will inherit both the parameters and the accu of the prev_job.
=cut
sub extend_param_stack {
my $self = shift @_;
if(@_) {
$self->{'_extend_param_stack'} = shift @_;
}
return $self->{'_extend_param_stack'};
}
=head2 to_analysis_url
Arg[1] : (optional) string $url
Usage : $self->to_analysis_url($url);
Function: Get/set method for the 'to' analysis objects URL for this rule
Returns : string
=cut
sub to_analysis_url {
my $self = shift @_;
if(@_) {
$self->{'_to_analysis_url'} = shift @_;
if( $self->{'_to_analysis'} ) {
$self->{'_to_analysis'} = undef;
}
} elsif( !$self->{'_to_analysis_url'} and my $target_object=$self->{'_to_analysis'} ) {
my $ref_dba = $self->from_analysis && $self->from_analysis->adaptor && $self->from_analysis->adaptor->db;
$self->{'_to_analysis_url'} = $target_object->url( $ref_dba ); # the URL may be shorter if DBA is the same for source and target
}
return $self->{'_to_analysis_url'};
}
=head2 to_analysis
Usage : $self->to_analysis($analysis);
Function: Get/set method for the goal analysis object of this rule.
Returns : Bio::EnsEMBL::Hive::Analysis
Args : Bio::EnsEMBL::Hive::Analysis
=cut
sub to_analysis {
my ($self, $target_object) = @_;
if( defined $target_object ) {
unless ($target_object->can('url')) {
throw( "to_analysis arg must support 'url' method, '$target_object' does not know how to do it");
}
$self->{'_to_analysis'} = $target_object;
}
if( !$self->{'_to_analysis'} and my $to_analysis_url = $self->to_analysis_url ) { # lazy-load through TheApiary
$self->{'_to_analysis'} = Bio::EnsEMBL::Hive::TheApiary->find_by_url( $to_analysis_url, $self->hive_pipeline );
}
return $self->{'_to_analysis'};
}
=head2 toString
Args : (none)
Example : print $df_rule->toString()."\n";
Description: returns a stringified representation of the rule
Returntype : string
=cut
sub toString {
my $self = shift @_;
my $short = shift @_;
my $on_condition = $self->on_condition;
return join('',
$short ? () : ( 'DataflowTarget: ' ),
defined($on_condition) ? 'WHEN '.$on_condition : 'DEFAULT ',
'--> ',
$self->to_analysis_url,
($self->input_id_template ? (' WITH TEMPLATE: '.$self->input_id_template) : ''),
);
}
1;