Raw content of Bio::EnsEMBL::Hive::AnalysisCtrlRule
<![CDATA[# Perl module for Bio::EnsEMBL::Hive::AnalysisCtrlRule
#
# Creator: Jessica Severin <jessica@ebi.ac.uk>
# Date of creation: 22.03.2004
#
# Copyright EMBL-EBI 2000-2004
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::EnsEMBL::Hive::AnalysisCtrlRule
=head1 SYNOPSIS
=head1 DESCRIPTION
An 'analysis control rule' is a high level blocking control structure where there is
a 'ctrled_analysis' which is 'BLOCKED' from running until all of its 'condition_analysis' are 'DONE'.
If a ctrled_analysis requires multiple analysis to be DONE before it can run, a separate
AnalysisCtrlRule must be created/stored for each condtion analysis.
Allows the 'condition' analysis to be specified with a network savy URL like
mysql://ensadmin:<pass>@ecs2:3361/compara_hive_test?analysis.logic_name='blast_NCBI34'
=head1 CONTACT
Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@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::Hive::AnalysisCtrlRule;
use strict;
use Bio::EnsEMBL::Hive::URLFactory;
use Bio::EnsEMBL::Hive::Extensions;
use Bio::EnsEMBL::Utils::Argument;
use Bio::EnsEMBL::Utils::Exception;
=head2 Constructor
Title : new
Usage : ...AnalysisCtrlRule->new;
Function: Constructor for empty AnalysisCtrlRule object
Returns : Bio::EnsEMBL::Hive::AnalysisCtrlRule
Args : none
=cut
sub new {
my ($class,@args) = @_;
my $self = bless {}, $class;
return $self;
}
sub adaptor {
my ( $self, $adaptor ) = @_;
$self->{'_adaptor'} = $adaptor if defined $adaptor;
return $self->{'_adaptor'};
}
=head2 ctrled_analysis_id
Arg[1] : (optional) int $dbID
Usage : $self->ctrled_analysis_id($dbID);
Function: Get/set method for the analysis which will be BLOCKED until all
of its condition analyses are 'DONE'. Specified as a dbID.
Returns : integer
=cut
sub ctrled_analysis_id {
my ($self,$analysis_id) = @_;
if($analysis_id) {
$self->{'_ctrled_analysis_id'} = $analysis_id;
$self->{'_ctrled_analysis'} = undef;
}
return $self->{'_ctrled_analysis_id'};
}
=head2 condition_analysis_url
Arg[1] : (optional) string $url
Usage : $self->condition_analysis_url($url);
Function: Get/set method for the analysis which must be 'DONE' in order for
the controlled analysis to be un-BLOCKED. Specified as a URL.
Returns : string
=cut
sub condition_analysis_url {
my ($self,$url) = @_;
if($url) {
$self->{'_condition_analysis_url'} = $url;
$self->{'_condition_analysis'} = undef;
}
return $self->{'_condition_analysis_url'};
}
=head2 ctrled_analysis
Arg[1] : (optional) Bio::EnsEMBL::Analysis object
Usage : $self->ctrled_analysis($anal);
Function: Get/set method for the analysis which will be BLOCKED until all
of its condition analyses are 'DONE'
Returns : Bio::EnsEMBL::Analysis
=cut
sub ctrled_analysis {
my ($self,$analysis) = @_;
# setter mode
if( defined $analysis ) {
unless ($analysis->isa('Bio::EnsEMBL::Analysis')) {
throw(
"ctrled_analysis arg must be a [Bio::EnsEMBL::Analysis]".
"not a [$analysis]");
}
$self->{'_ctrled_analysis'} = $analysis;
$self->{'_ctrled_analysis_id'} = $analysis->dbID;
}
# lazy load the analysis object if I can
if(!defined($self->{'_ctrled_analysis'})
and defined($self->ctrled_analysis_id)
and defined($self->adaptor))
{
$self->{'_ctrled_analysis'} =
$self->adaptor->db->get_AnalysisAdaptor->fetch_by_dbID($self->ctrled_analysis_id);
}
return $self->{'_ctrled_analysis'};
}
=head2 condition_analysis
Arg[1] : (optional) Bio::EnsEMBL::Analysis object
Usage : $self->condition_analysis($anal);
Function: Get/set method for the analysis which must be 'DONE' in order for
the controlled analysis to be un-BLOCKED
Returns : Bio::EnsEMBL::Analysis
=cut
sub condition_analysis {
my ($self,$analysis) = @_;
if( defined $analysis ) {
unless ($analysis->isa('Bio::EnsEMBL::Analysis')) {
throw(
"condition_analysis arg must be a [Bio::EnsEMBL::Analysis]".
"not a [$analysis]");
}
$self->{'_condition_analysis'} = $analysis;
#if the 'condition' and 'ctrled' share the same adaptor, then use a simple logic_name
#for the URL rather than a full network distributed URL
if($self->ctrled_analysis and ($self->ctrled_analysis->adaptor == $analysis->adaptor)) {
$self->{'_condition_analysis_url'} = $analysis->logic_name;
} else {
$self->{'_condition_analysis_url'} = $analysis->url;
}
}
# lazy load the analysis object if I can
if(!defined($self->{'_condition_analysis'}) and defined($self->condition_analysis_url)) {
$analysis = Bio::EnsEMBL::Hive::URLFactory->fetch($self->condition_analysis_url);
unless($analysis) {
$analysis =
$self->adaptor->db->get_AnalysisAdaptor->fetch_by_logic_name($self->condition_analysis_url);
}
$self->{'_condition_analysis'} = $analysis;
}
return $self->{'_condition_analysis'};
}
=head2 print_rule
Usage : $ctrlRule->print_rule;
Function: Prints a description of the rule for use in debugging.
=cut
sub print_rule {
my $self = shift;
print("AnalysisCtrlRule ",
" ctrled_analysis_id=", $self->ctrled_analysis_id,
" condition_analysis_url=", $self->condition_analysis_url,
"\n");
}
1;
]]>