Commit 7fe49577 authored by Jessica Severin's avatar Jessica Severin
Browse files

updated the perldoc

parent f8b850d6
......@@ -10,25 +10,29 @@
# POD documentation - main docs before the code
=head1 NAME
Bio::EnsEMBL::Hive::AnalysisCtrlRule
=head1 SYNOPSIS
=head1 DESCRIPTION
Needed a robust and simpler rule table
where Analyses in the pipeline can robustly define
new analyses and rules. New design has a single table where a 'rule'
is a simple link from one analysis to another.
Extended from design of SimpleRule concept to allow the 'to' analysis to
be specified with a network savy URL like
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 _
......@@ -53,6 +57,7 @@ use Bio::EnsEMBL::Utils::Exception;
Function: Constructor for empty AnalysisCtrlRule object
Returns : Bio::EnsEMBL::Hive::AnalysisCtrlRule
Args : none
=cut
sub new {
......@@ -70,12 +75,15 @@ sub adaptor {
=head2 ctrled_analysis_id
Title : ctrled_analysis_id
Arg[1] : (optional) int $dbID
Usage : $self->ctrled_analysis_id($dbID);
Function: Get/set method for the 'controlled' analysis objects dbID of this rule.
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) {
......@@ -87,12 +95,15 @@ sub ctrled_analysis_id {
=head2 condition_analysis_url
Title : condition_analysis_url
Arg[1] : (optional) string $url
Usage : $self->condition_analysis_url($url);
Function: Get/set method for the 'to' analysis objects URL for this rule
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) {
......@@ -104,12 +115,15 @@ sub condition_analysis_url {
=head2 ctrled_analysis
Title : ctrled_analysis
Arg[1] : (optional) Bio::EnsEMBL::Analysis object
Usage : $self->ctrled_analysis($anal);
Function: Get/set method for the condition analysis object of this rule.
Function: Get/set method for the analysis which will be BLOCKED until all
of its condition analyses are 'DONE'
Returns : Bio::EnsEMBL::Analysis
Args : Bio::EnsEMBL::Analysis
=cut
sub ctrled_analysis {
my ($self,$analysis) = @_;
......@@ -137,12 +151,15 @@ sub ctrled_analysis {
=head2 condition_analysis
Title : condition_analysis
Arg[1] : (optional) Bio::EnsEMBL::Analysis object
Usage : $self->condition_analysis($anal);
Function: Get/set method for the goal analysis object of this rule.
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
Args : Bio::EnsEMBL::Analysis
=cut
sub condition_analysis {
my ($self,$analysis) = @_;
......@@ -175,6 +192,14 @@ sub condition_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 ",
......
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