From ad756fa6b84842bdd9a8587162cacb34d52a6fbf Mon Sep 17 00:00:00 2001
From: Leo Gordon <lg4@ebi.ac.uk>
Date: Fri, 2 Nov 2012 15:14:57 +0000
Subject: [PATCH] parametrically slow down the LongMult test pipeline using
-take_time global parameter
---
.../EnsEMBL/Hive/PipeConfig/LongMult_conf.pm | 20 +++++++++++++++++++
.../Hive/RunnableDB/LongMult/AddTogether.pm | 4 ++++
.../Hive/RunnableDB/LongMult/PartMultiply.pm | 4 +++-
.../EnsEMBL/Hive/RunnableDB/LongMult/Start.pm | 9 ++++++++-
4 files changed, 35 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Hive/PipeConfig/LongMult_conf.pm b/modules/Bio/EnsEMBL/Hive/PipeConfig/LongMult_conf.pm
index 782707237..2408d37bd 100644
--- a/modules/Bio/EnsEMBL/Hive/PipeConfig/LongMult_conf.pm
+++ b/modules/Bio/EnsEMBL/Hive/PipeConfig/LongMult_conf.pm
@@ -75,6 +75,8 @@ sub default_options {
'first_mult' => '9650156169', # the actual numbers to be multiplied can also be specified from the command line
'second_mult' => '327358788',
+
+ 'take_time' => 0, # how much time (in seconds) should each job take -- to slow things down
};
}
@@ -98,6 +100,24 @@ sub pipeline_create_commands {
}
+=head2 pipeline_wide_parameters
+
+ Description : Interface method that should return a hash of pipeline_wide_parameter_name->pipeline_wide_parameter_value pairs.
+ The value doesn't have to be a scalar, can be any Perl structure now (will be stringified and de-stringified automagically).
+ Please see existing PipeConfig modules for examples.
+
+=cut
+
+sub pipeline_wide_parameters {
+ my ($self) = @_;
+ return {
+ %{$self->SUPER::pipeline_wide_parameters}, # here we inherit anything from the base class
+
+ 'take_time' => $self->o('take_time'),
+ };
+}
+
+
=head2 pipeline_analyses
Description : Implements pipeline_analyses() interface method of Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf that defines the structure of the pipeline: analyses, jobs, rules, etc.
diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/AddTogether.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/AddTogether.pm
index 774167d7c..fc63e8e23 100644
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/AddTogether.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/AddTogether.pm
@@ -33,6 +33,8 @@ use base ('Bio::EnsEMBL::Hive::Process');
param('b_multiplier'): The second long number (also a string of digits).
+ param('take_time'): How much time to spend sleeping (seconds).
+
=cut
sub fetch_input { # fetch all the (relevant) precomputed products
@@ -64,6 +66,8 @@ sub run { # call the function that will compute the stuff
my $product_pair = $self->param('product_pair');
$self->param('result', _add_together($b_multiplier, $product_pair));
+
+ sleep( $self->param('take_time') );
}
=head2 write_output
diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/PartMultiply.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/PartMultiply.pm
index 12a53d1f4..bdd5304b1 100644
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/PartMultiply.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/PartMultiply.pm
@@ -42,6 +42,8 @@ sub fetch_input {
param('digit'): A decimal digit that is a part of the second multiplier.
+ param('take_time'): How much time to spend sleeping (seconds).
+
=cut
sub run { # call the recursive function that will compute the stuff
@@ -52,7 +54,7 @@ sub run { # call the recursive function that will compute the stuff
$self->param('result', _rec_multiply($a_multiplier, $digit, 0) || 0);
- sleep(1); # slow it down a little
+ sleep( $self->param('take_time') );
}
=head2 write_output
diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/Start.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/Start.pm
index 4d16398ad..c5b591437 100644
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/Start.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/Start.pm
@@ -37,6 +37,8 @@ use base ('Bio::EnsEMBL::Hive::Process');
param('b_multiplier'): The second long number (also a string of digits).
+ param('take_time'): How much time to spend sleeping (seconds).
+
=cut
sub fetch_input {
@@ -58,16 +60,21 @@ sub fetch_input {
$self->param('output_ids', \@output_ids);
}
+
=head2 run
Description : Implements run() interface method of Bio::EnsEMBL::Hive::Process that is used to perform the main bulk of the job (minus input and output).
- Here we don't have any real work to do, just input and output, so run() remains empty.
+ Here we don't have any real work to do, just input and output, so run() just spends some time waiting.
=cut
sub run {
+ my $self = shift @_;
+
+ sleep( $self->param('take_time') );
}
+
=head2 write_output
Description : Implements write_output() interface method of Bio::EnsEMBL::Hive::Process that is used to deal with job's output after the execution.
--
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