From a67276fab9d745c0aa20644d6d43afae019e4fa9 Mon Sep 17 00:00:00 2001
From: Leo Gordon <lg4@ebi.ac.uk>
Date: Sat, 28 Sep 2013 11:16:25 +0100
Subject: [PATCH] moved stringification of analysis.parameters into Analysis
object
---
modules/Bio/EnsEMBL/Hive/Analysis.pm | 7 ++++++-
modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm | 3 +--
2 files changed, 7 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Hive/Analysis.pm b/modules/Bio/EnsEMBL/Hive/Analysis.pm
index bfdb13172..ebe92edeb 100644
--- a/modules/Bio/EnsEMBL/Hive/Analysis.pm
+++ b/modules/Bio/EnsEMBL/Hive/Analysis.pm
@@ -39,6 +39,8 @@ use strict;
use Bio::EnsEMBL::Utils::Argument ('rearrange');
+use Bio::EnsEMBL::Hive::Utils ('stringify');
+
use base ( 'Bio::EnsEMBL::Storable', # inherit dbID(), adaptor() and new() methods
);
@@ -82,7 +84,10 @@ sub module {
sub parameters {
my $self = shift;
- $self->{'_parameters'} = shift if(@_);
+ if(@_) {
+ my $parameters = shift @_;
+ $self->{'_parameters'} = ref($parameters) ? stringify($parameters) : $parameters;
+ }
return $self->{'_parameters'};
}
diff --git a/modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm b/modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm
index 39ec715bf..fd4c0c8d1 100644
--- a/modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm
+++ b/modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm
@@ -62,7 +62,6 @@ use warnings;
use Bio::EnsEMBL::ApiVersion ();
-use Bio::EnsEMBL::Hive::Utils ('stringify');
use Bio::EnsEMBL::Hive::Utils::URL;
use Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor;
@@ -579,7 +578,7 @@ sub run {
$analysis = Bio::EnsEMBL::Hive::Analysis->new(
-logic_name => $logic_name,
-module => $module,
- -parameters => stringify($parameters_hash), # have to stringify it here, because Analysis code is external wrt Hive code
+ -parameters => $parameters_hash,
-resource_class_id => $rc_id,
-failed_job_tolerance => $failed_job_tolerance,
-max_retry_count => $max_retry_count,
--
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