From 08c0c4d3eed466d74026d3744f210b0080ebdec3 Mon Sep 17 00:00:00 2001
From: Leo Gordon <lg4@ebi.ac.uk>
Date: Tue, 21 Jan 2014 10:08:19 +0000
Subject: [PATCH] Inherited more classes from Storable even though they may not
have dbID()
---
modules/Bio/EnsEMBL/Hive/Accumulator.pm | 25 ++++-------------
modules/Bio/EnsEMBL/Hive/AnalysisCtrlRule.pm | 27 +++++-------------
modules/Bio/EnsEMBL/Hive/AnalysisStats.pm | 1 -
modules/Bio/EnsEMBL/Hive/NakedTable.pm | 28 ++++++-------------
.../Bio/EnsEMBL/Hive/ResourceDescription.pm | 24 ++++------------
5 files changed, 28 insertions(+), 77 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Hive/Accumulator.pm b/modules/Bio/EnsEMBL/Hive/Accumulator.pm
index ad3e4a31a..dfad3f988 100644
--- a/modules/Bio/EnsEMBL/Hive/Accumulator.pm
+++ b/modules/Bio/EnsEMBL/Hive/Accumulator.pm
@@ -32,20 +32,20 @@
package Bio::EnsEMBL::Hive::Accumulator;
use strict;
-use Scalar::Util ('weaken');
-
use Bio::EnsEMBL::Utils::Argument ('rearrange');
use Bio::EnsEMBL::Hive::Utils ('stringify');
+use base ( 'Bio::EnsEMBL::Hive::Storable' ); # inherit dbID(), adaptor() and new() methods
+
+
sub new {
my $class = shift @_;
- my $self = bless {}, $class;
+ my $self = $class->SUPER::new( @_ ); # deal with Storable stuff
- my ($adaptor, $struct_name, $signature_template) =
- rearrange([qw(adaptor struct_name signature_template) ], @_);
+ my ($struct_name, $signature_template) =
+ rearrange([qw(struct_name signature_template) ], @_);
- $self->adaptor($adaptor) if(defined($adaptor));
$self->struct_name($struct_name) if(defined($struct_name));
$self->signature_template($signature_template) if(defined($signature_template));
@@ -53,18 +53,6 @@ sub new {
}
-sub adaptor {
- my $self = shift @_;
-
- if(@_) {
- $self->{'_adaptor'} = shift @_;
- weaken $self->{'_adaptor'};
- }
-
- return $self->{'_adaptor'};
-}
-
-
sub struct_name {
my $self = shift @_;
@@ -126,6 +114,5 @@ sub dataflow {
$self->adaptor->store( \@rows );
}
-
1;
diff --git a/modules/Bio/EnsEMBL/Hive/AnalysisCtrlRule.pm b/modules/Bio/EnsEMBL/Hive/AnalysisCtrlRule.pm
index a86d7220c..0e0cafb7f 100644
--- a/modules/Bio/EnsEMBL/Hive/AnalysisCtrlRule.pm
+++ b/modules/Bio/EnsEMBL/Hive/AnalysisCtrlRule.pm
@@ -42,14 +42,15 @@
package Bio::EnsEMBL::Hive::AnalysisCtrlRule;
use strict;
-use Scalar::Util ('weaken');
-
use Bio::EnsEMBL::Utils::Argument ('rearrange');
use Bio::EnsEMBL::Utils::Exception ('throw');
use Bio::EnsEMBL::Hive::URLFactory;
use Bio::EnsEMBL::Hive::Extensions;
+use base ( 'Bio::EnsEMBL::Hive::Storable' ); # inherit dbID(), adaptor() and new() methods
+
+
=head2 new
Title : new
@@ -62,14 +63,11 @@ use Bio::EnsEMBL::Hive::Extensions;
sub new {
my $class = shift @_;
- my $self = bless {}, $class;
-
- my ( $dbID, $adaptor, $condition_analysis_url, $ctrled_analysis_id ) =
- rearrange( [ qw (DBID ADAPTOR CONDITION_ANALYSIS_URL CTRLED_ANALYSIS_ID) ], @_ );
- # database persistence:
- $self->dbID( $dbID ) if(defined($dbID));
- $self->adaptor( $adaptor ) if(defined($adaptor));
+ my $self = $class->SUPER::new( @_ ); # deal with Storable stuff
+
+ my ( $condition_analysis_url, $ctrled_analysis_id ) =
+ rearrange( [ qw (CONDITION_ANALYSIS_URL CTRLED_ANALYSIS_ID) ], @_ );
# simple scalars:
$self->condition_analysis_url( $condition_analysis_url ) if(defined($condition_analysis_url));
@@ -78,17 +76,6 @@ sub new {
return $self;
}
-sub adaptor {
- my $self = shift @_;
-
- if(@_) {
- $self->{'_adaptor'} = shift @_;
- weaken $self->{'_adaptor'};
- }
-
- return $self->{'_adaptor'};
-}
-
=head2 ctrled_analysis_id
diff --git a/modules/Bio/EnsEMBL/Hive/AnalysisStats.pm b/modules/Bio/EnsEMBL/Hive/AnalysisStats.pm
index 6b96e5f0a..fe3103c88 100644
--- a/modules/Bio/EnsEMBL/Hive/AnalysisStats.pm
+++ b/modules/Bio/EnsEMBL/Hive/AnalysisStats.pm
@@ -36,7 +36,6 @@
package Bio::EnsEMBL::Hive::AnalysisStats;
use strict;
-use Scalar::Util ('weaken');
use Bio::EnsEMBL::Utils::Argument ('rearrange');
use Bio::EnsEMBL::Utils::Exception ('throw');
diff --git a/modules/Bio/EnsEMBL/Hive/NakedTable.pm b/modules/Bio/EnsEMBL/Hive/NakedTable.pm
index bddd5aca7..ca6b36737 100644
--- a/modules/Bio/EnsEMBL/Hive/NakedTable.pm
+++ b/modules/Bio/EnsEMBL/Hive/NakedTable.pm
@@ -32,19 +32,19 @@
package Bio::EnsEMBL::Hive::NakedTable;
use strict;
-use Scalar::Util ('weaken');
-
use Bio::EnsEMBL::Utils::Argument ('rearrange');
+use base ( 'Bio::EnsEMBL::Hive::Storable' ); # inherit dbID(), adaptor() and new() methods
+
+
sub new {
my $class = shift @_;
- my $self = bless {}, $class;
+ my $self = $class->SUPER::new( @_ ); # deal with Storable stuff
- my ($adaptor, $table_name, $insertion_method) =
- rearrange([qw(adaptor table_name insertion_method) ], @_);
+ my ($table_name, $insertion_method) =
+ rearrange([qw(table_name insertion_method) ], @_);
- $self->adaptor($adaptor) if(defined($adaptor));
$self->table_name($table_name) if(defined($table_name));
$self->insertion_method($insertion_method) if(defined($insertion_method));
@@ -52,18 +52,6 @@ sub new {
}
-sub adaptor {
- my $self = shift @_;
-
- if(@_) {
- $self->{'_adaptor'} = shift @_;
- weaken $self->{'_adaptor'};
- }
-
- return $self->{'_adaptor'};
-}
-
-
sub table_name {
my $self = shift @_;
@@ -73,6 +61,7 @@ sub table_name {
return $self->{'_table_name'};
}
+
sub insertion_method {
my $self = shift @_;
@@ -82,6 +71,7 @@ sub insertion_method {
return $self->{'_insertion_method'} || 'INSERT_IGNORE';
}
+
sub url {
my $self = shift @_;
my $ref_dba = shift @_; # if reference dba is the same as 'our' dba, a shorter url can be generated
@@ -94,6 +84,7 @@ sub url {
}
}
+
sub dataflow {
my ( $self, $output_ids, $emitting_job ) = @_;
@@ -117,6 +108,5 @@ sub dataflow {
$adaptor->store( \@rows );
}
-
1;
diff --git a/modules/Bio/EnsEMBL/Hive/ResourceDescription.pm b/modules/Bio/EnsEMBL/Hive/ResourceDescription.pm
index 2d3ee6d1c..0bc99694c 100644
--- a/modules/Bio/EnsEMBL/Hive/ResourceDescription.pm
+++ b/modules/Bio/EnsEMBL/Hive/ResourceDescription.pm
@@ -40,19 +40,19 @@
package Bio::EnsEMBL::Hive::ResourceDescription;
use strict;
-use Scalar::Util ('weaken');
-
use Bio::EnsEMBL::Utils::Argument ('rearrange');
+use base ( 'Bio::EnsEMBL::Hive::Storable' ); # inherit dbID(), adaptor() and new() methods
+
+
sub new {
my $class = shift @_;
- my $self = bless {}, $class;
+ my $self = $class->SUPER::new( @_ ); # deal with Storable stuff
- my ($adaptor, $resource_class_id, $meadow_type, $submission_cmd_args, $worker_cmd_args) =
- rearrange([qw(adaptor resource_class_id meadow_type submission_cmd_args worker_cmd_args) ], @_);
+ my ($resource_class_id, $meadow_type, $submission_cmd_args, $worker_cmd_args) =
+ rearrange([qw(resource_class_id meadow_type submission_cmd_args worker_cmd_args) ], @_);
- $self->adaptor($adaptor) if(defined($adaptor));
$self->resource_class_id($resource_class_id);
$self->meadow_type($meadow_type);
$self->submission_cmd_args($submission_cmd_args);
@@ -62,18 +62,6 @@ sub new {
}
-sub adaptor {
- my $self = shift @_;
-
- if(@_) {
- $self->{'_adaptor'} = shift @_;
- weaken $self->{'_adaptor'};
- }
-
- return $self->{'_adaptor'};
-}
-
-
sub resource_class_id {
my $self = shift @_;
--
GitLab