From 9a1f8e72a836f67523754b565492b43d778b6f3c Mon Sep 17 00:00:00 2001
From: Leo Gordon <lg4@ebi.ac.uk>
Date: Tue, 21 Jan 2014 09:42:20 +0000
Subject: [PATCH] removed dependency on Core's DBSQL::BaseAdaptor and Storable
by introducing own lightweight Hive::Storable
---
modules/Bio/EnsEMBL/Hive/Analysis.pm | 2 +-
modules/Bio/EnsEMBL/Hive/AnalysisJob.pm | 2 +-
modules/Bio/EnsEMBL/Hive/AnalysisStats.pm | 2 +-
modules/Bio/EnsEMBL/Hive/DBSQL/BaseAdaptor.pm | 56 ++++++++-
.../Bio/EnsEMBL/Hive/DBSQL/MetaContainer.pm | 2 +-
modules/Bio/EnsEMBL/Hive/DataflowRule.pm | 2 +-
modules/Bio/EnsEMBL/Hive/ResourceClass.pm | 2 +-
modules/Bio/EnsEMBL/Hive/Storable.pm | 118 ++++++++++++++++++
modules/Bio/EnsEMBL/Hive/Worker.pm | 2 +-
9 files changed, 179 insertions(+), 9 deletions(-)
create mode 100644 modules/Bio/EnsEMBL/Hive/Storable.pm
diff --git a/modules/Bio/EnsEMBL/Hive/Analysis.pm b/modules/Bio/EnsEMBL/Hive/Analysis.pm
index 2dfec22ce..740b98cd3 100644
--- a/modules/Bio/EnsEMBL/Hive/Analysis.pm
+++ b/modules/Bio/EnsEMBL/Hive/Analysis.pm
@@ -41,7 +41,7 @@ use Bio::EnsEMBL::Utils::Argument ('rearrange');
use Bio::EnsEMBL::Hive::Utils ('stringify');
-use base ( 'Bio::EnsEMBL::Storable', # inherit dbID(), adaptor() and new() methods
+use base ( 'Bio::EnsEMBL::Hive::Storable', # inherit dbID(), adaptor() and new() methods
);
diff --git a/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm b/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
index 8ca1dffdc..43f186860 100644
--- a/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
+++ b/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
@@ -44,7 +44,7 @@ use Bio::EnsEMBL::Hive::Utils ('stringify', 'destringify');
use Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;
use Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor;
-use base ( 'Bio::EnsEMBL::Storable', # inherit dbID(), adaptor() and new() methods
+use base ( 'Bio::EnsEMBL::Hive::Storable', # inherit dbID(), adaptor() and new() methods
'Bio::EnsEMBL::Hive::Params', # inherit param management functionality
);
diff --git a/modules/Bio/EnsEMBL/Hive/AnalysisStats.pm b/modules/Bio/EnsEMBL/Hive/AnalysisStats.pm
index f424579f8..6b96e5f0a 100644
--- a/modules/Bio/EnsEMBL/Hive/AnalysisStats.pm
+++ b/modules/Bio/EnsEMBL/Hive/AnalysisStats.pm
@@ -42,7 +42,7 @@ use Bio::EnsEMBL::Utils::Argument ('rearrange');
use Bio::EnsEMBL::Utils::Exception ('throw');
use Bio::EnsEMBL::Hive::Analysis;
-use base ( 'Bio::EnsEMBL::Storable' ); # inherit dbID(), adaptor() and new() methods
+use base ( 'Bio::EnsEMBL::Hive::Storable' ); # inherit dbID(), adaptor() and new() methods
## Minimum amount of time in msec that a worker should run before reporting
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/BaseAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/BaseAdaptor.pm
index 1fa5ee4b2..b5f71fca5 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/BaseAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/BaseAdaptor.pm
@@ -39,8 +39,6 @@ use strict;
no strict 'refs'; # needed to allow AUTOLOAD create new methods
use DBI 1.6; # the 1.6 functionality is important for detecting autoincrement fields and other magic.
-use base ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
-
sub default_table_name {
die "Please define table_name either by setting it via table_name() method or by redefining default_table_name() in your adaptor class";
@@ -68,6 +66,60 @@ sub default_input_column_mapping {
};
}
+# ---------------------------------------------------------------------------
+
+sub new {
+ my ( $class, $dbobj ) = @_;
+
+ my $self = bless {}, $class;
+
+ if ( !defined $dbobj || !ref $dbobj ) {
+ throw("Don't have a db [$dbobj] for new adaptor");
+ }
+
+ if ( ref($dbobj) =~ /DBConnection$/ ) {
+ $self->dbc($dbobj);
+ } elsif( UNIVERSAL::can($dbobj, 'dbc') ) {
+ $self->dbc( $dbobj->dbc );
+ $self->db( $dbobj );
+ } else {
+ throw("I was given [$dbobj] for a new adaptor");
+ }
+
+ return $self;
+}
+
+
+sub db {
+ my $self = shift @_;
+
+ if(@_) { # setter
+ $self->{_db} = shift @_;
+ }
+ return $self->{_db};
+}
+
+
+sub dbc {
+ my $self = shift @_;
+
+ if(@_) { # setter
+ $self->{_dbc} = shift @_;
+ }
+ return $self->{_dbc};
+}
+
+
+sub prepare {
+ my ( $self, $sql ) = @_;
+
+ # Uncomment next line to cancel caching on the SQL side.
+ # Needed for timing comparisons etc.
+ #$sql =~ s/SELECT/SELECT SQL_NO_CACHE/i;
+
+ return $self->dbc->prepare($sql);
+}
+
sub overflow_limit {
my $self = shift @_;
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/MetaContainer.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/MetaContainer.pm
index 9706ee967..7580bc621 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/MetaContainer.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/MetaContainer.pm
@@ -37,7 +37,7 @@ package Bio::EnsEMBL::Hive::DBSQL::MetaContainer;
use strict;
use Bio::EnsEMBL::Hive::Utils ('stringify', 'destringify');
-use base ('Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor', 'Bio::EnsEMBL::DBSQL::BaseMetaContainer');
+use base ('Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor');
sub default_table_name {
diff --git a/modules/Bio/EnsEMBL/Hive/DataflowRule.pm b/modules/Bio/EnsEMBL/Hive/DataflowRule.pm
index dfcab628a..48e809b98 100644
--- a/modules/Bio/EnsEMBL/Hive/DataflowRule.pm
+++ b/modules/Bio/EnsEMBL/Hive/DataflowRule.pm
@@ -59,7 +59,7 @@ use Bio::EnsEMBL::Utils::Exception ('throw');
use Bio::EnsEMBL::Hive::Utils ('stringify');
use Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor;
-use base ( 'Bio::EnsEMBL::Storable', # inherit dbID(), adaptor() and new() methods
+use base ( 'Bio::EnsEMBL::Hive::Storable', # inherit dbID(), adaptor() and new() methods
);
diff --git a/modules/Bio/EnsEMBL/Hive/ResourceClass.pm b/modules/Bio/EnsEMBL/Hive/ResourceClass.pm
index 20df3ab67..4756ef78a 100644
--- a/modules/Bio/EnsEMBL/Hive/ResourceClass.pm
+++ b/modules/Bio/EnsEMBL/Hive/ResourceClass.pm
@@ -41,7 +41,7 @@ use strict;
use Bio::EnsEMBL::Utils::Argument ('rearrange');
-use base ( 'Bio::EnsEMBL::Storable', # inherit dbID(), adaptor() and new() methods
+use base ( 'Bio::EnsEMBL::Hive::Storable', # inherit dbID(), adaptor() and new() methods
);
diff --git a/modules/Bio/EnsEMBL/Hive/Storable.pm b/modules/Bio/EnsEMBL/Hive/Storable.pm
new file mode 100644
index 000000000..f08d088d3
--- /dev/null
+++ b/modules/Bio/EnsEMBL/Hive/Storable.pm
@@ -0,0 +1,118 @@
+=pod
+
+=head1 NAME
+
+ Bio::EnsEMBL::Hive::Storable
+
+=head1 SYNOPSIS
+
+ my $dbID = $storable_object->dbID();
+ my $adaptor = $storable_object->adaptor();
+
+=head1 DESCRIPTION
+
+ Storable is a base class for anything that can be stored.
+ It provides two getters/setters: dbID() and adaptor().
+
+=head1 LICENSE
+
+ Copyright [1999-2013] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+
+ Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software distributed under the License
+ is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and limitations under the License.
+
+=head1 CONTACT
+
+ Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
+
+=head1 APPENDIX
+
+ The rest of the documentation details each of the object methods.
+ Internal methods are usually preceded with a _
+
+=cut
+
+
+package Bio::EnsEMBL::Hive::Storable;
+
+use strict;
+use warnings;
+
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+use Scalar::Util qw(weaken);
+
+
+=head2 new
+
+ Arg [-ADAPTOR] : Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor
+ Arg [-dbID] : database internal id
+ Caller : internal calls
+ Description : create a new Storable object
+ Returntype : Bio::EnsEMBL::Hive::Storable
+ Exceptions : Adaptor not a Bio::EnsEMBL::DBSQL::BaseAdaptor
+ Status : Stable
+
+=cut
+
+sub new {
+ my $caller = shift;
+ my $class = ref($caller) || $caller;
+
+ my $self = bless {}, $class;
+
+ my ($adaptor, $dbID) = rearrange(['ADAPTOR', 'dbID'], @_);
+ $self->dbID( $dbID ) if defined( $dbID );
+ $self->adaptor($adaptor) if defined( $adaptor );
+
+ return $self;
+}
+
+
+=head2 dbID
+
+ Arg [1] : int $dbID
+ Description: getter/setter for the database internal id
+ Returntype : int
+ Exceptions : none
+ Caller : general, set from adaptor on store
+ Status : Stable
+
+=cut
+
+sub dbID {
+ my $self = shift;
+ $self->{'dbID'} = shift if(@_);
+ return $self->{'dbID'};
+}
+
+
+=head2 adaptor
+
+ Arg [1] : Bio::EnsEMBL::DBSQL::BaseAdaptor $adaptor
+ Description: get/set for this objects Adaptor
+ Returntype : Bio::EnsEMBL::DBSQL::BaseAdaptor
+ Exceptions : none
+ Caller : general, set from adaptor on store
+ Status : Stable
+
+=cut
+
+sub adaptor {
+ my $self = shift;
+
+ if(@_) {
+ $self->{'adaptor'} = shift;
+ weaken( $self->{'adaptor'} ) if defined( $self->{'adaptor'} );
+ }
+
+ return $self->{'adaptor'};
+}
+
+1;
+
diff --git a/modules/Bio/EnsEMBL/Hive/Worker.pm b/modules/Bio/EnsEMBL/Hive/Worker.pm
index 780b1d40b..11ef740a1 100644
--- a/modules/Bio/EnsEMBL/Hive/Worker.pm
+++ b/modules/Bio/EnsEMBL/Hive/Worker.pm
@@ -89,7 +89,7 @@ use Bio::EnsEMBL::Hive::Utils::RedirectStack;
use Bio::EnsEMBL::Hive::Utils::Stopwatch;
use Bio::EnsEMBL::Hive::Utils ('stringify');
-use base ( 'Bio::EnsEMBL::Storable', # inherit dbID(), adaptor() and new() methods
+use base ( 'Bio::EnsEMBL::Hive::Storable', # inherit dbID(), adaptor() and new() methods
);
--
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