INCUBATORS-17: use reconciliation attributes to get the speciation an…

…d duplication counts.
iPlantCollaborativeOpenSource · Feb 18, 2011 · 34b78b6 · 34b78b6
1 parent c278696
commit 34b78b6
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Showing 4 changed files with 52 additions and 8 deletions.
diff --git a/MANIFEST b/MANIFEST
@@ -14,6 +14,7 @@ lib/IPlant/DB/TreeRec/Result/DuplicationCount.pm
 lib/IPlant/DB/TreeRec/Result/Duplications.pm
 lib/IPlant/DB/TreeRec/Result/DuplicationSearch.pm
 lib/IPlant/DB/TreeRec/Result/Family.pm
+lib/IPlant/DB/TreeRec/Result/FamilyAttribute.pm
 lib/IPlant/DB/TreeRec/Result/FamilyMember.pm
 lib/IPlant/DB/TreeRec/Result/GeneIdSearch.pm
 lib/IPlant/DB/TreeRec/Result/GoAccessionSearch.pm
@@ -27,6 +28,7 @@ lib/IPlant/DB/TreeRec/Result/ProteinTreeAttribute.pm
 lib/IPlant/DB/TreeRec/Result/ProteinTreeMember.pm
 lib/IPlant/DB/TreeRec/Result/ProteinTreeNode.pm
 lib/IPlant/DB/TreeRec/Result/ProteinTreeNodeAttribute.pm
+lib/IPlant/DB/TreeRec/Result/ProteinTreeNodePath.pm
 lib/IPlant/DB/TreeRec/Result/Reconciliation.pm
 lib/IPlant/DB/TreeRec/Result/ReconciliationAttribute.pm
 lib/IPlant/DB/TreeRec/Result/ReconciliationNode.pm
@@ -44,6 +46,7 @@ lib/IPlant/DB/TreeRec/Result/SpeciesTreeNodePath.pm
 lib/IPlant/DB/TreeRec/ResultSet/Family.pm
 lib/IPlant/DB/TreeRec/ResultSet/ProteinTree.pm
 lib/IPlant/DB/TreeRec/ResultSet/Reconciliation.pm
+lib/IPlant/DB/TreeRec/ResultSet/ReconciliationAttribute.pm
 lib/IPlant/DB/TreeRec/ResultSet/SpeciesTree.pm
 lib/IPlant/DB/TreeRec/ResultSet/SpeciesTreeNode.pm
 lib/IPlant/TreeRec.pm

diff --git a/lib/IPlant/DB/TreeRec/ResultSet/ReconciliationAttribute.pm b/lib/IPlant/DB/TreeRec/ResultSet/ReconciliationAttribute.pm
@@ -0,0 +1,38 @@
+package IPlant::DB::TreeRec::ResultSet::ReconciliationAttribute;
+
+use warnings;
+use strict;
+
+use IPlant::TreeRec::X;
+
+use base 'DBIx::Class::ResultSet';
+
+##########################################################################
+# Usage      : @values = $dbh->resultset('ReconciliationAttribute')
+#                  ->get_values( $reconciliation_id, $attribute_name );
+#
+# Purpose    : Retrieves the attribute values for all attributes of the
+#              reconciliation with the given ID that have the given name.
+#
+# Returns    : The list of values.
+#
+# Parameters : $reconciliation_id - the reconciliation identifier.
+#              $attribute_name    - the name of the attribute.
+#
+# Throws     : No exceptions.
+sub get_values {
+    my ( $self, $reconciliation_id, $attribute_name ) = @_;
+
+    # Find the tree.
+    my @results = $self->search(
+        {   'reconciliation_id' => $reconciliation_id,
+            'cvterm.name'       => $attribute_name,
+        },
+        { 'join' => 'cvterm' }
+    );
+
+    return map { $_->value() } @results;
+}
+
+1;
+__END__
diff --git a/lib/IPlant/TreeRec/GeneFamilyInfo.pm b/lib/IPlant/TreeRec/GeneFamilyInfo.pm
@@ -438,10 +438,11 @@ Readonly my %EMPTY_SUMMARY => (
         my $dbh = $dbh_of{ ident $self };
 
         # Get the number of duplications.
-        my @results = eval { $dbh->resultset('DuplicationCount')
-            ->search( {}, { 'bind' => [ $reconciliation_id ] } ) };
-        warn $EVAL_ERROR if $EVAL_ERROR;
-        return scalar @results > 0 ? $results[0]->duplication_count() : 0;
+        my @results = eval {
+            $dbh->resultset('ReconciliationAttribute')
+                ->get_values( $reconciliation_id, 'duplication' );
+        };
+        return scalar @results > 0 ? $results[0] : 0;
     }
 
     ##########################################################################
@@ -466,9 +467,10 @@ Readonly my %EMPTY_SUMMARY => (
         my $dbh = $dbh_of{ ident $self };
 
         # Get the number of speciations.
-        my @results = eval { $dbh->resultset('SpeciationCount')
-            ->search( {}, { 'bind' => [ $reconciliation_id ] } ) };
-        warn $EVAL_ERROR if $EVAL_ERROR;
+        my @results = eval {
+            $dbh->resultset('ReconciliationAttribute')
+                ->get_values( $reconciliation_id, 'speciation' );
+        };
         return scalar @results > 0 ? $results[0]->speciation_count() : 0;
     }
 

diff --git a/t/IPlant-TreeRec.t b/t/IPlant-TreeRec.t
@@ -5,7 +5,7 @@ use strict;
 
 #########################
 
-use Test::More tests => 71;
+use Test::More tests => 72;
 BEGIN { use_ok('IPlant::DB::TreeRec') };
 BEGIN { use_ok('IPlant::DB::TreeRec::Result::Cv') };
 BEGIN { use_ok('IPlant::DB::TreeRec::Result::Cvterm') };
@@ -49,6 +49,7 @@ BEGIN { use_ok('IPlant::DB::TreeRec::Result::SpeciesTreeNodePath') };
 BEGIN { use_ok('IPlant::DB::TreeRec::ResultSet::Family') };
 BEGIN { use_ok('IPlant::DB::TreeRec::ResultSet::ProteinTree') };
 BEGIN { use_ok('IPlant::DB::TreeRec::ResultSet::Reconciliation') };
+BEGIN { use_ok('IPlant::DB::TreeRec::ResultSet::ReconciliationAttribute') };
 BEGIN { use_ok('IPlant::DB::TreeRec::ResultSet::SpeciesTree') };
 BEGIN { use_ok('IPlant::DB::TreeRec::ResultSet::SpeciesTreeNode') };
 BEGIN { use_ok('IPlant::TreeRec') };