refactor to move some gene search code into GeneSearch util module fr…

…om gene plugin module
htgt · Aug 22, 2012 · d24fbe2 · d24fbe2
1 parent 8c7bc75
commit d24fbe2
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Showing 2 changed files with 101 additions and 69 deletions.
diff --git a/lib/LIMS2/Model/Plugin/Gene.pm b/lib/LIMS2/Model/Plugin/Gene.pm
@@ -4,12 +4,9 @@ use strict;
 use warnings FATAL => 'all';
 
 use Moose::Role;
-use Const::Fast;
 use Data::Dump 'pp';
 use namespace::autoclean;
-
-const my $MGI_ACCESSION_ID_RX => qr/^MGI:\d+$/;
-const my $ENSEMBL_GENE_ID_RX  => qr/^ENS[A-Z]*G\d+$/;
+use LIMS2::Model::Util::GeneSearch qw( retrieve_solr_gene retrieve_ensembl_gene normalize_solr_result );
 
 requires qw( schema check_params throw retrieve log trace );
 
@@ -45,11 +42,12 @@ sub search_genes {
     my @genes;
 
     if ( $species eq 'Mouse' ) {
-        @genes = map { $self->_normalize_solr_result( $_ ) }
+        @genes = map { normalize_solr_result( $_ ) }
             @{ $self->solr_query( $validated_params->{search_term} ) };
     }
     elsif ( $species eq 'Human' ) {
-        @genes = ( $self->retrieve_gene( $validated_params ) || () );
+        my $genes = $self->retrieve_gene( $validated_params ) || [];
+        @genes = @{ $genes };
     }
     else {
         LIMS2::Exception::Implementation->throw( "search_genes() for species '$species' not implemented" );
@@ -82,83 +80,23 @@ sub retrieve_gene {
     if ( $species eq 'Mouse' ) {
         return $self->_gene_cache_mouse->compute(
             $validated_params->{search_term}, undef, sub {
-                $self->_retrieve_solr_gene( $validated_params );
+                retrieve_solr_gene( $self, $validated_params );
             }
         );
     }
 
     if ( $species eq 'Human' ) {
         return $self->_gene_cache_human->compute(
             $validated_params->{search_term}, undef, sub {
-                $self->_retrieve_ensembl_gene( $validated_params );
+                retrieve_ensembl_gene( $self, $validated_params );
             }
         );
     }
 
-    $self->throw( Implementation => "retrieve_gene() for species $species not implemented" );
+    $self->throw( Implementation => "retrieve_gene() for species '$species' not implemented" );
 }
 ## use critic
 
-sub _retrieve_solr_gene {
-    my ( $self, $params ) = @_;
-
-    my $search_term = $params->{search_term};
-
-    my $genes;
-
-    if ( $search_term =~ $MGI_ACCESSION_ID_RX ) {
-        $genes = $self->solr_query( [ mgi_accession_id => $search_term ] );
-    }
-    elsif ( $search_term =~ $ENSEMBL_GENE_ID_RX ) {
-        $genes = $self->solr_query( [ ensembl_gene_id => $search_term ] );
-    }
-    else {
-        $genes = $self->solr_query( [ marker_symbol_str => $search_term ] );
-    }
-
-    if ( @{$genes} == 0 ) {
-        $self->throw( NotFound => { entity_class => 'Gene', search_params => $params } );
-    }
-
-    if ( @{$genes} > 1 ) {
-        $self->throw( Implementation => "Retrieval of gene Mouse/$search_term returned " . @{$genes} . " genes" );
-    }
-
-    return $self->_normalize_solr_result( shift @{$genes} );
-}
-
-sub _retrieve_ensembl_gene {
-    my ( $self, $params ) = @_;
-
-    if ( $params->{search_term} =~ $ENSEMBL_GENE_ID_RX ) {
-        my $gene = $self->ensembl_gene_adaptor( $params->{species} )->fetch_by_stable_id( $params->{search_term} )
-            or $self->throw( NotFound => { entity_class => 'Gene', search_params => $params } );
-        return { gene_id => $gene->stable_id, gene_symbol => $gene->external_name };
-    }
-
-    my $genes = $self->ensembl_gene_adaptor( $params->{species} )->fetch_all_by_external_name( $params->{search_term} );
-
-    if ( @{$genes} == 0 ) {
-        $self->throw( NotFound => { entity_class => 'Gene', search_params => $params } );
-    }
-
-    if ( @{$genes} > 1 ) {
-        $self->throw( Implementation => "Retrieval of gene $params->{species}/$params->{search_term} returned " . @{$genes} . " genes" );
-    }
-
-    return { gene_id => $genes->[0]->stable_id, gene_symbol => $genes->[0]->external_name };
-}
-
-sub _normalize_solr_result {
-    my ( $self, $solr_result ) = @_;
-
-    my %normalized = %{ $solr_result };
-
-    $normalized{gene_id}     = delete $normalized{mgi_accession_id};
-    $normalized{gene_symbol} = delete $normalized{marker_symbol};
-
-    return \%normalized;
-}
 
 1;
 

diff --git a/lib/LIMS2/Model/Util/GeneSearch.pm b/lib/LIMS2/Model/Util/GeneSearch.pm
@@ -0,0 +1,94 @@
+package LIMS2::Model::Util::GeneSearch;
+
+use strict;
+use warnings FATAL => 'all';
+
+use Sub::Exporter -setup => {
+    exports => [
+        qw(
+            retrieve_solr_gene
+            retrieve_ensembl_gene
+            normalize_solr_result
+          )
+    ]
+};
+
+use Log::Log4perl qw( :easy );
+use Const::Fast;
+use LIMS2::Exception::NotFound;
+use LIMS2::Exception::Implementation;
+
+const my $MGI_ACCESSION_ID_RX => qr/^MGI:\d+$/;
+const my $ENSEMBL_GENE_ID_RX  => qr/^ENS[A-Z]*G\d+$/;
+
+sub retrieve_solr_gene {
+    my ( $model, $params ) = @_;
+
+    my $search_term = $params->{search_term};
+
+    my $genes;
+
+    if ( $search_term =~ $MGI_ACCESSION_ID_RX ) {
+        $genes = $model->solr_query( [ mgi_accession_id => $search_term ] );
+    }
+    elsif ( $search_term =~ $ENSEMBL_GENE_ID_RX ) {
+        $genes = $model->solr_query( [ ensembl_gene_id => $search_term ] );
+    }
+    else {
+        $genes = $model->solr_query( [ marker_symbol_str => $search_term ] );
+    }
+
+    if ( @{$genes} == 0 ) {
+        LIMS2::Exception::NotFound->throw( { entity_class => 'Gene', search_params => $params } );
+    }
+
+    if ( @{$genes} > 1 ) {
+        LIMS2::Exception::Implementation->throw(
+            "Retrieval of gene Mouse/$search_term returned " . @{$genes} . " genes" );
+    }
+
+    return normalize_solr_result( shift @{$genes} );
+}
+
+sub retrieve_ensembl_gene {
+    my ( $model, $params ) = @_;
+
+    if ( $params->{search_term} =~ $ENSEMBL_GENE_ID_RX ) {
+        my $gene = $model->ensembl_gene_adaptor( $params->{species} )
+            ->fetch_by_stable_id( $params->{search_term} )
+                or LIMS2::Exception::NotFound->throw( { entity_class => 'Gene', search_params => $params } );
+
+        return { gene_id => $gene->stable_id, gene_symbol => $gene->external_name };
+    }
+
+    my $genes = $model->ensembl_gene_adaptor( $params->{species} )
+        ->fetch_all_by_external_name( $params->{search_term} );
+
+    if ( @{$genes} == 0 ) {
+        LIMS2::Exception::NotFound->throw( { entity_class => 'Gene', search_params => $params } );
+    }
+
+    if ( @{$genes} > 1 ) {
+        LIMS2::Exception::Implementation->throw(
+            "Retrieval of gene $params->{species}/$params->{search_term} returned "
+            . @{$genes} . " genes"
+        );
+    }
+
+    return { gene_id => $genes->[0]->stable_id, gene_symbol => $genes->[0]->external_name };
+}
+
+sub normalize_solr_result {
+    my ( $solr_result ) = @_;
+
+    my %normalized = %{ $solr_result };
+
+    $normalized{gene_id}     = delete $normalized{mgi_accession_id};
+    $normalized{gene_symbol} = delete $normalized{marker_symbol};
+
+    return \%normalized;
+}
+
+1;
+
+__END__