SequenceOntologyMapper no longer required and functional cache

modules/Bio/EnsEMBL/IO/Translator/BulkFetcherFeature.pm

@@ -72,6 +72,9 @@ my %field_callbacks = (
     so_term          => 'so_term'
 );
 
+# caching of biotype to SO terms to improve speed
+my $so_cache = {};
+
 =head2 new
 
     Returntype   : Bio::EnsEMBL::IO::Translator::BulkFetcherFeature
@@ -81,7 +84,7 @@ my %field_callbacks = (
 sub new {
   my ($class, %args) = @_;
   
-  my @required_args = qw/version xref_mapping_file biotype_mapper adaptor/;
+  my @required_args = qw/version xref_mapping_file adaptor/;
   my @missing_args;
   map { push @missing_args, $_ unless exists $args{$_} } @required_args;
   confess "Missing arguments required by Bio::EnsEMBL::IO::Translator::BulkFetcherFeature" . join(',', @missing_args)
@@ -90,9 +93,6 @@ sub new {
   # this connects Ensembl to Identifiers.org amongst other things
   my $xref_mapping = Bio::EnsEMBL::Utils::RDF::Mapper->new($args{xref_mapping_file});
 
-  croak "Bio::EnsEMBL::IO::Translator::Feature requires a sequence ontology mapper"
-    unless $args{biotype_mapper}->isa('Bio::EnsEMBL::Utils::SequenceOntologyMapper');
-
   croak "Bio::EnsEMBL::IO::Translator::BulkFetcherFeature requires a DBAdaptor"
     unless $args{adaptor} and $args{adaptor}->isa('Bio::EnsEMBL::DBSQL::DBAdaptor');
   $args{meta_adaptor} = $args{adaptor}->get_MetaContainer();
@@ -104,9 +104,10 @@ sub new {
   croak "Unable to get a transcript adaptor"
     unless $args{transcript_adaptor}->isa('Bio::EnsEMBL::DBSQL::TranscriptAdaptor');
       
+  $args{biotype_adaptor} = $args{adaptor}->get_BiotypeAdaptor();
+
   delete $args{adaptor};
 
-  $args{ontology_cache} = {};
   $args{mapping} = $xref_mapping;
   
   my $self = $class->SUPER::new(\%args);
@@ -133,14 +134,9 @@ sub production_name {
   return $self->{production_name};
 }
 
-sub ontology_cache {
-  my $self = shift;
-  return $self->{ontology_cache};
-}
-
-sub ontology_adaptor {
+sub biotype_adaptor {
   my $self = shift;
-  return $self->{ontology_adaptor};
+  return $self->{biotype_adaptor};
 }
 
 sub meta_adaptor {
@@ -494,58 +490,25 @@ sub protein_features {
 =cut
 
 sub so_term {
-  my $self = shift;
-  my $object = shift;
-
-  my $so_term;
-  my ($type, $biotype) = ($self->type($object), $self->biotype($object));
-
-  if (!defined $biotype) {
-    # warn "Could not find biotype for SO term mapping\n";
-    return;
-  }
-
-  eval { 
-    if ($type eq 'gene') {
-      $so_term = $self->biotype_mapper->gene_biotype_to_name($biotype);
-    } elsif ($type eq 'transcript') {
-      $so_term = $self->biotype_mapper->transcript_biotype_to_name($biotype);
-    } else {
-      $so_term = $self->_ontology_id($biotype);
-    }
-  };
-
-  # TODO: better exception handling, e.g. look up ontology_cache?!
-  if ($@) { 
-    if (! exists $self->{ontology_cache}->{$biotype}) {
-      warn sprintf "Failed to map biotype %s to SO term\n", $biotype;
-      $self->{ontology_cache}->{$biotype} = undef;
-    }
-  }
-  
-  return $so_term;
-}
-
-# SO terms often required for dumping RDF
-sub _ontology_id {
-  my ($self, $term) = @_;
-  my $ontology_cache = $self->ontology_cache;
-  return $self->{$ontology_cache->{$term}} if $term and exists $self->{$ontology_cache->{$term}};
-
-  my ($typeterm) = @{ $self->ontology_adaptor->fetch_all_by_name( $term, 'SO' ) };
-    
-  unless ($typeterm) {
-    if($term) {
-      warn "Can't find SO term for biotype '$term'";
-      $self->{$ontology_cache->{$term}} = undef;  
-    }
-    return;
-  }
-    
-  my $id = $typeterm->accession;
-  $self->{$ontology_cache->{$term}} = $id;
-  
-  return $id;
+  my ($self, $object) = @_;
+
+  my $type = $self->type($object);
+  my $biotype = $self->biotype($object);
+
+  # Only type gene and transcript supported
+  return unless ($type eq 'gene' || $type eq 'transcript');
+
+  # look if term is cached
+  my $so_acc = $so_cache->{$type}{$biotype};
+
+  # if so return it
+  return $so_acc if defined $so_acc;
+
+  # else retrieve the so term using the biotype adaptor, and cache it
+  $so_acc = $self->biotype_adaptor->fetch_by_name_object_type($biotype, $type)->so_acc;
+  $so_cache->{$type}{$biotype} = $so_acc;
+
+  return $so_acc;
 }
 
 1;

modules/t/rdf/bulkfetcherfeature_translator.t

@@ -24,14 +24,9 @@ use Test::Exception;
 use JSON;
 
 use Bio::EnsEMBL::Test::MultiTestDB;
-use Bio::EnsEMBL::Utils::SequenceOntologyMapper;
 
 use_ok 'Bio::EnsEMBL::IO::Translator::BulkFetcherFeature';
 
-my $omulti = Bio::EnsEMBL::Test::MultiTestDB->new('ontology', "$Bin/..");
-my $ontology_adaptor =
-  $omulti->get_DBAdaptor('ontology')->get_OntologyTermAdaptor();
-
 my $multi = Bio::EnsEMBL::Test::MultiTestDB->new(undef, "$Bin/..");
 my $adaptor = $multi->get_DBAdaptor('core');
 my $meta_adaptor = $adaptor->get_MetaContainer();
@@ -41,11 +36,11 @@ my ($version, $production_name) =
    $meta_adaptor->list_value_by_key('species.production_name')->[0]
   );
 
-my $translator =
-  Bio::EnsEMBL::IO::Translator::BulkFetcherFeature->new(version => $version,
+my $translator = Bio::EnsEMBL::IO::Translator::BulkFetcherFeature->new(
+    version           => $version,
     xref_mapping_file => "$Bin/xref_LOD_mapping.json",
-							biotype_mapper    => Bio::EnsEMBL::Utils::SequenceOntologyMapper->new($omulti->get_DBAdaptor('ontology')->get_OntologyTermAdaptor()),
-							adaptor           => $adaptor);
+    adaptor           => $adaptor
+);
 
 ok($translator->version == $version, 'version');
 ok($translator->production_name eq $production_name, 'production name');
@@ -58,8 +53,7 @@ my $gene = from_json(slurp_file("$Bin/gene.json"));
 #
 # compare gene
 #
-my %gene_attrs =
-  (
+my %gene_attrs = (
    type => 'gene',
    id   => 'ENSG00000127720',
    name => 'METTL25',
@@ -74,13 +68,16 @@ my %gene_attrs =
    taxon_id => 9606,
    provenance => 'ANNOTATED',
    so_term => 'SO:0001217'
-  );
+);
+
 foreach my $attr (keys %gene_attrs) {
   is($translator->$attr($gene), $gene_attrs{$attr}, "gene $attr");
 }
+
 cmp_deeply($translator->synonyms($gene), [ 'C12orf26', 'FLJ22789' ], 'gene synonyms');
-cmp_deeply($translator->xrefs($gene)->[5],
-	   { display_id => 'METTL25',
+cmp_deeply(
+    $translator->xrefs($gene)->[5],
+     {display_id => 'METTL25',
        primary_id => 84190,
        info_type  => 'DEPENDENT',
        info_text  => '',
@@ -96,8 +93,7 @@ is($translator->uri($gene), "http://rdf.ebi.ac.uk/resource/ensembl/ENSG000001277
 my $transcripts = $translator->transcripts($gene);
 is(scalar @{$transcripts}, 11, 'number of transcripts');
 my $transcript = $transcripts->[0];
-my %transcript_attrs =
-  (
+my %transcript_attrs = (
    id => 'ENST00000248306',
    type => 'transcript',
    name => 'METTL25-201',
@@ -112,10 +108,12 @@ my %transcript_attrs =
    taxon_id => 9606,
    provenance => 'INFERRED_FROM_TRANSCRIPT',
    so_term => 'SO:0000234'
-  );
+);
+
 foreach my $attr (keys %transcript_attrs) {
   is($translator->$attr($transcript), $transcript_attrs{$attr}, "transcript $attr");
 }
+
 cmp_deeply($translator->synonyms($transcript), [], 'transcript synonyms');
 is(scalar @{$translator->xrefs($transcript)}, 19, 'number of transcript xrefs');
 cmp_deeply($translator->xrefs($transcript)->[13],
@@ -132,8 +130,7 @@ is($translator->uri($transcript), "http://rdf.ebi.ac.uk/resource/ensembl.transcr
 # compare exon
 is(scalar @{$translator->exons($transcript)}, 12, 'number of transcript exons');
 my $exon = $translator->exons($transcript)->[3];
-my %exon_attrs =
-  (
+my %exon_attrs = (
    end => 82476718,
    seq_region_name => '12',
    coord_system_name => 'chromosome',
@@ -144,10 +141,12 @@ my %exon_attrs =
    rank => 10,
    start => 82476644,
    so_term => undef
-  );
+);
+
 foreach my $attr (keys %exon_attrs) {
   is($translator->$attr($exon), $exon_attrs{$attr}, "exon $attr");
 }
+
 is($translator->uri($exon), "http://rdf.ebi.ac.uk/resource/ensembl.exon/ENSE00003483236", 'exon URI');
 
 # compare translation, its xrefs and protein features

modules/t/test-genome-DBs/homo_sapiens/core/biotype.txt

+64	protein_coding	gene	core,otherfeatures,rnaseq,vega,presite	\N	\N	coding	SO:0001217
+65	protein_coding	transcript	core,otherfeatures,rnaseq,vega,presite	\N	\N	coding	SO:0000234