Merge pull request #114 from markmcdowall/patch-1

Update DBEntryAdaptor.pm

modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm

@@ -896,10 +896,11 @@ sub _store_object_xref_mapping {
           my $group = $annotext->{$ax_group};
           my $gsth = $self->prepare( " 
                   INSERT INTO associated_group 
-                    SET description = ?;" );
-          $sth->bind_param( 1, $ax_group,     SQL_INTEGER );
+                    ( description )
+                  VALUES ( ? )" );
+          $gsth->bind_param( 1, $ax_group,     SQL_VARCHAR );
           $gsth->execute();
-          my $associatedGid = $self->last_insert_id();
+          my $associatedGid = $self->last_insert_id('associated_group_id', undef, 'associated_group');
           
           foreach my $ax_rank (sort keys %{ $group }) {
             my @ax = @{ $group->{$ax_rank} };
@@ -907,9 +908,14 @@ sub _store_object_xref_mapping {
             my $associatedXid = undef;
             my $sourceXid = undef;
             
-            $ax[0]->is_stored( $self->dbc ) || $self->store($ax[0]);
+            if (!$ax[0]->dbID) {
+              $self->store($ax[0]);
+            }
             $associatedXid = $ax[0]->dbID;
-            $ax[1]->is_stored( $self->dbc ) || $self->store($ax[1]);
+
+            if (!$ax[1]->dbID) {
+              $self->store($ax[1]);
+            }
             $sourceXid = $ax[1]->dbID;
             
             if (!defined $associatedXid || !defined $sourceXid) {
@@ -1622,7 +1628,11 @@ $where_sql";
                                 ? $self->fetch_by_dbID($source_associated_xref_id)
                                 : undef );
             if ( defined($associated_xref) ) {
-              $exDB->add_linked_associated_xref( $associated_xref, $source_associated_xref, $condition_type || '', $associate_group_id, $associate_group_rank );
+              my $ct = '';
+              if ( defined $condition_type ) {
+                $ct = $condition_type;
+              }
+              $exDB->add_linked_associated_xref( $associated_xref, $source_associated_xref, $ct, $associate_group_id, $associate_group_rank );
             }
           }
 
@@ -1673,7 +1683,11 @@ $where_sql";
                                 ? $self->fetch_by_dbID($source_associated_xref_id)
                                 : undef );
         if ( defined($associated_xref) ) {
-          $seen{$refID}->add_linked_associated_xref( $associated_xref, $source_associated_xref, $condition_type || '', $associate_group_id, $associate_group_rank );
+          my $ct = '';
+          if ( defined $condition_type ) {
+            $ct = $condition_type;
+          }
+          $seen{$refID}->add_linked_associated_xref( $associated_xref, $source_associated_xref, $ct, $associate_group_id, $associate_group_rank );
         }
         
         $linkage_types{$refID}->{$linkage_key} = 1;

modules/t/associated_xref.t

+# Copyright [1999-2016] 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.
+
+use strict;
+use warnings;
+
+use Test::More;
+use Test::Warnings;
+
+use Bio::EnsEMBL::Test::MultiTestDB;
+use Bio::EnsEMBL::Test::TestUtils;
+use Bio::EnsEMBL::Transcript;
+use Bio::EnsEMBL::DBSQL::DBEntryAdaptor;
+use Bio::EnsEMBL::DBEntry;
+
+note( "Startup test" );
+#
+# 1 Test started
+#
+ok(1);
+
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
+
+my $db = $multi->get_DBAdaptor( "core" );
+
+note( "Test database instantiated" );
+#
+# 2 Database instatiated
+#
+ok( $db );
+
+my $dbEntryAdaptor = $db->get_DBEntryAdaptor();
+
+#
+# 3 Get a gene to attach the term to
+#
+my $ga  = $db->get_adaptor('Gene');
+my $gene = $ga->fetch_by_stable_id("ENSG00000171456");
+debug("Gene->fetch_by_stable_id()");
+ok($gene);
+
+$multi->hide("core", 'xref', 'object_xref', 'associated_xref', 'associated_group');
+
+#
+# 4 Loading ontology terms and adding associate_xrefs
+#
+my $ont_xref = Bio::EnsEMBL::OntologyXref->new
+  (
+   -primary_id => "GO:0000001", 
+   -dbname => "GO",
+   -release => "1", 
+   -display_id => "Test GO term",
+   -description => "Amuch longer description of the GO term",
+   -info_type => "DIRECT",
+   -analysis => undef,
+   );   
+
+my $pmid_xref = Bio::EnsEMBL::DBEntry->new (
+                  -primary_id => "123456789",
+                  -dbname     => "PUBMED",
+                  -release    => "1",
+                  -display_id => "PMID:123456789",
+                  -description => "A paper",
+                  -info_type  => "DIRECT"
+                );
+
+my $during_xref = Bio::EnsEMBL::DBEntry->new (
+                  -primary_id => "GO:0007067",
+                  -dbname     => "GO",
+                  -release    => "1",
+                  -display_id => "mitotic nuclear division",
+                  -description => "A cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell.",
+                  -info_type  => "DIRECT"
+                );
+
+my $with_xref = Bio::EnsEMBL::DBEntry->new (
+                  -primary_id => "Q9BR19",
+                  -dbname     => "Uniprot/SPTREMBL",
+                  -release    => "1",
+                  -display_id => "Q9BR19",
+                  -info_type  => "DIRECT"
+                );
+
+$ont_xref->add_linkage_type( "IC", $pmid_xref ); # Linkage type on own
+
+$ont_xref->add_associated_xref(
+  $during_xref,
+  $pmid_xref,
+  "during",
+  1,
+  1
+);
+
+$ont_xref->add_associated_xref(
+  $with_xref,
+  $pmid_xref,
+  "with",
+  1,
+  2
+);
+
+
+my $ont_xref_id = $dbEntryAdaptor->store($ont_xref, $gene->dbID, "Gene");
+note("Xref_id from insert: ".$ont_xref_id);
+
+
+#
+# HC1 - Check that there are 2 entries in the associated_xref table
+#
+my $assoc_count = $db->dbc->prepare( 'select count(*) from associated_xref' );
+#$assoc_count->bind_param(1, $ont_xref_id);
+$assoc_count->execute();
+
+my ( $assoc_xref_count )  = $assoc_count->fetchrow_array();
+$assoc_count->finish();
+is($assoc_xref_count, 2, "Count in the associated_xref table.");
+
+
+#
+# HC2 - Check that there is a single entry in the associated_group table
+#
+$assoc_count = $db->dbc->prepare( 'select count(*) from associated_group' );
+$assoc_count->execute();
+
+( $assoc_xref_count )  = $assoc_count->fetchrow_array();
+
+is($assoc_xref_count, 1, "Count in the associated_group table.");
+$assoc_count->finish();
+
+
+#
+# 5 Retrieve associated_xref entries from the db.
+#
+my $gene2 = $ga->fetch_by_stable_id("ENSG00000171456");
+debug("Gene->fetch_by_stable_id()");
+ok($gene2, "Found the required gene");
+
+my @gene_DBentries = @{ $gene2->get_all_DBEntries() };
+my $ont_xref_retrieved = 0;
+my $ont_xref_hasAssoc  = 0;
+foreach my $dbentry (@gene_DBentries) {
+  if (ref $dbentry eq 'Bio::EnsEMBL::OntologyXref') {
+    if ($dbentry->dbname eq 'GO' and $dbentry->primary_id eq 'GO:0000001') {
+      $ont_xref_retrieved = 1;
+      my $annot_ext = $dbentry->get_all_associated_xrefs();
+      $ont_xref_hasAssoc  = scalar(keys %{ $annot_ext });
+    }
+  }
+}
+
+#
+# HC3 - Test the retrieval of the ontology term with paired asociated_xrefs
+#
+is($ont_xref_retrieved, 1, "Ontology DBEntry has been retrieved");
+is($ont_xref_hasAssoc, 1, "Count of the number associated xrefs");
+
+$multi->restore;
+
+done_testing();