Merge pull request #133 from Ensembl/stable_id_display_xref

Stable id display xref

lib/Bio/EnsEMBL/DataCheck/Checks/StableIdDisplayXref.pm

@@ -0,0 +1,62 @@
+=head1 LICENSE
+
+Copyright [2018-2019] 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.
+
+=cut
+
+package Bio::EnsEMBL::DataCheck::Checks::StableIdDisplayXref;
+
+use warnings;
+use strict;
+
+use Moose;
+use Test::More;
+use Bio::EnsEMBL::DataCheck::Test::DataCheck;
+
+extends 'Bio::EnsEMBL::DataCheck::DbCheck';
+
+use constant {
+  NAME           => 'StableIdDisplayXref',
+  DESCRIPTION    => 'Genes/Transcript display_xref does not have display_label set as stable_id',
+  GROUPS         => ['xref'],
+  DB_TYPES       => ['core'],
+  TABLES         => ['gene','transcript','xref']
+};
+
+sub tests {
+  my ($self) = @_;
+  $self->check_display_xref('gene');
+  $self->check_display_xref('transcript');
+}
+
+sub check_display_xref {
+  my ($self, $table) = @_;
+  my $species_id = $self->dba->species_id;
+  my $desc = "No $table found with stable_id set as display_xrefs";
+  my $diag = "$table found with stable_id set as display_xrefs";
+  my $sql  = qq/
+    SELECT stable_id FROM
+      $table tb JOIN 
+      xref x on (tb.display_xref_id=x.xref_id) JOIN
+      seq_region sr USING (seq_region_id) INNER JOIN
+      coord_system cs USING (coord_system_id)
+    WHERE x.display_label=tb.stable_id AND
+      cs.species_id = $species_id
+  /;
+
+  is_rows_zero($self->dba, $sql, $desc, $diag);
+}
+
+1;

lib/Bio/EnsEMBL/DataCheck/index.json

@@ -1225,6 +1225,15 @@
       "name" : "StableIDUnique",
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::StableIDUnique"
    },
+   "StableIdDisplayXref" : {
+      "datacheck_type" : "critical",
+      "description" : "Genes/Transcript display_xref does not have display_label set as stable_id",
+      "groups" : [
+         "xref"
+      ],
+      "name" : "StableIdDisplayXref",
+      "package_name" : "Bio::EnsEMBL::DataCheck::Checks::StableIdDisplayXref"
+   },
    "StructuralVariationFeature" : {
       "datacheck_type" : "critical",
       "description" : "StructuralVariationFeature table data is present and correct",