Merge e9c1076 into c508cec

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

@@ -0,0 +1,63 @@
+
+=head1 LICENSE
+
+Copyright [2018-2023] 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::CompareSpeciesAlias;
+
+use warnings;
+use strict;
+
+use Moose;
+use Test::More;
+
+extends 'Bio::EnsEMBL::DataCheck::DbCheck';
+
+use constant {
+    NAME           => 'CompareSpeciesAlias',
+    DESCRIPTION    => 'Comparison of aliases between releases',
+    GROUPS         => [ 'core_handover' ],
+    DB_TYPES       => [ 'core' ],
+    TABLES         => [ 'meta' ],
+    DATACHECK_TYPE => 'advisory'
+
+};
+
+sub skip_tests {
+    my ($self) = @_;
+    my $old_dba = $self->get_old_dba();
+    if (not defined $old_dba) {
+        return (1, 'New database');
+    }
+}
+
+
+sub tests {
+    my ($self) = @_;
+    my $old_dba = $self->get_old_dba();
+    my $mca = $self->dba->get_adaptor('MetaContainer');
+    my $old_mca = $old_dba->get_adaptor('MetaContainer');
+
+    my @new_alias = $mca->list_value_by_key('species.alias');
+    my @old_alias = $old_mca->list_value_by_key('species.alias');
+
+    my $description = 'Number of species.aliases did not decrease';
+    ok($#old_alias <= $#new_alias, $description );
+
+}
+
+1;

lib/Bio/EnsEMBL/DataCheck/index.json

@@ -994,6 +994,15 @@
       "name" : "CompareSource",
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::CompareSource"
    },
+   "CompareSpeciesAlias" : {
+      "datacheck_type" : "advisory",
+      "description" : "Comparison of aliases between releases",
+      "groups" : [
+         "core_handover"
+      ],
+      "name" : "CompareSpeciesAlias",
+      "package_name" : "Bio::EnsEMBL::DataCheck::Checks::CompareSpeciesAlias"
+   },
    "CompareStableIdsMapping" : {
       "datacheck_type" : "critical",
       "description" : "Stable IDs have been mapped between old and new databases",