Merge pull request #385 from Ensembl/bugfix/ont_advisory

Make ontology term comparisons advisory.

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

@@ -39,15 +39,13 @@ use constant {
 sub tests {
   my ($self) = @_;
 
-  my $desc = 'Critical terms are present in term table';
-  my @critical_terms = (
-      "'EFO:0003900'"
-  );
-  my $len = @critical_terms;
+  my @critical_terms = qw/EFO:0003900/;
 
-  my $sql = "SELECT COUNT(*) FROM term WHERE accession IN (".join(', ', @critical_terms).")";
-
-  is_rows($self->dba, $sql, $len, $desc);
+  foreach (@critical_terms) {
+    my $desc = "Critical term $_ is present in term table";
+    my $sql = "SELECT accession FROM term WHERE accession = '$_'";
+    is_rows($self->dba, $sql, 1, $desc);
+  }
 }
 
 1;

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

@@ -29,9 +29,9 @@ extends 'Bio::EnsEMBL::DataCheck::DbCheck';
 
 use constant {
   NAME           => 'CompareOntologyTerm',
-  DESCRIPTION    => 'Compare Term counts between current and previous ontology database',
+  DESCRIPTION    => 'Compare namespace counts between current and previous ontology database',
   GROUPS         => ['ontologies'],
-  DATACHECK_TYPE => 'critical',
+  DATACHECK_TYPE => 'advisory',
   DB_TYPES       => ['ontology'],
   TABLES         => ['ontology', 'term']
 };

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

@@ -0,0 +1,58 @@
+=head1 LICENSE
+
+Copyright [2018-2021] 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::CompareOntologyTotal;
+
+use warnings;
+use strict;
+
+use Moose;
+use Test::More;
+use Bio::EnsEMBL::DataCheck::Test::DataCheck;
+
+extends 'Bio::EnsEMBL::DataCheck::DbCheck';
+
+use constant {
+  NAME           => 'CompareOntologyTotal',
+  DESCRIPTION    => 'Compare total counts between current and previous ontology database',
+  GROUPS         => ['ontologies'],
+  DATACHECK_TYPE => 'critical',
+  DB_TYPES       => ['ontology'],
+  TABLES         => ['ontology', 'term']
+};
+
+sub tests {
+  my ($self) = @_;
+
+  # Inherited code from DbCheck will always fail if the previous
+  # release's database cannot be found - so don't need to test
+  # for that here.
+  my $old_dba = $self->get_old_dba();
+
+  my $desc = 'Ontology term totals have not decreased in '.
+             $self->dba->dbc->dbname.' compared to '.$old_dba->dbc->dbname;
+  my $sql  = q/
+    SELECT ontology.name, COUNT(*) FROM
+      term INNER JOIN
+      ontology USING (ontology_id)
+    GROUP BY ontology.name
+  /;
+  row_subtotals($self->dba, $old_dba, $sql, undef, 1.00, $desc);
+}
+
+1;

lib/Bio/EnsEMBL/DataCheck/index.json

@@ -723,14 +723,23 @@
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::CompareMetaKeys"
    },
    "CompareOntologyTerm" : {
-      "datacheck_type" : "critical",
-      "description" : "Compare Term counts between current and previous ontology database",
+      "datacheck_type" : "advisory",
+      "description" : "Compare namespace counts between current and previous ontology database",
       "groups" : [
          "ontologies"
       ],
       "name" : "CompareOntologyTerm",
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::CompareOntologyTerm"
    },
+   "CompareOntologyTotal" : {
+      "datacheck_type" : "critical",
+      "description" : "Compare total counts between current and previous ontology database",
+      "groups" : [
+         "ontologies"
+      ],
+      "name" : "CompareOntologyTotal",
+      "package_name" : "Bio::EnsEMBL::DataCheck::Checks::CompareOntologyTotal"
+   },
    "ComparePhenotypeFeatures" : {
       "datacheck_type" : "advisory",
       "description" : "Compare phenotype feature counts between two databases, categorised by source",