Merge bdfa9cf into d835b91

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

@@ -0,0 +1,65 @@
+=head1 LICENSE
+
+Copyright [2018] 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::SampleRegulatoryFeatureExists;
+
+use warnings;
+use strict;
+
+use Moose;
+use Test::More;
+use Bio::EnsEMBL::DataCheck::Test::DataCheck;
+use Bio::EnsEMBL::DataCheck::Utils qw/sql_count/;
+
+extends 'Bio::EnsEMBL::DataCheck::DbCheck';
+
+use constant {
+  NAME        => 'SampleRegulatoryFeatureExists',
+  DESCRIPTION => 'Check if the current regulatory build has a sample regulatory feature',
+  GROUPS      => ['funcgen_integrity', 'funcgen_Post_regulatory_build'],
+  DB_TYPES    => ['funcgen'],
+  TABLES      => ['regulatory_build','regulatory_feature'],
+};
+
+sub skip_tests {
+  my ($self) = @_;
+
+  my $sql = q/
+    SELECT COUNT(name) FROM regulatory_build 
+    WHERE is_current=1
+  /;
+
+  if (! sql_count($self->dba, $sql) ) {
+    return (1, 'The database has no regulatory build');
+  }
+}
+
+sub tests {
+  my ($self) = @_;
+  my $desc = "Current regulatory build has a sample regulatory feature";
+  my $sql  = qq/
+    SELECT regulatory_build.name FROM
+      regulatory_build JOIN 
+      regulatory_feature ON (regulatory_build.sample_regulatory_feature_id=regulatory_feature.regulatory_feature_id and regulatory_build.regulatory_build_id=regulatory_feature.regulatory_build_id) 
+    WHERE regulatory_feature.stable_id is not null
+  /;
+  is_rows_nonzero($self->dba, $sql, $desc);
+}
+
+1;
+

lib/Bio/EnsEMBL/DataCheck/index.json

@@ -201,6 +201,16 @@
       "name" : "PhenotypeDescription",
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::PhenotypeDescription"
    },
+   "SampleRegulatoryFeatureExists" : {
+      "datacheck_type" : "critical",
+      "description" : "Check if the current regulatory build has a sample regulatory feature",
+      "groups" : [
+         "funcgen_integrity",
+         "funcgen_Post_regulatory_build"
+      ],
+      "name" : "SampleRegulatoryFeatureExists",
+      "package_name" : "Bio::EnsEMBL::DataCheck::Checks::SampleRegulatoryFeatureExists"
+   },
    "SchemaVersion" : {
       "datacheck_type" : "critical",
       "description" : "Check that the schema version meta_key matches the DB name",