Merge pull request #512 from Ensembl/update/check_annotation_source

Update/check annotation source

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

@@ -0,0 +1,56 @@
+=head1 LICENSE
+Copyright [2018-2022] 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::AnnotationSource;
+
+use warnings;
+use strict;
+
+use Moose;
+use Test::More;
+
+extends 'Bio::EnsEMBL::DataCheck::DbCheck';
+
+use constant {
+  NAME           => 'AnnotationSource',
+  DESCRIPTION    => 'If present, the annotation_source meta key must be from an approved list',
+  GROUPS         => ['rapid_release'],
+  DATACHECK_TYPE => 'critical',
+  DB_TYPES       => ['core'],
+  TABLES         => ['meta']
+};
+sub tests{
+  my ($self) = @_;
+
+  my $mca = $self->dba->get_adaptor('MetaContainer');
+
+ SKIP: {
+     my $method = $mca->single_value_by_key('genebuild.method');
+     if($method ne 'braker' && $method ne 'import' && $method ne 'external_annotation_import') {
+         skip "Annotation source key not needed for Ensembl builds", 1;
+     }
+
+     my $desc = "'species.annotation_source' meta_key exists";
+     my $annotation_source = lc($mca->single_value_by_key('species.annotation_source'));
+     ok($annotation_source, $desc);
+
+     my $sources = 'braker|genbank|refseq|community|flybase|wormbase|veupathdb|noninsdc';
+     my $source_desc = "Source is allowed";
+
+     skip 'species.annotation_source meta key does not exist', 1 unless defined $annotation_source;
+
+     like($annotation_source, qr/^$sources$/, $source_desc);
+  }
+
+
+}

lib/Bio/EnsEMBL/DataCheck/index.json

@@ -115,6 +115,15 @@
       "name" : "AnalysisWebDataFormat",
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::AnalysisWebDataFormat"
    },
+   "AnnotationSource" : {
+      "datacheck_type" : "critical",
+      "description" : "If present, the annotation_source meta key must be from an approved list",
+      "groups" : [
+         "rapid_release"
+      ],
+      "name" : "AnnotationSource",
+      "package_name" : "Bio::EnsEMBL::DataCheck::Checks::AnnotationSource"
+   },
    "Archive" : {
       "datacheck_type" : "critical",
       "description" : "Gene archive table is up to date",