Fix/check beta sample location meta value

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

@@ -43,13 +43,13 @@ sub tests {
   my $desc_1 = 'Sample gene has displayable analysis';
   my $diag_1 = 'Undisplayed analysis';
   my $sql_1  = qq/
-      SELECT gene_id 
+      SELECT gene_id
         FROM gene g
-  INNER JOIN meta m 
-          ON g.stable_id = m.meta_value 
-         AND m.meta_key = 'sample.gene_param'
+  INNER JOIN meta m
+          ON g.stable_id = m.meta_value
+         AND m.meta_key = 'genebuild.sample_gene'
   INNER JOIN analysis a ON g.analysis_id = a.analysis_id
-  INNER JOIN analysis_description ad 
+  INNER JOIN analysis_description ad
           ON g.analysis_id = ad.analysis_id AND ad.displayable = 0
     /;
 
@@ -58,13 +58,13 @@ sub tests {
   my $desc_2 = 'Sample gene has associated web_data';
   my $diag_2 = 'web_data is not set';
   my $sql_2  = qq/
-      SELECT gene_id 
+      SELECT gene_id
         FROM gene g
-  INNER JOIN meta m 
-          ON g.stable_id = m.meta_value 
-         AND m.meta_key = 'sample.gene_param'
+  INNER JOIN meta m
+          ON g.stable_id = m.meta_value
+         AND m.meta_key = 'genebuild.sample_gene'
   INNER JOIN analysis a ON g.analysis_id = a.analysis_id
-  INNER JOIN analysis_description ad 
+  INNER JOIN analysis_description ad
           ON g.analysis_id = ad.analysis_id AND ad.web_data IS NULL
     /;
 

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

@@ -0,0 +1,117 @@
+=head1 LICENSE
+
+Copyright [2018-2025] 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::DisplayableSampleLocation;
+
+use warnings;
+use strict;
+
+use Moose;
+use Test::More;
+use Bio::EnsEMBL::DataCheck::Test::DataCheck;
+
+extends 'Bio::EnsEMBL::DataCheck::DbCheck';
+
+use constant {
+  NAME        => 'DisplayableSampleLocation',
+  DESCRIPTION => 'Sample location is displayable and has web_data attached to its analysis',
+  GROUPS      => ['analysis_description', 'core', 'geneset', 'meta_sample'],
+  DB_TYPES    => ['core'],
+  TABLES      => ['gene', 'meta', 'seq_region']
+};
+
+sub tests {
+  my ($self) = @_;
+
+  my $species_id = $self->dba->species_id;
+
+  my $desc_1 = 'Sample location metadata exists exactly once';
+  my $diag_1 = 'genebuild.sample_location meta key should exist exactly once per species';
+  my $sql_1  = qq/
+      SELECT COUNT(*) AS count
+        FROM meta
+       WHERE meta_key = 'genebuild.sample_location'
+         AND species_id = $species_id
+      HAVING count != 1
+    /;
+
+  is_rows_zero($self->dba, $sql_1, $desc_1, $diag_1);
+
+  my $desc_2 = 'Sample location metadata is valid format';
+  my $diag_2 = 'genebuild.sample_location format is invalid';
+  my $sql_2  = qq/
+      SELECT meta_id
+        FROM meta
+       WHERE meta_key = 'genebuild.sample_location'
+         AND species_id = $species_id
+         AND meta_value NOT REGEXP '^.+:[0-9]+-[0-9]+\$'
+    /;
+
+  is_rows_zero($self->dba, $sql_2, $desc_2, $diag_2);
+
+  my $desc_3 = 'Sample location coordinates are properly ordered';
+  my $diag_3 = 'genebuild.sample_location start coordinate is greater than end coordinate';
+  my $sql_3  = qq/
+      SELECT meta_id
+        FROM meta
+       WHERE meta_key = 'genebuild.sample_location'
+         AND species_id = $species_id
+         AND CAST(SUBSTRING_INDEX(SUBSTRING_INDEX(meta_value, ':', -1), '-', 1) AS UNSIGNED) >
+             CAST(SUBSTRING_INDEX(meta_value, '-', -1) AS UNSIGNED)
+    /;
+
+  is_rows_zero($self->dba, $sql_3, $desc_3, $diag_3);
+
+  my $desc_4 = 'Sample location references valid seq_region';
+  my $diag_4 = 'genebuild.sample_location seq_region does not exist or coordinates out of bounds';
+  my $sql_4  = qq/
+      SELECT m.meta_id
+        FROM meta m
+        LEFT JOIN seq_region sr
+          ON SUBSTRING_INDEX(m.meta_value, ':', 1) = sr.name
+         AND CAST(SUBSTRING_INDEX(SUBSTRING_INDEX(m.meta_value, ':', -1), '-', 1) AS UNSIGNED) >= 1
+         AND CAST(SUBSTRING_INDEX(m.meta_value, '-', -1) AS UNSIGNED) <= sr.length
+       WHERE m.meta_key = 'genebuild.sample_location'
+         AND m.species_id = $species_id
+         AND sr.seq_region_id IS NULL
+    /;
+
+  is_rows_zero($self->dba, $sql_4, $desc_4, $diag_4);
+
+  my $desc_5 = 'Sample location contains at least one gene';
+  my $diag_5 = 'genebuild.sample_location region has no genes';
+  my $sql_5  = qq/
+      SELECT m.meta_id
+        FROM meta m
+        JOIN seq_region sr
+          ON SUBSTRING_INDEX(m.meta_value, ':', 1) = sr.name
+        LEFT JOIN gene g
+          ON g.seq_region_id = sr.seq_region_id
+         AND g.seq_region_start <= CAST(SUBSTRING_INDEX(m.meta_value, '-', -1) AS UNSIGNED)
+         AND g.seq_region_end >= CAST(SUBSTRING_INDEX(SUBSTRING_INDEX(m.meta_value, ':', -1), '-', 1) AS UNSIGNED)
+       WHERE m.meta_key = 'genebuild.sample_location'
+         AND m.species_id = $species_id
+         AND g.gene_id IS NULL
+    /;
+
+  is_rows_zero($self->dba, $sql_5, $desc_5, $diag_5);
+
+}
+
+1;
+