Merge pull request #233 from helensch/fix/indiv-type

Updates to IndividualType and EmptyVariationTables
Ensembl · Apr 22, 2020 · 246dbce · 246dbce
2 parents 9680622 + f5c4132
commit 246dbce
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Showing 2 changed files with 26 additions and 6 deletions.
diff --git a/lib/Bio/EnsEMBL/DataCheck/Checks/EmptyVariationTables.pm b/lib/Bio/EnsEMBL/DataCheck/Checks/EmptyVariationTables.pm
@@ -146,7 +146,7 @@ sub get_tables_to_check {
   # Remove citation tables for species without citation database
   my @species_with_citations = qw/
      bos_taurus
-     canis_familiaris
+     canis_lupus_familiaris
      capra_hircus
      danio_rerio
      equus_caballus

diff --git a/lib/Bio/EnsEMBL/DataCheck/Checks/IndividualType.pm b/lib/Bio/EnsEMBL/DataCheck/Checks/IndividualType.pm
@@ -24,6 +24,7 @@ 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';
 
@@ -35,6 +36,16 @@ use constant {
   TABLES      => ['individual'],
 };
 
+sub skip_tests {
+  my ($self) = @_;
+
+  my $sql = 'SELECT COUNT(*) FROM individual';
+
+  if (! sql_count($self->dba, $sql) ) {
+    return (1, 'No individual records.');
+  }
+}
+
 sub tests {
   my ($self) = @_;
 
@@ -49,18 +60,20 @@ sub tests {
         WHERE individual_type_id != 1
     /;
     is_rows_zero($self->dba, $sql_1, $desc, $diag);
+    return;
   }
 
-  if($species =~ /canis_familiaris|danio_rerio|
+  if($species =~ /canis_lupus_familiaris|danio_rerio|
                   gallus_gallus|rattus_norvegicus|
                   bos_taurus|ornithorhynchus_anatinus|
                   pongo_abelii/) {
-  my $sql_2 = q/
+    my $sql_2 = q/
       SELECT COUNT(*)
       FROM individual
       WHERE individual_type_id != 2
-  /; 
-  is_rows_zero($self->dba, $sql_2, $desc, $diag);
+    /;
+    is_rows_zero($self->dba, $sql_2, $desc, $diag);
+    return;
   } 
 
   if($species =~ /anopheles_gambiae/) {
@@ -71,6 +84,7 @@ sub tests {
         AND individual_type_id != 3
     /;
     is_rows_zero($self->dba, $sql_3, $desc, $diag);
+    return;
   }
 
   if($species =~ /homo_sapiens|pan_troglodytes|tetraodon_nigroviridis/) {
@@ -80,9 +94,15 @@ sub tests {
         WHERE individual_type_id != 3
     /;
     is_rows_zero($self->dba, $sql_4, $desc, $diag);
+    return;
+  }
+
+  # There are individual records but no species specific individual type checks
+  # SKIP the check so that it is not reported as a failure
+  SKIP: {
+     skip "No individual_type_id check" , 1;
   }
 
 }
 
 1;
-