Extended DC to add extra check to make sure dbprimary_acc and display…

…_label does not have empty rows
Ensembl · Aug 29, 2019 · 9e7b196 · 9e7b196
1 parent be29aa1
commit 9e7b196
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Showing 2 changed files with 16 additions and 7 deletions.
diff --git a/lib/Bio/EnsEMBL/DataCheck/Checks/XrefHTML.pm → ...EnsEMBL/DataCheck/Checks/XrefHTMLBlank.pm b/lib/Bio/EnsEMBL/DataCheck/Checks/XrefHTML.pm → ...EnsEMBL/DataCheck/Checks/XrefHTMLBlank.pm
@@ -16,7 +16,7 @@ limitations under the License.
 
 =cut
 
-package Bio::EnsEMBL::DataCheck::Checks::XrefHTML;
+package Bio::EnsEMBL::DataCheck::Checks::XrefHTMLBlank;
 
 use warnings;
 use strict;
@@ -28,8 +28,8 @@ use Bio::EnsEMBL::DataCheck::Test::DataCheck;
 extends 'Bio::EnsEMBL::DataCheck::DbCheck';
 
 use constant {
-  NAME           => 'XrefHTML',
-  DESCRIPTION    => 'Xrefs dont have HTML markups',
+  NAME           => 'XrefHTMLBlank',
+  DESCRIPTION    => 'Xrefs dont have HTML markups nor blank rows',
   GROUPS         => ['xref'],
   DB_TYPES       => ['core'],
   TABLES         => ['xref'],
@@ -46,6 +46,15 @@ sub tests {
     WHERE display_label LIKE '%<%>%<\/%>%'/;
 
   is_rows_zero($self->dba, $sql, $desc, $diag);
+
+  foreach my $column ('dbprimary_acc','display_label'){
+    my $desc = "$column has no empty string values";
+    my $sql  = qq/
+      SELECT COUNT(*) FROM xref
+      WHERE $column = ''
+    /;
+    is_rows_zero($self->dba, $sql, $desc);
+  }
 }
 
 1;
diff --git a/lib/Bio/EnsEMBL/DataCheck/index.json b/lib/Bio/EnsEMBL/DataCheck/index.json
@@ -1369,14 +1369,14 @@
       "name" : "VariationSubset",
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::VariationSubset"
    },
-   "XrefHTML" : {
+   "XrefHTMLBlank" : {
       "datacheck_type" : "critical",
-      "description" : "Xrefs dont have HTML markups",
+      "description" : "Xrefs dont have HTML markups nor blank rows",
       "groups" : [
          "xref"
       ],
-      "name" : "XrefHTML",
-      "package_name" : "Bio::EnsEMBL::DataCheck::Checks::XrefHTML"
+      "name" : "XrefHTMLBlank",
+      "package_name" : "Bio::EnsEMBL::DataCheck::Checks::XrefHTMLBlank"
    },
    "XrefTypes" : {
       "datacheck_type" : "advisory",