Merge bfb6526 into c59936e

Ensembl · Sep 9, 2019 · dabe3e1 · dabe3e1
2 parents c59936e + bfb6526
commit dabe3e1
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Showing 2 changed files with 26 additions and 16 deletions.
diff --git a/...EnsEMBL/DataCheck/Checks/XrefHTMLBlank.pm → ...io/EnsEMBL/DataCheck/Checks/XrefFormat.pm b/...EnsEMBL/DataCheck/Checks/XrefHTMLBlank.pm → ...io/EnsEMBL/DataCheck/Checks/XrefFormat.pm
@@ -16,7 +16,7 @@ limitations under the License.
 
 =cut
 
-package Bio::EnsEMBL::DataCheck::Checks::XrefHTMLBlank;
+package Bio::EnsEMBL::DataCheck::Checks::XrefFormat;
 
 use warnings;
 use strict;
@@ -28,8 +28,8 @@ use Bio::EnsEMBL::DataCheck::Test::DataCheck;
 extends 'Bio::EnsEMBL::DataCheck::DbCheck';
 
 use constant {
-  NAME           => 'XrefHTMLBlank',
-  DESCRIPTION    => 'Xrefs dont have HTML markups nor blank rows',
+  NAME           => 'XrefFormat',
+  DESCRIPTION    => 'Xrefs do not have HTML markup, non-printing characters, or blank values',
   GROUPS         => ['xref'],
   DB_TYPES       => ['core'],
   TABLES         => ['xref'],
@@ -39,22 +39,32 @@ use constant {
 sub tests {
   my ($self) = @_;
 
-  my $desc = 'No xrefs appear to have HTML markup in the display_label';
-  my $diag = 'Xrefs appear to have HTML markup (<*>*</*>) in the display_label';
-  my $sql  = qq/
+  my $desc_1 = 'No xrefs appear to have HTML markup in the display_label';
+  my $diag_1 = 'HTML markup';
+  my $sql_1  = qq/
     SELECT display_label FROM xref
     WHERE display_label LIKE '%<%>%<\/%>%'/;
 
-  is_rows_zero($self->dba, $sql, $desc, $diag);
+  is_rows_zero($self->dba, $sql_1, $desc_1, $diag_1);
 
   foreach my $column ('dbprimary_acc','display_label'){
-    my $desc = "$column has no empty string values";
-    my $sql  = qq/
-      SELECT COUNT(*) FROM xref
+    my $desc_2 = "$column has no empty string values";
+    my $diag_2 = 'Empty value';
+    my $sql_2  = qq/
+      SELECT dbprimary_acc,display_label FROM xref
       WHERE $column = ''
     /;
-    is_rows_zero($self->dba, $sql, $desc);
+    is_rows_zero($self->dba, $sql_2, $desc_2, $diag_2);
   }
+
+  my $desc_3 = 'No xrefs descriptions have newlines, tabs or carriage returns';
+  my $diag_3 = 'Non-printing character';
+  my $sql_3  = qq/
+    SELECT dbprimary_acc,display_label FROM xref 
+    WHERE description like '%\r%' or description like '%\n%' or description like '%\t%'
+  /;
+
+  is_rows_zero($self->dba, $sql_3, $desc_3, $diag_3);
 }
 
-1;
+1;
diff --git a/lib/Bio/EnsEMBL/DataCheck/index.json b/lib/Bio/EnsEMBL/DataCheck/index.json
@@ -1433,14 +1433,14 @@
       "name" : "VariationSubset",
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::VariationSubset"
    },
-   "XrefHTMLBlank" : {
+   "XrefFormat" : {
       "datacheck_type" : "critical",
-      "description" : "Xrefs dont have HTML markups nor blank rows",
+      "description" : "Xrefs do not have HTML markup, non-printing characters, or blank values",
       "groups" : [
          "xref"
       ],
-      "name" : "XrefHTMLBlank",
-      "package_name" : "Bio::EnsEMBL::DataCheck::Checks::XrefHTMLBlank"
+      "name" : "XrefFormat",
+      "package_name" : "Bio::EnsEMBL::DataCheck::Checks::XrefFormat"
    },
    "XrefPrefixes" : {
       "datacheck_type" : "critical",