Merge e75d913 into a9a58c6

Ensembl · Apr 28, 2021 · 8872e8d · 8872e8d
2 parents a9a58c6 + e75d913
commit 8872e8d
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Showing 2 changed files with 25 additions and 15 deletions.
diff --git a/...MBL/DataCheck/Checks/AttribValuesExist.pm → ...MBL/DataCheck/Checks/TranscriptSupport.pm b/...MBL/DataCheck/Checks/AttribValuesExist.pm → ...MBL/DataCheck/Checks/TranscriptSupport.pm
@@ -16,7 +16,7 @@ limitations under the License.
 
 =cut
 
-package Bio::EnsEMBL::DataCheck::Checks::AttribValuesExist;
+package Bio::EnsEMBL::DataCheck::Checks::TranscriptSupport;
 
 use warnings;
 use strict;
@@ -28,19 +28,19 @@ use Bio::EnsEMBL::DataCheck::Test::DataCheck;
 extends 'Bio::EnsEMBL::DataCheck::DbCheck';
 
 use constant {
-  NAME           => 'AttribValuesExist',
-  DESCRIPTION    => 'Check that TSL and GENCODE attributes exist',
+  NAME           => 'TranscriptSupport',
+  DESCRIPTION    => 'Check for presence of TSL and GENCODE attributes, and CCDS xrefs',
   GROUPS         => ['core', 'geneset_support_level'],
   DATACHECK_TYPE => 'critical',
   DB_TYPES       => ['core'],
-  TABLES         => ['attrib_type', 'transcript', 'transcript_attrib']
+  TABLES         => ['attrib_type', 'external_db', 'object_xref', 'transcript', 'transcript_attrib', 'xref']
 };
 
 sub skip_tests {
   my ($self) = @_;
 
   if ( $self->species !~ /^(homo_sapiens|mus_musculus)$/ ) {
-    return (1, 'GENCODE/TSL attribs are only required for human and mouse');
+    return (1, 'GENCODE/TSL/CCDS are only required for human and mouse');
   }
 }
 
@@ -76,6 +76,16 @@ sub tests {
     WHERE code like 'tsl%'
   /;
   is_rows_nonzero($self->dba, $sql_2, $desc_2);
+
+  my $desc_3 = 'CCDS xrefs exist';
+  my $sql_3  = q/
+    SELECT COUNT(*) FROM
+      object_xref INNER JOIN
+      xref USING (xref_id) INNER JOIN
+      external_db USING (external_db_id)
+    WHERE db_name = 'CCDS';
+  /;
+  is_rows_nonzero($self->dba, $sql_3, $desc_3);
 }
 
 1;
diff --git a/lib/Bio/EnsEMBL/DataCheck/index.json b/lib/Bio/EnsEMBL/DataCheck/index.json
@@ -151,16 +151,6 @@
       "name" : "AssemblySeqregion",
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::AssemblySeqregion"
    },
-   "AttribValuesExist" : {
-      "datacheck_type" : "critical",
-      "description" : "Check that TSL and GENCODE attributes exist",
-      "groups" : [
-         "core",
-         "geneset_support_level"
-      ],
-      "name" : "AttribValuesExist",
-      "package_name" : "Bio::EnsEMBL::DataCheck::Checks::AttribValuesExist"
-   },
    "BlankEnums" : {
       "datacheck_type" : "critical",
       "description" : "Enum columns do not have empty string values",
@@ -2363,6 +2353,16 @@
       "name" : "TranscriptDisplayXrefSuffix",
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::TranscriptDisplayXrefSuffix"
    },
+   "TranscriptSupport" : {
+      "datacheck_type" : "critical",
+      "description" : "Check for presence of TSL and GENCODE attributes, and CCDS xrefs",
+      "groups" : [
+         "core",
+         "geneset_support_level"
+      ],
+      "name" : "TranscriptSupport",
+      "package_name" : "Bio::EnsEMBL::DataCheck::Checks::TranscriptSupport"
+   },
    "TranscriptVariation" : {
       "datacheck_type" : "critical",
       "description" : "TranscriptVariation data is present and correct",