Health check DescriptionNewlines converted to datacheck

Ensembl · Mar 17, 2020 · 10da1c5 · 10da1c5
1 parent 63d968e
commit 10da1c5
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Showing 2 changed files with 77 additions and 8 deletions.
diff --git a/lib/Bio/EnsEMBL/DataCheck/Checks/DescriptionNewlines.pm b/lib/Bio/EnsEMBL/DataCheck/Checks/DescriptionNewlines.pm
@@ -0,0 +1,52 @@
+=head1 LICENSE
+
+Copyright [2018-2020] 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::DescriptionNewlines;
+
+use warnings;
+use strict;
+
+use Moose;
+use Test::More;
+use Bio::EnsEMBL::DataCheck::Test::DataCheck;
+
+extends 'Bio::EnsEMBL::DataCheck::DbCheck';
+
+use constant {
+  NAME           => 'DescriptionNewlines',
+  DESCRIPTION    => 'Check for newlines and tabs in gene descriptions',
+  GROUPS         => ['xref'],
+  DATACHECK_TYPE => 'critical',
+  TABLES         => ['gene']
+};
+
+sub tests {
+  my ($self) = @_;
+
+  my $desc_1 = 'gene description does not contain  newlines and/or tabs';
+  my $sql_1  = qq/
+  	SELECT COUNT(*) 
+        FROM gene 
+        WHERE (LOCATE('\n', description) > 0 OR LOCATE('\t', description) > 0)
+  /;
+
+  is_rows_zero($self->dba, $sql_1, $desc_1);
+}
+
+1;
+
diff --git a/lib/Bio/EnsEMBL/DataCheck/index.json b/lib/Bio/EnsEMBL/DataCheck/index.json
@@ -897,6 +897,15 @@
       "name" : "DensitySNPs",
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::DensitySNPs"
    },
+   "DescriptionNewlines" : {
+      "datacheck_type" : "critical",
+      "description" : "Check for newlines and tabs in gene descriptions",
+      "groups" : [
+         "xref"
+      ],
+      "name" : "DescriptionNewlines",
+      "package_name" : "Bio::EnsEMBL::DataCheck::Checks::DescriptionNewlines"
+   },
    "DisplayableGenes" : {
       "datacheck_type" : "advisory",
       "description" : "Genes are displayable and have web_data attached to their analysis",
@@ -944,7 +953,8 @@
       "datacheck_type" : "critical",
       "description" : "Xrefs have been added twice with different descriptions or versions",
       "groups" : [
-         "xref"
+         "xref",
+         "core"
       ],
       "name" : "DuplicateXref",
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::DuplicateXref"
@@ -1090,7 +1100,8 @@
       "datacheck_type" : "critical",
       "description" : "All GO xrefs have an evidence",
       "groups" : [
-         "xref"
+         "xref",
+         "core"
       ],
       "name" : "GOXrefEvidence",
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::GOXrefEvidence"
@@ -1671,7 +1682,8 @@
       "datacheck_type" : "critical",
       "description" : "Protein coding gene/transcript display xrefs are not shared between species inside a collection. This can lead to species-specific synonyms being applied to the wrong species",
       "groups" : [
-         "xref"
+         "xref",
+         "core"
       ],
       "name" : "SharedDisplayXref",
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::SharedDisplayXref"
@@ -1747,7 +1759,8 @@
       "datacheck_type" : "critical",
       "description" : "Genes/Transcript display_xref does not have display_label set as stable_id",
       "groups" : [
-         "xref"
+         "xref",
+         "core"
       ],
       "name" : "StableIdDisplayXref",
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::StableIdDisplayXref"
@@ -1786,7 +1799,8 @@
       "datacheck_type" : "critical",
       "description" : "Transcripts do not have a display xref with a -20* suffix. These are created by the non-vert Xref pipeline unless a flag is enabled: http://www.ebi.ac.uk/seqdb/confluence/display/EnsGen/Xref+mapping#Xrefmapping-CustomisingXrefMapping(DisplayXrefs)",
       "groups" : [
-         "xref"
+         "xref",
+         "core"
       ],
       "name" : "TranscriptDisplayXrefSuffix",
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::TranscriptDisplayXrefSuffix"
@@ -1804,7 +1818,8 @@
       "datacheck_type" : "critical",
       "description" : "Gene display xrefs are only attached to UniProtKB Gene Names (Uniprot_gn)",
       "groups" : [
-         "xref"
+         "xref",
+         "core"
       ],
       "name" : "UniProtDisplayXref",
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::UniProtDisplayXref"
@@ -1824,7 +1839,8 @@
       "datacheck_type" : "critical",
       "description" : "Uniprot xrefs do not have Unreviewed as their primary DB accession",
       "groups" : [
-         "xref"
+         "xref",
+         "core"
       ],
       "name" : "UnreviewedXrefs",
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::UnreviewedXrefs"
@@ -1946,7 +1962,8 @@
       "datacheck_type" : "critical",
       "description" : "Xrefs do not have HTML markup, non-printing characters, or blank values",
       "groups" : [
-         "xref"
+         "xref",
+         "core"
       ],
       "name" : "XrefFormat",
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::XrefFormat"