Load allele comments when importing JSON

Refs #1779
pombase · May 23, 2019 · 9127b53 · 9127b53
1 parent 0ace6b3
commit 9127b53
Show file tree

Hide file tree

Showing 3 changed files with 8 additions and 2 deletions.
diff --git a/lib/Canto/Track/LoadUtil.pm b/lib/Canto/Track/LoadUtil.pm
@@ -936,6 +936,7 @@ sub create_sessions_from_json
 
         my $type = $allele_details->{type} || 'other';
         my $name = $allele_details->{name} || undef;
+        my $comment = $allele_details->{comment} || undef;
         my $description = $allele_details->{description} || undef;
         my $synonyms = $allele_details->{synonyms};
         my @args = ($allele_uniquename, $type, $name, $description, $gene, $synonyms);
@@ -958,6 +959,7 @@ sub create_sessions_from_json
           allele_display_name => lc $allele_object->display_name(),
           gene_display_name => lc $gene_display_name,
           identifier => "genotype-$allele_uniquename",
+          comment => $comment,
           taxonid => $default_organism_taxonid,
         };
       }
@@ -971,7 +973,8 @@ sub create_sessions_from_json
       for my $genotype_details (@genotype_details) {
         $genotype_manager->make_genotype(undef, undef, [$genotype_details->{allele}],
                                          $genotype_details->{taxonid},
-                                         $genotype_details->{identifier});
+                                         $genotype_details->{identifier}, undef,
+                                         $genotype_details->{comment});
       }
     }
 

diff --git a/t/60_load_util.t b/t/60_load_util.t
@@ -1,6 +1,6 @@
 use strict;
 use warnings;
-use Test::More tests => 15;
+use Test::More tests => 16;
 use Test::Exception;
 
 use Canto::TestUtil;
@@ -52,6 +52,8 @@ is($FBal0119310_allele->description(), 'description of FBal0119310');
 my $genotype_FBal0119310 =
   $created_cursdb->resultset('Genotype')->find({ identifier => "genotype-FBal0119310" });
 
+is($genotype_FBal0119310->comment(), 'comment on FBal0119310');
+
 my $FBal0119310_genotype_allele = ($genotype_FBal0119310->alleles()->all())[0];
 is ($FBal0119310_genotype_allele->allele_id(), $FBal0119310_allele->allele_id());
 

diff --git a/t/data/sessions_from_json_test.json b/t/data/sessions_from_json_test.json
@@ -9,6 +9,7 @@
         "type": "other",
         "name": "Dmel\\Cdk2_UAS.Tag:MYC",
         "description": "description of FBal0119310",
+        "comment": "comment on FBal0119310",
         "synonyms": ["UAS-Cdk2-myc", "UAS-Cdk2"]
       },
       "FBal0064432": {