Remove the exogenous_promoter field

Merge the contents of exogenous_promoter into the promoter_gene field. Refs #2823
pombase · Apr 17, 2024 · d0d3fb8 · d0d3fb8
1 parent 96a71c1
commit d0d3fb8
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Showing 31 changed files with 34 additions and 100 deletions.
diff --git a/Makefile.PL b/Makefile.PL
@@ -46,7 +46,7 @@ requires 'Exception::Class' => 1.40;
 requires 'Class::Container' => 0.12;
 requires 'Config::Any' => 0.27;
 requires 'DBD::Pg';
-requires 'DBD::SQLite' => 1.50;
+requires 'DBD::SQLite' => 1.74;
 requires 'DBIx::Class' => 0.082840;
 requires 'DBIx::Class::ResultClass::HashRefInflator';
 requires 'DBIx::Class::ResultSet::Data::Pageset' => 0.06;

diff --git a/canto.yaml b/canto.yaml
@@ -27,7 +27,7 @@ canto_url: https://curation.pombase.org/
 
 app_version: v1819
 
-schema_version: 35
+schema_version: 36
 
 ## Set this to create a Canto instance for a particular organism.  If not set,
 ## Canto will be in multi-organism mode and the multi_organism_mode will be set.

diff --git a/db_templates/curs_db_template.sqlite3 b/db_templates/curs_db_template.sqlite3
diff --git a/db_templates/ontology_index_dir/segments b/db_templates/ontology_index_dir/segments
diff --git a/db_templates/track_db_template.sqlite3 b/db_templates/track_db_template.sqlite3
diff --git a/etc/curs.sql b/etc/curs.sql
@@ -20,7 +20,6 @@ CREATE TABLE allele (
        name text,
        comment text,
        promoter_gene text,
-       exogenous_promoter text,
        gene integer REFERENCES gene(gene_id)
 );
 

diff --git a/lib/Canto/Curs/AlleleManager.pm b/lib/Canto/Curs/AlleleManager.pm
@@ -177,7 +177,6 @@ sub allele_from_json
   my $description = $json_allele->{description};
   my $expression = $json_allele->{expression};
   my $promoter_gene = $json_allele->{promoter_gene};
-  my $exogenous_promoter = $json_allele->{exogenous_promoter};
   my $allele_type = $json_allele->{type};
   my $gene_id = $json_allele->{gene_id};
   my $comment = $json_allele->{comment};
@@ -194,8 +193,7 @@ sub allele_from_json
 
     if ($allele) {
       if (($expression // '') eq ($allele->expression() // '') and
-          ($promoter_gene // '') eq ($allele->promoter_gene() // '') and
-          ($exogenous_promoter // '') eq ($allele->exogenous_promoter() // '')) {
+          ($promoter_gene // '') eq ($allele->promoter_gene() // '')) {
         return $allele;
       } else {
         # fall through and find another allele that matches, or create
@@ -254,8 +252,7 @@ sub allele_from_json
     if (($allele->name() // '') eq ($name // '') &&
         ($allele->description() // '') eq ($description // '') &&
         ($allele->expression() // '') eq ($expression // '') &&
-        ($allele->promoter_gene() // '') eq ($promoter_gene // '') &&
-        ($allele->exogenous_promoter() // '') eq ($exogenous_promoter // '')) {
+        ($allele->promoter_gene() // '') eq ($promoter_gene // '')) {
       set_allele_synonyms($schema, $allele, \@allele_synonyms);
 
       return $allele;
@@ -300,7 +297,6 @@ sub allele_from_json
     comment => $comment || undef,
     expression => $expression || undef,
     promoter_gene => $promoter_gene || undef,
-    exogenous_promoter => $exogenous_promoter || undef,
   );
 
   if ($allele_type =~ /_/) {
@@ -344,7 +340,6 @@ sub create_simple_allele
   my $name = shift;
   my $description = shift;
   my $promoter_gene = shift;
-  my $exogenous_promoter = shift;
   my $gene = shift;
   my $synonyms = shift;
 
@@ -354,7 +349,6 @@ sub create_simple_allele
     name => $name || undef,
     description => $description || undef,
     promoter_gene => $promoter_gene || undef,
-    exogenous_promoter => $exogenous_promoter || undef,
   );
 
   if ($allele_type !~ /^aberration/) {

diff --git a/lib/Canto/Curs/GenotypeManager.pm b/lib/Canto/Curs/GenotypeManager.pm
@@ -135,18 +135,16 @@ sub allele_hashes_in_config_order
       my $a_type = $a->{type};
       my $a_expression = $a->{expression};
       my $a_promoter_gene = $a->{promoter_gene};
-      my $a_exogenous_promoter = $a->{exogenous_promoter};
 
       my $b_name = $b->{name};
       my $b_description = $b->{description};
       my $b_type = $b->{type};
       my $b_expression = $b->{expression};
       my $b_promoter_gene = $b->{promoter_gene};
-      my $b_exogenous_promoter = $b->{exogenous_promoter};
 
-      "$a_name-$a_description-$a_type-$a_expression-$a_promoter_gene-$a_exogenous_promoter"
+      "$a_name-$a_description-$a_type-$a_expression-$a_promoter_gene"
         cmp
-      "$b_name-$b_description-$b_type-$b_expression-$b_promoter_gene-$b_exogenous_promoter"
+      "$b_name-$b_description-$b_type-$b_expression-$b_promoter_gene"
     } else {
       $res;
     }
@@ -174,7 +172,6 @@ sub _allele_string_from_json
     $ret{type} = $allele->type() // 'UNKNOWN';
     $ret{expression} = $allele->expression() // 'UNKNOWN';
     $ret{promoter_gene} = $allele->promoter_gene() // 'UNKNOWN';
-    $ret{exogenous_promoter} = $allele->exogenous_promoter() // 'UNKNOWN';
 
     $ret{allele} = $allele;
 

diff --git a/lib/Canto/Curs/Serialise.pm b/lib/Canto/Curs/Serialise.pm
@@ -550,9 +550,6 @@ sub _get_genotype_loci
     if ($allele->promoter_gene()) {
       $ret_hash{promoter_gene} = $allele->promoter_gene();
     }
-    if ($allele->exogenous_promoter()) {
-      $ret_hash{exogenous_promoter} = $allele->exogenous_promoter();
-    }
 
     my $locus = $allele_genotype->diploid();
 

diff --git a/lib/Canto/Curs/ServiceUtils.pm b/lib/Canto/Curs/ServiceUtils.pm
@@ -832,7 +832,6 @@ sub _allele_details_hash
     comment => $allele->comment(),
     allele_id => $allele->allele_id(),
     promoter_gene => $allele->promoter_gene(),
-    exogenous_promoter => $allele->exogenous_promoter(),
     synonyms => \@synonyms_list,
     notes => \%notes,
   );

diff --git a/lib/Canto/CursDB/Allele.pm b/lib/Canto/CursDB/Allele.pm
@@ -67,11 +67,6 @@ __PACKAGE__->table("allele");
   data_type: 'text'
   is_nullable: 1
 
-=head2 exogenous_promoter
-
-  data_type: 'text'
-  is_nullable: 1
-
 =head2 gene
 
   data_type: 'integer'
@@ -97,8 +92,6 @@ __PACKAGE__->add_columns(
   { data_type => "text", is_nullable => 1 },
   "promoter_gene",
   { data_type => "text", is_nullable => 1 },
-  "exogenous_promoter",
-  { data_type => "text", is_nullable => 1 },
   "gene",
   { data_type => "integer", is_foreign_key => 1, is_nullable => 1 },
 );
@@ -197,8 +190,8 @@ __PACKAGE__->belongs_to(
 );
 
 
-# Created by DBIx::Class::Schema::Loader v0.07049 @ 2023-06-14 20:50:03
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:tiJPC9Xx1sQThu4sXAHr4w
+# Created by DBIx::Class::Schema::Loader v0.07049 @ 2024-04-17 18:07:24
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:gIvlsUbVFK03pbSUaAW5MQ
 
 __PACKAGE__->many_to_many('genotypes' => 'allele_genotypes',
                           'genotype');
@@ -248,10 +241,6 @@ sub long_identifier
     $ret .= '{promoter:' . $self->promoter_gene() . '}';
   }
 
-  if ($self->exogenous_promoter()) {
-    $ret .= '{exogenous_promoter:' . $self->exogenous_promoter() . '}';
-  }
-
   return $ret;
 }
 

diff --git a/lib/Canto/DBUpgrade.pm b/lib/Canto/DBUpgrade.pm
@@ -781,6 +781,26 @@ CREATE TABLE genotype_interaction_with_phenotype (
 
     Canto::Track::curs_map($config, $track_schema, $update_proc);
   },
+
+  36 => sub {
+    my $config = shift;
+    my $track_schema = shift;
+
+    my $dbh = $track_schema->storage()->dbh();
+
+    my $update_proc = sub {
+      my $curs = shift;
+      my $curs_schema = shift;
+
+      my $curs_dbh = $curs_schema->storage()->dbh();
+
+      $curs_dbh->do("UPDATE allele SET promoter_gene = exogenous_promoter, exogenous_promoter = NULL WHERE exogenous_promoter IS NOT NULL;");
+      $curs_dbh->do("ALTER TABLE allele DROP COLUMN exogenous_promoter;");
+0    };
+
+    Canto::Track::curs_map($config, $track_schema, $update_proc);
+  },
+
 );
 
 sub upgrade_to

diff --git a/root/static/js/canto-modules.js b/root/static/js/canto-modules.js
@@ -4121,15 +4121,14 @@ var alleleEditDialogCtrl =
     $scope.alleleData.description = $scope.alleleData.description || '';
     $scope.alleleData.type = $scope.alleleData.type || '';
     $scope.alleleData.expression = $scope.alleleData.expression || '';
+    $scope.alleleData.promoter_gene = $scope.alleleData.promoter_gene || '';
     $scope.alleleData.evidence = $scope.alleleData.evidence || '';
     $scope.alleleData.synonyms = $scope.alleleData.synonyms || [];
     $scope.alleleData.existingSynonyms = [];
     $scope.alleleData.newSynonyms = [];
     $scope.genes = null;
-    $scope.promoterSelect = 'none';
 
     $scope.data = {
-      promoterGeneId: null,
       newSynonymsString: '',
       alleleGene: null,
       organismShortDisplayName: null,
@@ -4197,11 +4196,6 @@ var alleleEditDialogCtrl =
 
         $.map($scope.genes,
               (gene) => {
-                if (typeof($scope.alleleData.promoter_gene) != 'undefined') {
-                  if (gene.primary_identifier == $scope.alleleData.promoter_gene) {
-                    $scope.data.promoterGeneId = gene.gene_id;
-                  }
-                }
                 if (gene.primary_identifier == $scope.alleleData.gene_systematic_id) {
                   $scope.data.alleleGene = gene;
                   if (gene && gene.organism && gene.organism.full_name) {
@@ -4211,13 +4205,6 @@ var alleleEditDialogCtrl =
                 }
               });
 
-        if ($scope.data.promoterGeneId) {
-          $scope.promoterSelect = 'gene';
-        } else {
-          if ($scope.alleleData.exogenous_promoter) {
-            $scope.promoterSelect = 'exogenous';
-          }
-        }
       }).catch(function (err) {
         toaster.pop('note', "couldn't read the gene list from the server");
       });
@@ -4470,28 +4457,6 @@ var alleleEditDialogCtrl =
           $scope.okInProgress = true;
           splitSynonymsForStoring($scope.alleleData, $scope.data.newSynonymsString);
           copyObject($scope.alleleData, args.allele);
-          if ($scope.data.promoterGeneId == null) {
-            args.allele.promoter_gene = null;
-          } else {
-            $.map($scope.genes,
-                  (gene) => {
-                    if (gene.gene_id == $scope.data.promoterGeneId) {
-                      args.allele.promoter_gene = gene.primary_identifier;
-                    }
-                  });
-          }
-
-          if ($scope.showPromoterOpts()) {
-            if ($scope.promoterSelect != 'gene') {
-              delete args.allele.promoter_gene;
-            }
-            if ($scope.promoterSelect != 'exogenous') {
-              delete args.allele.exogenous_promoter;
-            }
-          } else {
-            delete args.allele.promoter_gene;
-            delete args.allele.exogenous_promoter;
-          }
 
           var strainName = null;
           if ($scope.strainData.selectedStrain) {
@@ -5070,8 +5035,7 @@ var genotypeEdit =
             allele1.gene_id === allele2.gene_id &&
             (allele1.expression || '') === (allele2.expression || '') &&
             (allele1.name || '') === (allele2.name || '') &&
-            (allele1.promoter_gene || '') === (allele2.promoter_gene || '') &&
-            (allele1.exogenous_promoter || '') === (allele2.exogenous_promoter || '');
+            (allele1.promoter_gene || '') === (allele2.promoter_gene || '');
         };
 
         $scope.findExistingAllele = function (alleleData) {

diff --git a/root/static/ng_templates/allele_edit.html b/root/static/ng_templates/allele_edit.html
@@ -236,27 +236,8 @@ <h4 class="modal-title">
       </table>
 
       <div class="curs-allele-promoter ng-cloak" ng-show="showPromoterOpts()">
-        Promoter:
-        <div>
-          <input id="promoter-none" type="radio" value="none" ng-model="promoterSelect">
-          <label for="promoter-none">Unspecified</label>
-        </div>
-        <div>
-          <input id="promoter-gene" type="radio" value="gene" ng-model="promoterSelect">
-          <label for="promoter-gene">Promoter swap
-            <span ng-if="data.organismShortDisplayName">({{data.organismShortDisplayName}})</span></label>
-          <feature-chooser
-            ng-if="genes && promoterSelect == 'gene'"
-            feature-type="gene" features="genes"
-            feature-editable="true"
-            chosen-feature-id="data.promoterGeneId"></feature-chooser>
-          <a ng-if="promoterSelect == 'gene'" ng-click="openSingleGeneAddDialog()">Add another gene</a>
-        </div>
-        <div>
-          <input id="promoter-exogenous" type="radio" value="exogenous" ng-model="promoterSelect">
-          <label for="promoter-exogenous">Exogenous gene promoter</label>
-          <input type="text" ng-if="promoterSelect == 'exogenous'" ng-model="alleleData.exogenous_promoter"/>
-        </div>
+        <label for="gene-promoter">Promoter (optional)</label>
+        <input id="gene-promoter" type="text" ng-model="alleleData.promoter_gene">
       </div>
 
       <div class="modal-footer">

diff --git a/t/80_curs_service_utils.t b/t/80_curs_service_utils.t
@@ -1067,7 +1067,6 @@ cmp_deeply($allele_res,
               'gene_systematic_id' => 'SPAC27D7.13c',
               'synonyms' => [],
               'notes' => {},
-              'exogenous_promoter' => undef,
               'promoter_gene' => undef,
             },
             {
@@ -1087,7 +1086,6 @@ cmp_deeply($allele_res,
               'notes' => {
                 'note_test_key' => 'note_test_value',
               },
-              'exogenous_promoter' => undef,
               'promoter_gene' => undef,
             },
             {
@@ -1134,7 +1132,6 @@ my $expected_genotype_detail_res =
         'synonyms' => [],
         'comment' => undef,
         'notes' => {},
-        'exogenous_promoter' => undef,
         'promoter_gene' => undef,
       },
       {
@@ -1152,7 +1149,6 @@ my $expected_genotype_detail_res =
         'synonyms' => [],
         'comment' => undef,
         'notes' => {},
-        'exogenous_promoter' => undef,
         'promoter_gene' => undef,
       },
     ],

diff --git a/t/85_allele_manager.t b/t/85_allele_manager.t
@@ -91,7 +91,7 @@ is ($no_name_allele_check->allele_id(), $no_name_allele->allele_id());
 
 
 $allele_manager->create_simple_allele('test_uniquename', 'unknown', 'some_name',
-                                      'some_description', undef, undef,
+                                      'some_description', undef,
                                       $SPBC1826_01c, []);
 
 my $new_simple_allele = $curs_schema->resultset('Allele')
@@ -105,7 +105,7 @@ is ($new_simple_allele->gene()->primary_identifier(), 'SPBC1826.01c');
 
 $allele_manager->create_simple_allele('test_aberration_uniquename', 'aberration',
                                       'some_aberration_name',
-                                      'some_aberration_description',  undef, undef,
+                                      'some_aberration_description',  undef,
                                       undef, []);
 
 my $new_aberration = $curs_schema->resultset('Allele')

diff --git a/t/90_curs_controller_service.t b/t/90_curs_controller_service.t
@@ -97,7 +97,6 @@ test_psgi $app, sub {
                    'comment' => undef,
                    'synonyms' => [],
                    'notes' => {},
-                   'exogenous_promoter' => undef,
                    'promoter_gene' => undef,
                 },
                  {
@@ -115,7 +114,6 @@ test_psgi $app, sub {
                    'comment' => undef,
                    'synonyms' => [],
                    'notes' => {},
-                   'exogenous_promoter' => undef,
                    'promoter_gene' => undef,
                  }
                ],

diff --git a/t/data/curs_aaaa0001.sqlite3 b/t/data/curs_aaaa0001.sqlite3
diff --git a/t/data/curs_aaaa0002.sqlite3 b/t/data/curs_aaaa0002.sqlite3
diff --git a/t/data/curs_aaaa0003.sqlite3 b/t/data/curs_aaaa0003.sqlite3
diff --git a/t/data/curs_aaaa0004.sqlite3 b/t/data/curs_aaaa0004.sqlite3
diff --git a/t/data/curs_aaaa0005.sqlite3 b/t/data/curs_aaaa0005.sqlite3
diff --git a/t/data/curs_aaaa0006.sqlite3 b/t/data/curs_aaaa0006.sqlite3
diff --git a/t/data/curs_aaaa0007.sqlite3 b/t/data/curs_aaaa0007.sqlite3
diff --git a/t/data/ontology_index/segments b/t/data/ontology_index/segments
diff --git a/t/data/track_0_curs_test_template.sqlite3 b/t/data/track_0_curs_test_template.sqlite3
diff --git a/t/data/track_1_curs_test_template.sqlite3 b/t/data/track_1_curs_test_template.sqlite3
diff --git a/t/data/track_3_curs_test_template.sqlite3 b/t/data/track_3_curs_test_template.sqlite3
diff --git a/t/data/track_curs_annotations_1_test_template.sqlite3 b/t/data/track_curs_annotations_1_test_template.sqlite3
diff --git a/t/data/track_curs_annotations_2_test_template.sqlite3 b/t/data/track_curs_annotations_2_test_template.sqlite3
diff --git a/t/data/track_empty_db_test_template.sqlite3 b/t/data/track_empty_db_test_template.sqlite3