Merge branch 'main' into release

griffithlab · Oct 2, 2024 · a6491d9 · a6491d9
2 parents b52fbe7 + de08b87
commit a6491d9
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Showing 5 changed files with 21 additions and 11 deletions.
diff --git a/server/Gemfile b/server/Gemfile
@@ -8,7 +8,7 @@ gem 'rails', '~> 7.1'
 # Use postgresql as the database for Active Record
 gem 'pg', '~> 1.1'
 # Use Puma as the app server
-gem 'puma', '5.6.8'
+gem 'puma', '5.6.9'
 # Use SCSS for stylesheets
 gem 'sass-rails', '>= 6'
 # Transpile app-like JavaScript. Read more: https://github.com/rails/webpacker

diff --git a/server/Gemfile.lock b/server/Gemfile.lock
@@ -273,7 +273,7 @@ GEM
     net-smtp (0.4.0.1)
       net-protocol
     net-ssh (7.2.1)
-    nio4r (2.7.0)
+    nio4r (2.7.3)
     nokogiri (1.16.5-aarch64-linux)
       racc (~> 1.4)
     nokogiri (1.16.5-arm-linux)
@@ -330,7 +330,7 @@ GEM
     psych (5.1.2)
       stringio
     public_suffix (5.0.4)
-    puma (5.6.8)
+    puma (5.6.9)
       nio4r (~> 2.0)
     raabro (1.4.0)
     racc (1.8.0)
@@ -579,7 +579,7 @@ DEPENDENCIES
   pg (~> 1.1)
   pry
   pry-rails
-  puma (= 5.6.8)
+  puma (= 5.6.9)
   rack-cors (~> 1.1.1)
   rack-mini-profiler (~> 2.0)
   rails (~> 7.1)

diff --git a/server/app/graphql/types/queries/typeahead_queries.rb b/server/app/graphql/types/queries/typeahead_queries.rb
@@ -81,13 +81,13 @@ def disease_typeahead(query_term:)
         base_query = Disease.where(deprecated: false)
         results = base_query.where("diseases.name ILIKE ?", "%#{query_term}%")
           .or(base_query.where("diseases.doid ILIKE ?", "#{query_term}%"))
-          .order("LENGTH(diseases.name) ASC")
+          #.order("LENGTH(diseases.name) ASC")
           .limit(10)
         if results.size < 10
           secondary_results = base_query.eager_load(:disease_aliases)
             .where("disease_aliases.name ILIKE ?", "%#{query_term}%")
             .where.not(id: results.select('id'))
-            .order("LENGTH(diseases.name) ASC")
+            #.order("LENGTH(diseases.name) ASC")
             .distinct
             .limit(10-results.size)
           return results + secondary_results
@@ -100,7 +100,7 @@ def therapy_typeahead(query_term:)
         base_query = Therapy.where(deprecated: false)
         results = base_query.where("therapies.name ILIKE ?", "#{query_term}%")
           .or(base_query.where("therapies.ncit_id ILIKE ?", "%#{query_term}%"))
-          .order("LENGTH(therapies.name) ASC")
+          #.order("LENGTH(therapies.name) ASC")
           .limit(10)
         if results.size < 10
           secondary_results = base_query.where('therapies.name ILIKE ?', "%#{query_term}%")
@@ -110,7 +110,7 @@ def therapy_typeahead(query_term:)
             tertiary_results = base_query.eager_load(:therapy_aliases)
               .where("therapy_aliases.name ILIKE ?", "%#{query_term}%")
               .where.not(id: results.select('id') + secondary_results.select('id'))
-              .order("LENGTH(therapies.name) ASC")
+              #.order("LENGTH(therapies.name) ASC")
               .distinct
               .limit(10-results.size)
 
@@ -131,14 +131,14 @@ def feature_typeahead(query_term:, feature_type: nil)
                      end
 
         results = base_query.where('features.name ILIKE ?', "#{query_term}%")
-          .order("LENGTH(features.name) ASC")
+          #.order("LENGTH(features.name) ASC")
           .limit(10)
 
         if results.size < 10
           secondary_results = base_query.eager_load(:feature_aliases)
             .where("feature_aliases.name ILIKE ?", "#{query_term}%")
             .where.not(id: results.select('id'))
-            .order("LENGTH(features.name) ASC")
+            #.order("LENGTH(features.name) ASC")
             .distinct
             .limit(10 - results.size)
           return (results + secondary_results).uniq

diff --git a/server/app/graphql/types/variants/gene_variant_type.rb b/server/app/graphql/types/variants/gene_variant_type.rb
@@ -42,7 +42,7 @@ def mane_select_transcript
     def open_revision_count
       Loaders::AssociationCountLoader.for(object.class, association: :open_revisions).load(object.id).then do |count|
         Loaders::AssociationLoader.for(Variants::GeneVariant, :coordinates).load(object).then do |coord|
-          Loaders::AssociationCountLoader.for(VariantCoordinate, association: :open_revisions).load(coord.id) do |coord_count|
+          Loaders::AssociationCountLoader.for(VariantCoordinate, association: :open_revisions).load(coord.id).then do |coord_count|
             count + coord_count
           end
         end

diff --git a/server/app/models/activities/create_variant.rb b/server/app/models/activities/create_variant.rb
@@ -32,9 +32,19 @@ def call_actions
 
       @variant = cmd.variant
       @molecular_profile = cmd.molecular_profile
+
+      stub_coordinates
+      variant.save!
+
       events << cmd.events
     end
 
+    def stub_coordinates
+      if variant.type == 'Variants::GeneVariant'
+        variant.coordinates = VariantCoordinate.generate_stub(variant, 'Gene Variant Coordinate')
+      end
+    end
+
     def linked_entities
       molecular_profile
     end