Merge branch 'main' into release

griffithlab · Feb 10, 2025 · 04bcd8d · 04bcd8d
2 parents 9428375 + 99ef5a0
commit 04bcd8d
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Showing 3 changed files with 14 additions and 7 deletions.
diff --git a/server/app/graphql/types/queries/typeahead_queries.rb b/server/app/graphql/types/queries/typeahead_queries.rb
@@ -80,14 +80,13 @@ def variants_typeahead(query_term:, feature_id: nil)
       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}%"))
+          .or(base_query.where("diseases.doid ILIKE ?", "#{query_term.gsub(/DOID:/i, "")}%"))
           .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")
             .distinct
             .limit(10-results.size)
           return results + secondary_results
@@ -110,7 +109,6 @@ 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")
               .distinct
               .limit(10-results.size)
 

diff --git a/server/app/jobs/populate_fusion_coordinates.rb b/server/app/jobs/populate_fusion_coordinates.rb
@@ -5,10 +5,19 @@ def perform(variant)
     end
 
     if variant.fusion.five_prime_partner_status == 'known'
+      if variant.five_prime_end_exon_coordinates.representative_transcript.blank?
+        return
+      end
+
       populate_coords(variant.five_prime_end_exon_coordinates, variant.five_prime_start_exon_coordinates)
       populate_representative_coordinates(variant.five_prime_coordinates, variant.five_prime_start_exon_coordinates, variant.five_prime_end_exon_coordinates)
     end
+
     if variant.fusion.three_prime_partner_status == 'known'
+      if variant.three_prime_start_exon_coordinates.representative_transcript.blank?
+        return
+      end
+
       populate_coords(variant.three_prime_start_exon_coordinates, variant.three_prime_end_exon_coordinates)
       populate_representative_coordinates(variant.three_prime_coordinates, variant.three_prime_start_exon_coordinates, variant.three_prime_end_exon_coordinates)
     end

diff --git a/server/app/models/variants/fusion_variant.rb b/server/app/models/variants/fusion_variant.rb
@@ -91,6 +91,10 @@ def forbidden_fields
       ]
     end
 
+    def on_revision_accepted
+      PopulateFusionCoordinates.perform_later(self)
+    end
+
     private
     def construct_five_prime_name(name_type:)
           construct_partner_name(
@@ -157,9 +161,5 @@ def populate_coordinates
         PopulateFusionCoordinates.perform_later(self)
       end
     end
-
-    def on_revision_accepted
-      PopulateFusionCoordinates.perform_later(self)
-    end
   end
 end