From 9695afbb0cdb6f914dde992ded135831d7592db1 Mon Sep 17 00:00:00 2001
From: Susanna Kiwala <susanna.kiwala@wustl.edu>
Date: Tue, 28 Jan 2025 10:08:47 -0600
Subject: [PATCH 1/2] Update short links to allow doid, ncit_id, and hpo_id

---
 server/app/lib/link_adaptors/phenotype.rb | 11 ++++++++++
 server/app/models/frontend_router.rb      | 26 ++++++++++++++++++-----
 2 files changed, 32 insertions(+), 5 deletions(-)
 create mode 100644 server/app/lib/link_adaptors/phenotype.rb

diff --git a/server/app/lib/link_adaptors/phenotype.rb b/server/app/lib/link_adaptors/phenotype.rb
new file mode 100644
index 000000000..aafe600bf
--- /dev/null
+++ b/server/app/lib/link_adaptors/phenotype.rb
@@ -0,0 +1,11 @@
+module LinkAdaptors
+  class Phenotype < Base
+    def display_name
+      obj.name
+    end
+
+    def base_path
+      "/phenotypes/#{obj.id}"
+    end
+  end
+end
diff --git a/server/app/models/frontend_router.rb b/server/app/models/frontend_router.rb
index b88634229..c3c6896d7 100644
--- a/server/app/models/frontend_router.rb
+++ b/server/app/models/frontend_router.rb
@@ -24,8 +24,16 @@ def url
   def query_info
     case id_type
     when /genes?/
-      [ 
-        Feature.where(feature_instance_type: "Features::Gene"), :feature_instance_id, 
+      [
+        Feature.where(feature_instance_type: "Features::Gene"), :id,
+      ]
+    when /fusions?/
+      [
+        Feature.where(feature_instance_type: "Features::Fusion"), :id,
+      ]
+    when /factors?/
+      [
+        Feature.where(feature_instance_type: "Features::Factor"), :id,
       ]
     when /features?/
       [ Feature, :id, ]
@@ -38,7 +46,7 @@ def query_info
     when /entrez_id/
       [ Features::Gene, :entrez_id ]
     when /entrez_name/
-      [ 
+      [
         Feature.where(feature_instance_type: "Features::Gene"), :name, -> { _1.upcase }
       ]
     when /variant_groups?/
@@ -47,10 +55,18 @@ def query_info
       [ Revision, :id ]
     when /diseases?/
       [ Disease, :id ]
+    when /doid/
+      [ Disease.where(deprecated: false), :doid, ]
     when /drugs?/
       [ Therapy, :id ]
     when /therapies?/
       [ Therapy, :id ]
+    when /ncit_id/
+      [ Therapy.where(deprecated: false), :ncit_id, ]
+    when /phenotypes?/
+      [ Phenotype, :id ]
+    when /hpo_id/
+      [ Phenotype, :hpo_id ]
     when /assertions?/
       [ Assertion, :id ]
     when /sources?/
@@ -62,8 +78,8 @@ def query_info
       when "AID"
         [ Assertion, :id ]
       when "GID"
-        [ 
-          Feature.where(feature_instance_type: "Features::Gene"), :feature_instance_id, 
+        [
+          Feature.where(feature_instance_type: "Features::Gene"), :id,
         ]
       when "FID"
         [ Feature, :id ]

From 4ed58e9d0cb4972b079dfffcea9e1977a987bf5b Mon Sep 17 00:00:00 2001
From: Adam Coffman <acc@fastmail.com>
Date: Tue, 28 Jan 2025 10:18:55 -0600
Subject: [PATCH 2/2] rank typeahead results by length of matched name

---
 .../app/graphql/types/queries/typeahead_queries.rb   | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/server/app/graphql/types/queries/typeahead_queries.rb b/server/app/graphql/types/queries/typeahead_queries.rb
index 396f43339..c972266a0 100644
--- 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