Merge branch 'main' into release

server/db/migrate/20240725165912_add_unique_index_to_new_views.rb

@@ -0,0 +1,6 @@
+class AddUniqueIndexToNewViews < ActiveRecord::Migration[7.1]
+  def change
+    add_index :user_browse_table_rows, :id, unique: true
+    add_index :organization_browse_table_rows, :id, unique: true
+  end
+end

server/db/schema.rb

@@ -10,12 +10,15 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-
-ActiveRecord::Schema[7.1].define(version: 2024_06_28_151626) do
-
+ActiveRecord::Schema[7.1].define(version: 2024_07_25_165912) do
   # These are extensions that must be enabled in order to support this database
   enable_extension "plpgsql"
 
+  # Custom types defined in this database.
+  # Note that some types may not work with other database engines. Be careful if changing database.
+  create_enum "exon_offset_direction", ["positive", "negative"]
+  create_enum "fusion_partner_status", ["known", "unknown", "multiple"]
+
   create_table "acmg_codes", id: :serial, force: :cascade do |t|
     t.text "code"
     t.text "description"
@@ -499,6 +502,17 @@
     t.index ["state"], name: "index_flags_on_state"
   end
 
+  create_table "fusions", force: :cascade do |t|
+    t.bigint "five_prime_gene_id"
+    t.bigint "three_prime_gene_id"
+    t.enum "five_prime_partner_status", default: "unknown", null: false, enum_type: "fusion_partner_status"
+    t.enum "three_prime_partner_status", default: "unknown", null: false, enum_type: "fusion_partner_status"
+    t.datetime "created_at", null: false
+    t.datetime "updated_at", null: false
+    t.index ["five_prime_gene_id"], name: "index_fusions_on_five_prime_gene_id"
+    t.index ["three_prime_gene_id"], name: "index_fusions_on_three_prime_gene_id"
+  end
+
   create_table "gene_aliases", id: :serial, force: :cascade do |t|
     t.string "name"
     t.index ["name"], name: "index_gene_aliases_on_name"
@@ -884,6 +898,7 @@
     t.text "coordinate_type", null: false
     t.datetime "created_at", null: false
     t.datetime "updated_at", null: false
+    t.enum "exon_offset_direction", enum_type: "exon_offset_direction"
     t.index ["chromosome"], name: "index_variant_coordinates_on_chromosome"
     t.index ["reference_build"], name: "index_variant_coordinates_on_reference_build"
     t.index ["representative_transcript"], name: "index_variant_coordinates_on_representative_transcript"
@@ -965,6 +980,7 @@
     t.bigint "feature_id"
     t.string "type", null: false
     t.string "ncit_id"
+    t.string "vicc_compliant_name"
     t.index "lower((name)::text) varchar_pattern_ops", name: "idx_case_insensitive_variant_name"
     t.index "lower((name)::text)", name: "variant_lower_name_idx"
     t.index ["chromosome"], name: "index_variants_on_chromosome"
@@ -981,6 +997,7 @@
     t.index ["stop"], name: "index_variants_on_stop"
     t.index ["stop2"], name: "index_variants_on_stop2"
     t.index ["variant_bases"], name: "index_variants_on_variant_bases"
+    t.index ["vicc_compliant_name"], name: "index_variants_on_vicc_compliant_name"
   end
 
   create_table "view_last_updated_timestamps", force: :cascade do |t|
@@ -1032,6 +1049,8 @@
   add_foreign_key "feature_aliases_features", "features"
   add_foreign_key "features_sources", "features"
   add_foreign_key "features_sources", "sources"
+  add_foreign_key "fusions", "genes", column: "five_prime_gene_id"
+  add_foreign_key "fusions", "genes", column: "three_prime_gene_id"
   add_foreign_key "gene_aliases_genes", "gene_aliases"
   add_foreign_key "gene_aliases_genes", "genes"
   add_foreign_key "genes_sources", "genes"
@@ -1401,7 +1420,8 @@
        LEFT JOIN organizations child ON ((child.parent_id = organizations.id)))
     GROUP BY organizations.id;
   SQL
-
+  add_index "organization_browse_table_rows", ["id"], name: "index_organization_browse_table_rows_on_id", unique: true
+
   create_view "user_browse_table_rows", materialized: true, sql_definition: <<-SQL
       SELECT users.id,
       users.email,
@@ -1432,4 +1452,6 @@
        LEFT JOIN events ON ((events.originating_user_id = users.id)))
     GROUP BY users.id;
   SQL
+  add_index "user_browse_table_rows", ["id"], name: "index_user_browse_table_rows_on_id", unique: true
+
 end