Call `set_discussion_id` again in DiffNote `before_validation` because the order is important

app/models/diff_note.rb

@@ -16,6 +16,9 @@ class DiffNote < Note
   after_initialize :ensure_original_discussion_id
   before_validation :set_original_position, :update_position, on: :create
   before_validation :set_line_code, :set_original_discussion_id
+  # We need to do this again, because it's already in `Note`, but is affected by
+  # `update_position` and needs to run after that.
+  before_validation :set_discussion_id
   after_save :keep_around_commits
 
   class << self

db/migrate/20160819221631_add_index_to_note_discussion_id.rb

@@ -0,0 +1,14 @@
+# See http://doc.gitlab.com/ce/development/migration_style_guide.html
+# for more information on how to write migrations for GitLab.
+
+class AddIndexToNoteDiscussionId < ActiveRecord::Migration
+  include Gitlab::Database::MigrationHelpers
+
+  DOWNTIME = false
+
+  disable_ddl_transaction!
+
+  def change
+    add_concurrent_index :notes, :discussion_id
+  end
+end

db/migrate/20160819221833_reset_diff_note_discussion_id_because_it_was_calculated_wrongly.rb

@@ -0,0 +1,12 @@
+# See http://doc.gitlab.com/ce/development/migration_style_guide.html
+# for more information on how to write migrations for GitLab.
+
+class ResetDiffNoteDiscussionIdBecauseItWasCalculatedWrongly < ActiveRecord::Migration
+  include Gitlab::Database::MigrationHelpers
+
+  DOWNTIME = false
+
+  def up
+    execute "UPDATE notes SET discussion_id = NULL WHERE discussion_id IS NOT NULL AND type = 'DiffNote'"
+  end
+end

db/schema.rb

@@ -11,7 +11,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema.define(version: 20160818205718) do
+ActiveRecord::Schema.define(version: 20160819221833) do
 
   # These are extensions that must be enabled in order to support this database
   enable_extension "plpgsql"
@@ -700,6 +700,7 @@ ActiveRecord::Schema.define(version: 20160818205718) do
   add_index "notes", ["author_id"], name: "index_notes_on_author_id", using: :btree
   add_index "notes", ["commit_id"], name: "index_notes_on_commit_id", using: :btree
   add_index "notes", ["created_at"], name: "index_notes_on_created_at", using: :btree
+  add_index "notes", ["discussion_id"], name: "index_notes_on_discussion_id", using: :btree
   add_index "notes", ["line_code"], name: "index_notes_on_line_code", using: :btree
   add_index "notes", ["note"], name: "index_notes_on_note_trigram", using: :gin, opclasses: {"note"=>"gin_trgm_ops"}
   add_index "notes", ["noteable_id", "noteable_type"], name: "index_notes_on_noteable_id_and_noteable_type", using: :btree