diff --git a/app/controllers/phases_controller.rb b/app/controllers/phases_controller.rb
index 15d45f3..21084a9 100644
--- a/app/controllers/phases_controller.rb
+++ b/app/controllers/phases_controller.rb
@@ -29,17 +29,19 @@
     # where guidance is a hash with the text and the org name
     theme_guidance = {}
 
-    guidance_groups.each do |guidance_group|
-      guidance_group.guidances.where(published: true).each do |guidance|
-        guidance.themes.each do |theme|
-          title = theme.title
-          if !theme_guidance.has_key?(title)
-            theme_guidance[title] = Array.new
+    guidance_groups.includes(guidances:[:themes]).each do |guidance_group|
+      guidance_group.guidances.each do |guidance|
+        if guidance.published
+          guidance.themes.each do |theme|
+            title = theme.title
+            if !theme_guidance.has_key?(title)
+              theme_guidance[title] = Array.new
+            end
+            theme_guidance[title] << {
+              text: guidance.text,
+              org: guidance_group.name + ':'
+            }
           end
-          theme_guidance[title] << {
-            text: guidance.text,
-            org: guidance_group.name + ':'
-          }
         end
       end
     end
diff --git a/app/controllers/users_controller.rb b/app/controllers/users_controller.rb
index 57b504f..b26a62e 100644
--- a/app/controllers/users_controller.rb
+++ b/app/controllers/users_controller.rb
@@ -41,7 +41,7 @@
       else
         if perms.include? perm
           @user.perms << perm
-          if perm.name == Perm.use_api.id
+          if perm.id == Perm.use_api.id
             @user.keep_or_generate_token!
           end
         end
diff --git a/app/models/plan.rb b/app/models/plan.rb
index 1eee8a6..8688f34 100644
--- a/app/models/plan.rb
+++ b/app/models/plan.rb
@@ -159,7 +159,7 @@
     # find all the themes in this plan
     # and get the guidance groups they belong to
     ggroups = []
-    self.template.phases.each do |phase|
+    Template.includes(phases: [sections: [questions: [themes: [guidances: [guidance_group: :org]]]]]).find(self.template_id).phases.each do |phase|
       phase.sections.each do |section|
         section.questions.each do |question|
           question.themes.each do |theme|
diff --git a/app/models/user.rb b/app/models/user.rb
index c1350f6..f900030 100644
--- a/app/models/user.rb
+++ b/app/models/user.rb
@@ -53,7 +53,7 @@
 
   ##
   # Scopes
-  default_scope { includes(:org, :perms, :plans) }
+  default_scope { includes(:org, :perms) }
 
 
 
diff --git a/db/migrate/20170702012742_ensure_indexes_in_place.rb b/db/migrate/20170702012742_ensure_indexes_in_place.rb
new file mode 100644
index 0000000..6bd9410
--- /dev/null
+++ b/db/migrate/20170702012742_ensure_indexes_in_place.rb
@@ -0,0 +1,40 @@
+class EnsureIndexesInPlace < ActiveRecord::Migration
+  def change
+    #users_perms
+    remove_index :users_perms, name: 'index_users_perms_on_user_id_and_perm_id'
+    add_index :users_perms, :user_id
+    #user_identifiers
+    add_index :user_identifiers, :user_id
+    #roles
+    add_index :roles, :user_id
+    add_index :roles, :plan_id
+    #org_token_permissions
+    add_index :org_token_permissions, :org_id
+    #users
+    add_index :users, :org_id
+    remove_index :users, :confirmation_token
+    remove_index :users, :invitation_token
+    remove_index :users, :reset_password_token
+    #notes
+    add_index :notes, :answer_id
+    #guidance_groups
+    add_index :guidance_groups, :org_id
+    #guidance
+    add_index :guidances, :guidance_group_id
+    #themes_in_guidance
+    add_index :themes_in_guidance, :theme_id
+    add_index :themes_in_guidance, :guidance_id
+    #annotations
+    add_index :annotations, :question_id
+    #question_themes
+    remove_index :questions_themes, name: 'question_theme_index'
+    remove_index :questions_themes, name: 'theme_question_index'
+    add_index :questions_themes, :question_id
+    #question_options
+    add_index :question_options, :question_id
+    #answers_question_options
+    remove_index :answers_question_options, name: 'answer_question_option_index'
+    remove_index :answers_question_options, name: 'question_option_answer_index'
+    add_index :answers_question_options, :answer_id
+  end
+end
diff --git a/db/schema.rb b/db/schema.rb
index fd97cce..1c7f711 100644
--- a/db/schema.rb
+++ b/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: 20170428083711) do
+ActiveRecord::Schema.define(version: 20170702012742) do
 
   # These are extensions that must be enabled in order to support this database
   enable_extension "plpgsql"
@@ -25,6 +25,8 @@
     t.datetime "updated_at"
   end
 
+  add_index "annotations", ["question_id"], name: "index_annotations_on_question_id", using: :btree
+
   create_table "answers", force: :cascade do |t|
     t.text     "text"
     t.integer  "plan_id"
@@ -40,8 +42,7 @@
     t.integer "question_option_id", null: false
   end
 
-  add_index "answers_question_options", ["answer_id", "question_option_id"], name: "answer_question_option_index", using: :btree
-  add_index "answers_question_options", ["question_option_id", "answer_id"], name: "question_option_answer_index", using: :btree
+  add_index "answers_question_options", ["answer_id"], name: "index_answers_question_options_on_answer_id", using: :btree
 
   create_table "exported_plans", force: :cascade do |t|
     t.integer  "plan_id"
@@ -93,6 +94,8 @@
     t.boolean  "published"
   end
 
+  add_index "guidance_groups", ["org_id"], name: "index_guidance_groups_on_org_id", using: :btree
+
   create_table "guidances", force: :cascade do |t|
     t.text     "text"
     t.integer  "guidance_group_id"
@@ -102,6 +105,8 @@
     t.boolean  "published"
   end
 
+  add_index "guidances", ["guidance_group_id"], name: "index_guidances_on_guidance_group_id", using: :btree
+
   create_table "identifier_schemes", force: :cascade do |t|
     t.string   "name"
     t.string   "description"
@@ -129,6 +134,8 @@
     t.datetime "updated_at"
   end
 
+  add_index "notes", ["answer_id"], name: "index_notes_on_answer_id", using: :btree
+
   create_table "org_token_permissions", force: :cascade do |t|
     t.integer  "org_id"
     t.integer  "token_permission_type_id"
@@ -136,6 +143,8 @@
     t.datetime "updated_at"
   end
 
+  add_index "org_token_permissions", ["org_id"], name: "index_org_token_permissions_on_org_id", using: :btree
+
   create_table "orgs", force: :cascade do |t|
     t.string   "name"
     t.string   "abbreviation"
@@ -219,6 +228,8 @@
     t.datetime "updated_at"
   end
 
+  add_index "question_options", ["question_id"], name: "index_question_options_on_question_id", using: :btree
+
   create_table "questions", force: :cascade do |t|
     t.text     "text"
     t.text     "default_value"
@@ -238,8 +249,7 @@
     t.integer "theme_id",    null: false
   end
 
-  add_index "questions_themes", ["question_id", "theme_id"], name: "question_theme_index", using: :btree
-  add_index "questions_themes", ["theme_id", "question_id"], name: "theme_question_index", using: :btree
+  add_index "questions_themes", ["question_id"], name: "index_questions_themes_on_question_id", using: :btree
 
   create_table "regions", force: :cascade do |t|
     t.string  "abbreviation"
@@ -256,6 +266,9 @@
     t.integer  "access",     default: 0, null: false
   end
 
+  add_index "roles", ["plan_id"], name: "index_roles_on_plan_id", using: :btree
+  add_index "roles", ["user_id"], name: "index_roles_on_user_id", using: :btree
+
   create_table "sections", force: :cascade do |t|
     t.string   "title"
     t.text     "description"
@@ -319,6 +332,9 @@
     t.integer "guidance_id"
   end
 
+  add_index "themes_in_guidance", ["guidance_id"], name: "index_themes_in_guidance_on_guidance_id", using: :btree
+  add_index "themes_in_guidance", ["theme_id"], name: "index_themes_in_guidance_on_theme_id", using: :btree
+
   create_table "token_permission_types", force: :cascade do |t|
     t.string   "token_type"
     t.text     "text_description"
@@ -334,14 +350,16 @@
     t.integer  "identifier_scheme_id"
   end
 
+  add_index "user_identifiers", ["user_id"], name: "index_user_identifiers_on_user_id", using: :btree
+
   create_table "users", force: :cascade do |t|
     t.string   "firstname"
     t.string   "surname"
     t.string   "email",                  default: "", null: false
     t.string   "orcid_id"
     t.string   "shibboleth_id"
-    t.datetime "created_at"
-    t.datetime "updated_at"
+    t.datetime "created_at",                          null: false
+    t.datetime "updated_at",                          null: false
     t.string   "encrypted_password",     default: ""
     t.string   "reset_password_token"
     t.datetime "reset_password_sent_at"
@@ -367,17 +385,15 @@
     t.integer  "language_id"
   end
 
-  add_index "users", ["confirmation_token"], name: "index_users_on_confirmation_token", unique: true, using: :btree
   add_index "users", ["email"], name: "index_users_on_email", unique: true, using: :btree
-  add_index "users", ["invitation_token"], name: "index_users_on_invitation_token", unique: true, using: :btree
-  add_index "users", ["reset_password_token"], name: "index_users_on_reset_password_token", unique: true, using: :btree
+  add_index "users", ["org_id"], name: "index_users_on_org_id", using: :btree
 
   create_table "users_perms", id: false, force: :cascade do |t|
     t.integer "user_id"
     t.integer "perm_id"
   end
 
-  add_index "users_perms", ["user_id", "perm_id"], name: "index_users_perms_on_user_id_and_perm_id", using: :btree
+  add_index "users_perms", ["user_id"], name: "index_users_perms_on_user_id", using: :btree
 
   add_foreign_key "annotations", "orgs"
   add_foreign_key "annotations", "questions"