diff --git a/app/models/organisation.rb b/app/models/organisation.rb
index 0aa0c88..0828218 100644
--- a/app/models/organisation.rb
+++ b/app/models/organisation.rb
@@ -1,101 +1,148 @@
 class Organisation < ActiveRecord::Base
 
-	#associations between tables
-	belongs_to :organisation_type
-	has_many :guidance_groups
-	has_many :dmptemplates
-	has_many :sections
-	has_many :users
-	has_many :option_warnings
-	has_many :suggested_answers
-	has_many :org_token_permissions
+    #associations between tables
+    belongs_to :organisation_type
+    has_many :guidance_groups
+    has_many :dmptemplates
+    has_many :sections
+    has_many :users, through: :user_org_roles
+    has_many :option_warnings
+    has_many :suggested_answers
+    has_and_belongs_to_many :token_permission_types, join_table: "org_token_permissions"
 
     has_many :user_org_roles
 
     belongs_to :parent, :class_name => 'Organisation'
-	has_many :children, :class_name => 'Organisation', :foreign_key => 'parent_id'
+    has_many :children, :class_name => 'Organisation', :foreign_key => 'parent_id'
 
-	accepts_nested_attributes_for :organisation_type
-	accepts_nested_attributes_for :dmptemplates
+    accepts_nested_attributes_for :organisation_type
+    accepts_nested_attributes_for :dmptemplates
+    accepts_nested_attributes_for :token_permission_types
 
-	attr_accessible :abbreviation, :banner_text, :description, :domain, :logo_file_name, :name, :stylesheet_file_id, :target_url, :organisation_type_id, :wayfless_entity, :parent_id, :sort_name
+    attr_accessible :abbreviation, :banner_text, :description, :domain, :logo_file_name, :name, :stylesheet_file_id, :target_url, :organisation_type_id, :wayfless_entity, :parent_id, :sort_name, :token_permission_type_ids
+    ##
+    # returns the name of the current organisation
+    #
+    # @return [String] the name of the organisation
+    def to_s
+        name
+    end
 
-	def to_s
-		name
-	end
+    ##
+    # returns the abbreviation for the organisation if it exists, name otherwise
+    #
+    # @return [String] abbreviation or name
+    def short_name
+        if abbreviation.nil? then
+            return name
+        else
+            return abbreviation
+        end
+    end
 
-	def short_name
-		if abbreviation.nil? then
-			return name
-		else
-			return abbreviation
-		end
-	end
+    ##
+    # returns all organisations who have parents of a given organisation type
+    #
+    # @params org_type [String] the name of an organisation type
+    # @return [Array<Organisation>] a list of organisations
+    def self.orgs_with_parent_of_type(org_type)
+        parents = OrganisationType.find_by(name: (org_type)).organisations
+        children = Array.new
+        parents.each do |parent|
+            children += parent.children
+        end
+        return children
+    end
 
-	#retrieves info off a child org
-	def self.orgs_with_parent_of_type(org_type)
-		parents = OrganisationType.find_by_name(org_type).organisations
-		children = Array.new
-		parents.each do |parent|
-		  	children += parent.children
-		end
-		return children
-	end
+    ##
+    # returns a list of all guidance groups belonging to other organisations
+    #
+    # @return [Array<GuidanceGroup>]
+    def self.other_organisations
+        #DISCUSS  - What does this method do?
+        org_types = [I18n.t('helpers.org_type.organisation')]
+        organisations_list = []
+        org_types.each do |ot|
+            new_org_obejct = OrganisationType.find_by(name: ot)
 
+            org_with_guidance = GuidanceGroup.joins(new_org_obejct.organisations)
 
-	def self.other_organisations
-		org_types = [I18n.t('helpers.org_type.organisation')]
-		organisations_list = []
-		org_types.each do |ot|
-			new_org_obejct = OrganisationType.find_by_name(ot)
+            organisations_list = organisations_list + org_with_guidance
+        end
+        return organisations_list
+    end
 
-			org_with_guidance = GuidanceGroup.joins(new_org_obejct.organisations)
+    ##
+    # returns a list of all sections of a given version from this organisation and it's parents
+    #
+    # @params version_id [Integer] version number of the section
+    # @return [Array<Section>] list of sections
+    def all_sections(version_id)
+        if parent.nil?
+            secs = sections.where("version_id = ?", version_id)
+            if secs.nil? then
+                secs = Array.new
+            end
+            return secs
+        else
+            return sections.where("version_id = ? ", version_id).all + parent.all_sections(version_id)
+        end
+    end
 
-			organisations_list = organisations_list + org_with_guidance
-		end
-		return organisations_list
-	end
+    ##
+    # returns the guidance groups of this organisation and all of it's children
+    #
+    # @return [Array<GuidanceGroup>] list of guidance groups
+    def all_guidance_groups
+        ggs = guidance_groups
+        children.each do |c|
+            ggs = ggs + c.all_guidance_groups
+        end
+        return ggs
+    end
 
-	def all_sections(version_id)
-		if parent.nil?
-			secs = sections.where("version_id = ?", version_id)
-			if secs.nil? then
-				secs = Array.new
-			end
-			return secs
-		else
-			return sections.where("version_id = ? ", version_id).all + parent.all_sections(version_id)
-		end
-	end
+    ##
+    # returns the highest parent organisation in the tree
+    #
+    # @return [organisation] the root organisation
+    def root
+        if parent.nil?
+            return self
+        else
+            return parent.root
+        end
+    end
 
-	def all_guidance_groups
-		ggs = guidance_groups
-		children.each do |c|
-			ggs = ggs + c.all_guidance_groups
-		end
-		return ggs
-	end
+    ##
+    # takes in the id of, and returns an OptionWarning
+    #
+    # @params option_id [number] the id of the desired warning
+    # @return [OptionWarning] the specified warning
+    def warning(option_id)
+        warning = option_warnings.find_by(option_id: option_id)
+        if warning.nil? && !parent.nil? then
+            return parent.warning(option_id)
+        else
+            return warning
+        end
+    end
 
-	def root
-		if parent.nil?
-			return self
-		else
-			return parent.root
-		end
-	end
+    ##
+    # returns all published templates belonging to the organisation
+    #
+    # @return [Array<Dmptemplate>] published dmptemplates
+    def published_templates
+        return dmptemplates.where("published = ?", 1)
+    end
 
-	def warning(option_id)
-		warning = option_warnings.find_by_option_id(option_id)
-		if warning.nil? && !parent.nil? then
-			return parent.warning(option_id)
-		else
-			return warning
-		end
-	end
-
-	def published_templates
-		return dmptemplates.where("published = ?", 1)
-	end
+    def check_api_credentials
+        if token_permission_types.count == 0
+            users.each do |user|
+                user.api_token = ""
+                user.save!
+            end
+        end
+    end
 
 
 end