class CodeRunner

# Every code module defines a custom child class of CodeRunner::Run. This class will also include a module which customizes it to work on the current system. The result is a class which knows how to run and analyses the results of the given code on the given system. 
# 
# Every simulation that is carried out has an instance of this custom class created for it, and this object, known as a run, contains both the results and the input parameters pertaining to that simulation. All these runs are then stored in the variable run_list in a runner (an instance of the CodeRunner class). The result is that every run has a runner that it can talk to, and that runner has a set of runs that it can talk to.
#
# Every run has its own directory, where all the input and output files from the simulation are stored. CodeRunner data for the run is stored in this folder in the files <tt>code_runner_info.rb</tt> and <tt>code_runner_results.rb</tt>.  
#
# As soon as the simulation is complete, CodeRunner call Run#process_directory to carry out any anlysis, and the results are stored in <tt>code_runner_results.rb</tt>. For speed CodeRunner also caches the data in the file <tt>.code_runner_run_data</tt> in binary format. This cache will be used after the initial analysis unless CodeRunner is specifically told to reanalyse this run.
#
# All input parameters and results are available during run time as instance variables of the run class.
#
# The class CodeRunner::Run itself defines a base set of methods which are added to by the code module. 
	
class Run
	include Log
# # include CodeRunner::HeuristicRunMethods

# 		class_vars = [:conditions, :sort, :sys, :debug, :script_folder, :necessary_system_runner_methods, :necessary_code_runner_methods, :recalc_all, :parallel]


# @@ruby_command = "ruby" #redefine if necessary
# @@input_file_extension = nil
# @@use_file_name_as_run_name = nil
# @@successful_trial_system = nil
# 
# @@readout_real_run_list = true
# @@print_out_real_run_list = true
# @@readout_component_run_list = false
# @@print_out_component_run_list = false


# class_accessor :readout_real_run_list, :print_out_real_run_list, :readout_component_run_list, :print_out_component_run_list, 

class_accessor :current_status, :runner

# Use the instance method #queue_status (defined in the system module) to put a list of current jobs obtained from the system into the class variable @@current_status

def self.update_status(runner)
	if runner.no_run
		@@current_status =  ""
	else
		#eputs 'Getting queue status...'
		@@current_status = new(runner).queue_status
	end
# 	puts @@current_status
end


def gets #No reading from the command line thank you very much!
	$stdin.gets
end
def self.gets
	$stdin.gets
end


(SUBMIT_OPTIONS + [:code, :version, :readout_list, :naming_pars, :other_pars, :all, :ruby_command, :run_sys_name, :modlet, :executable]).each do |variable|
	#define accessors for class options and instance options
# 	class_accessor(variable)
	attr_accessor variable
# 	set(variable, nil) unless class_variables.include? ("@@" + variable).to_sym
end

class_accessor :run_sys_name
@@run_sys_name = nil
# 	@@necessary_class_variables.keys.each{|v| send(:attr_accessor, v)}

# @runnmaxes = {}

attr_accessor :maxes, :max_complete, :version, :code, :nprocs, :executable_name, :runner, :sys, :naming_pars, :code_runner_version, :real_id

# Purely for testing purposes; see the test suite

attr_accessor :run_test_flags

# Access to a hash which is stored in the runner (not the run). The hash will persist while the runner is in the object space.
#
# E.g.
# 	cache[:my_stuff_to_store] = something_to_store

def cache
	@runner.cache[:runs] ||= {} 
	@runner.cache[:runs][@id] ||= {} 
	@runner.cache[:runs][@id]
end

# Empty the cache for this run
def clear_cache
	@runner.cache[:runs] ||= {} 
	@runner.cache[:runs][@id] = {} 
end

# The hard cache persists after the current program ceases because
# it is written in the .code_runner_run_data file.
# It will disappear if the -a or -A flags are specified at any point
# If you edit the hard cache you ''must'' call <tt>save</tt> afterwards
# or your changes may not be kept
def hard_cache
	@hard_cache ||={}
	@hard_cache
end 
#def save_hard_cache
	#Dir.chdir(@directory)




	class RunClassPropertyFetcher
		def initialize(the_class)
			@my_class = the_class
		end
		def method_missing(method, value=nil)
			#eputs 'STARTING'
			if method.to_s =~ /=$/
				raise 'rcps should not be set outside class methods'
				@my_class.instance_variable_set("@"+method.to_s.sub(/=/, ''), value)
			else
				the_class = @my_class
				loop do 
 					#p the_class, method
# 					p the_class.instance_variables
# 					p the_class.instance_variables.map{|v| the_class.instance_variable_get(v)}
					if method.to_s =~ /\?$/
						return false unless the_class
						return true if the_class.instance_variables.include?(("@"+method.to_s.sub(/\?$/,'')).to_sym)
					else
						raise NoMethodError.new("Run class property #{method} not found.") unless the_class
						return the_class.instance_variable_get("@"+method.to_s) if the_class.instance_variables.include?(("@"+method.to_s).to_sym)
					end
						the_class = the_class.superclass
				end
					
			end
		end
			
			def [](prop)
				send(prop.to_sym)
			end
# 			def []=(prop, value)
# 				set(prop.to_sym, value)
# 			end
# 		end
				
	end

# Access properties of the run class. These properties are stored as instance variables of the run class object. (Remember, in Ruby, every Class is an Object (and Object is a Class!)).
# 
# E.g.
# 	puts rcp.variables

def self.rcp
	@rcp ||= RunClassPropertyFetcher.new(self)
end

# Calls Run.rcp

def rcp 
	self.class.rcp
end

# Create a new run. <tt>runner</tt> should be an instance of the class CodeRunner.

def initialize(runner)
	logf('initialize')
# 	raise "runner must be either a CodeRunner or a RemoteCoderunner: it is a #{runner.class}" unless [CodeRunner, RemoteCodeRunner].include? runner.class
	@runner = runner
# 	raise CRFatal.new("Code not defined: #{CODE}") unless @@code and @@code.class == String and @@code =~ /\S/  
	@sys, @code = rcp.sys, rcp.code
	@naming_pars = rcp.naming_pars.dup
	raise CRFatal.new("@modlet not specified for #{self.class}") if rcp.modlet_required and not rcp.modlet
# 	@modlet = @@modlet; @modlet_location = @@modlet_location
# # 	@executable_location = executable_location
# 		@@necessary_run_variables.each{|v,clas| instance_eval("@#{v} = nil")}
		
# 		initialize_code_specific
	
# 	@script_folder  = @@script_folder
# 	@recalc_all = @@recalc_all
	@wall_mins = @runner.wall_mins if @runner
 	@smaxes = {}; @csmaxes = {}; @max_complete = {};
end

# Here we redefine the inspect function p to raise an error if anything is written to standard out
# while in server mode. This is because the server mode uses standard out to communicate
# and writing to standard out can break it. All messages, debug information and so on, should always
# be written to standard error.

def p(*args)
	if @runner and @runner.server
		raise "Writing to stdout in server mode will break things!"
	else
		super(*args)
	end
end

# Here we redefine the function puts to raise an error if anything is written to standard out
# while in server mode. This is because the server mode uses standard out to communicate
# and writing to standard out can break it. All messages, debug information and so on, should always
# be written to standard error.

def puts(*args)
	if @runner and @runner.server
		raise "Writing to stdout in server mode will break things!"
	else
		super(*args)
	end
end
 
# Here we redefine the function print to raise an error if anything is written to standard out
# while in server mode. This is because the server mode uses standard out to communicate
# and writing to standard out can break it. All messages, debug information and so on, should always
# be written to standard error.

def print(*args)
	if @runner and @runner.server
		raise "Writing to stdout in server mode will break things!"
	else
		super(*args)
	end
end


# Analyse the directory of the run. This should be called from the directory where the files of the run are located. This method reads in the CodeRunner data already available in <tt>code_runner_info.rb</tt> and <tt>code_runner_results.rb</tt>, and then calls <tt>process_directory_code_specific</tt> which is defined in the code module.

def process_directory
	
	# Clear the cache
  # EGH removed the two lines below because code module need the cache
  # to last, e.g. if it contains references to other files
	#@runner.cache[:runs]||={}
	#@runner.cache[:runs][@id] = {}
	logf(:process_directory)
	raise CRFatal.new("Something has gone horribly wrong: runner.class is #{@runner.class} instead of CodeRunner") unless @runner.class.to_s == "CodeRunner"

	begin
		@code_runner_version = Version.new(File.read('.code_runner_version.txt'))
		File.read('code_runner_info.rb')
	rescue Errno::ENOENT # version may be less than 0.5.1 when .code_runner_version.txt was introduced
		@code_runner_version = Version.new('0.5.0')
	end
	
	@directory = Dir.pwd
	@relative_directory = File.expand_path(Dir.pwd).sub(File.expand_path(@runner.root_folder) + '/', '')
# 	p @directory
	@readme = nil
	
	#if @code_runner_version < Version.new('0.5.1')
		#begin
			#update_from_version_0_5_0_and_lower
		#rescue Errno::ENOENT => err # No code runner files were found
			#unless @runner.heuristic_analysis
				#puts err
				#raise CRFatal.new("No code runner files found: suggest using heuristic analysis (flag -H if you are using the code_runner script)")
			#end
			#unless @runner.current_request == :traverse_directories
				#@runner.requests.push :traverse_directories unless @runner.requests.include? :traverse_directories
				#raise CRMild.new("can't begin heuristic analysis until there has been a sweep over all directories") # this will get rescued
			#end
			#@runner.increment_max_id	
			#@id = @runner.max_id
			#@job_no = -1
			#run_heuristic_analysis
		#end
	#end
		begin
			read_info
		rescue Errno::ENOENT => err # No code runner files were found
			unless @runner.heuristic_analysis
				puts err
				raise CRFatal.new("No code runner files found: suggest using heuristic analysis (flag -H if you are using the code_runner script)")
			end
			unless @runner.current_request == :traverse_directories
				@runner.requests.push :traverse_directories unless @runner.requests.include? :traverse_directories
				raise CRMild.new("can't begin heuristic analysis until there has been a sweep over all directories") # this will get rescued
			end
			@runner.increment_max_id	
			@id = @runner.max_id
			@job_no = -1
			run_heuristic_analysis
		end
	
	
  @cr_has_read_results = false
  if FileTest.exist? 'code_runner_results.rb'
    begin
      read_results
      @cr_has_read_results = true
    rescue NoMethodError, SyntaxError => err
      puts err
      puts 'Results file possibly corrupted for ' + @run_name
    end	
  end

	@running = (@@current_status =~ Regexp.new(@job_no.to_s)) ? true : false 
	if @running and methods.include? :get_run_status
		@status = get_run_status(@job_no, @@current_status) rescue :Unknown
	else
		@status ||= :Unknown
	end
	#logi '@@current_status', @@current_status, '@job_no', @job_no
	#logi '@running', @running
  if not @cr_has_read_results or @running or not [:Complete, :Failed].include? @status or @runner.recalc_all or @runner.reprocess_all
    process_directory_code_specific	
  end 
  
  # Sometimes the run can be completed and still in the queue, in
  # which case process_directory_code_specific may set @status==:Complete
  # or @status==:Failed even though @running = true. Here we update
  # @running if this is the case. This will have no effect on any subsequent
  # update as CodeRunner does not use @running as a criterion for deciding
  # whether or not to recheck a run and call process_directory again.
  @running = false if [:Complete, :Failed].include? @status
	
	raise CRFatal.new("status must be one of #{PERMITTED_STATI.inspect}") unless PERMITTED_STATI.include? @status
	@max = {}
	write_results
	@component_runs = []
	generate_component_runs
	save
  commit_results if @runner.is_in_repo? and not @running
	return self
end

# Read input parameters from the file <tt>code_runner_info.rb</tt>

def read_info
	eval(File.read('code_runner_info.rb')).each do |key, value|
		set(key, value)
	end
end

# Read results from the file <tt>code_runner_results.rb</tt>

def read_results
	return if @runner.recalc_all
	eval(File.read('code_runner_results.rb')).each do |key, value|
		set(key, value)
	end
end

# Write results to the file <tt>code_runner_results.rb</tt>

def write_results
	logf(:write_results)
	Dir.chdir(@directory){File.open("code_runner_results.rb", 'w'){|file| file.puts results_file}}
end

# Return the text of the results file.

def results_file
	logf(:results_file)
	return <<EOF
# <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
# #{rcp.code_long} Results
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
#
# This is a syntactically correct Ruby file, which is used by CodeRunner. Please do not edit unless you know what you are doing.
# Directory:	#{@directory}
# Runname:	#{@run_name}
# ID:		#{@id}

# Results:
#{(rcp.results+rcp.run_info - [:component_runs]).inject({}){|hash, (var,type_co)| hash[var] = send(var); hash}.pretty_inspect}

# <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
EOF

end

# Return a line of data for printing to file in CodeRunner#readout, organised according to the run class property rcp.readout_list 

def data_string
	rcp.readout_list.inject(""){|str,var| str+"#{send(var)}code_runner_spacer"}.gsub(/\s/, '_').gsub(/code_runner_spacer/, "\t") + "\n" 
end

# Used for the status with comments command.

def comment_line
	"#{id}: #{@comment}"
	sprintf("%2d:%d %1s:%2.1f(%s) %3s%1s %s",  @id, @job_no, @status.to_s[0,1],  @run_time.to_f / 60.0, @nprocs.to_s, percent_complete, "%", @comment)
end

# Cache the run object in the file <tt>.code_runner_run_data</tt>

def save
	
	logf(:save)
	raise CRFatal.new("Something has gone horribly wrong: runner.class is #{@runner.class} instead of CodeRunner") unless @runner.class.to_s =~ /^CodeRunner(::Merged)?/
	runner, @runner = @runner, nil
	@system_triers, old_triers = nil, @system_triers
	@component_runs.each{|run| run.runner = nil} if @component_runs
	#@component_runs.each{|run| run.runner = nil} if @component_runs
# 	logi(self)
	#pp self
	Dir.chdir(@directory){File.open(".code_runner_run_data", 'w'){|file| file.puts Marshal.dump(self)}}
	@runner = runner
	@component_runs.each{|run| run.runner = runner} if @component_runs
	@system_triers = old_triers 
end


# Load the run object from the file <tt>.code_runner_run_data</tt>

def self.load(dir, runner)
	raise CRFatal.new("runner supplied in Run.load was not an instance of code runner; runner.class = #{runner.class}") unless runner.class.to_s == "CodeRunner"
	begin
		raise CRMild.new("No saved run data") unless FileTest.exist? (dir+"/.code_runner_run_data")
		run = Marshal.load(File.read(dir+"/.code_runner_run_data"))
	rescue ArgumentError => err
		raise err unless err.message =~ /undefined class/
		#NB this means that all code_names have to contain only lowercase letters:
# 		code, modlet = err.message.scan(/CodeRunner\:\:([A-Z][a-z0-9]+)((?:[A-Z]\w+)+)?Run/)[0]
# 		code, modlet = err.message.scan(/CodeRunner\:\:([A-Z][a-z0-9_]+)(?:::([A-Z]\w+))?/)[0]
# 		ep code, modlet; exit
# 		code.gsub!(/([a-z0-9])([A-Z])/, '\1_\2')
# 		modlet.gsub!(/([a-z0-9])([A-Z])/, '\1_\2')
# 		ep err, modlet, code
# 		runner.setup_run_class(code.downcase, modlet: modlet.downcase)
# 		retry
		CodeRunner.repair_marshal_run_class_not_found_error(err)
		run = Marshal.load(File.read(dir+"/.code_runner_run_data"))		
	end
	run.runner = runner
	raise CRFatal.new("Something has gone horribly wrong: runner.class is #{run.runner.class} instead of CodeRunner") unless run.runner.class.to_s == "CodeRunner"
	run.directory = dir
	# For backwards compatibility with versions < 0.14
	run.instance_variable_set(:@component_run_list, run.instance_variable_get(:@phantom_run_list)) if run.instance_variable_get(:@phantom_run_list) 
	run.component_runs.each{|r| runner.add_component_run(r); r.runner = runner} if run.component_runs
	#@component_runs = []
	return run
end

# Return the name of the defaults file currently in use.

def defaults_file_name
	if @runner.defaults_file
		return "#{@runner.defaults_file}_defaults.rb"
	else
		return "#{rcp.code}_defaults.rb"
	end
end

@code_module_folder = "/dev/null"

# A list of places where defaults files may be found

def self.defaults_location_list
  locs = [rcp.user_defaults_location, rcp.code_module_folder + "/defaults_files"]
  if Repository.repo_folder
    repo = Repository.open_in_subfolder(Dir.pwd)
    folder = repo.dir.to_s + '/defaults_files/' + rcp.code + 'crmod/'
    FileUtils.makedirs folder
    locs.unshift folder
  end
  locs
end

def defaults_location_list
  self.class.defaults_location_list
end

# Return the folder where the default defaults file is located.

def defaults_location
  location = defaults_location_list.find{|folder| FileTest.exist? folder and Dir.entries(folder).include? defaults_file_name}
  raise "Can't find defaults_file #{defaults_file_name} in #{defaults_location_list.join(',')}." unless location
  location
end

# Return true if the run is completed, false otherwise

def is_complete
	@status == :Complete
end

alias :ctd :is_complete

# This function is a hook which is used by system modules. For runs it is defined as the id. 

def job_identifier
	id
end

class NoRunnerError < StandardError
	def new(mess)
		super("No Runner: a runner was needed for this Run method call "+mess)
	end
end

# Update instance variables using the given defaults file. Give warnings if the defaults file contains variables which are not simulation input parameters

def evaluate_defaults_file(filename)
	text = File.read(filename)
	text.scan(/^\s*@(\w+)/) do
		var_name = $~[1].to_sym
		next if var_name == :defaults_file_description
		unless rcp.variables.include? var_name
			warning("---#{var_name}---, specified in #{File.expand_path(filename)}, is not a variable. This could be an error")
		end
	end
	instance_eval(text)
end

#  This function set the input parameters of the run using the following sources in ascending order of priority: main defaults file (in the code module folder), local defaults file (in the local Directory), parameters (an inspected hash usually specified on the command line).

def update_submission_parameters(parameters, start_from_defaults=true)
	logf(:update_submission_parameters)
	if start_from_defaults
		#upgrade_defaults_from_0_5_0 if self.class.constants.include? :DEFAULTS_FILE_NAME_0_5_0
		main_defaults_file = "#{defaults_location}/#{defaults_file_name}"
		main_defaults_file_text = 		File.read(main_defaults_file)
		evaluate_defaults_file(main_defaults_file)

		unless FileTest.exist?(defaults_file_name)
			main_defaults_file_text.gsub!(/^/, "#")
			header = <<EOF
#############################################################
# CodeRunner Local Defaults File 
############################################################
#
# This is a local copy of the central defaults file, which 
# was copied from the central defaults file 
#		#{defaults_file_name} 
# 
# to the folder
# 	#{Dir.pwd}
#
# at 
# 	#{Time.now}
#
# by CodeRunner version #{CODE_RUNNER_VERSION}
#
# All lines in the original file have been commented out:
# they are kept as a reference to make adding local defaults easier. 
# It is suggested that local changes are placed at the top 
# of this file, not in the body of the commented out section.
#
# Local changes override the central defaults file. However,
# if the central defaults file changes, any variables which 
# are not overidden here will change for any future simulations
# in this folder.
#
##############################################################






# Begin Copy of Central Defaults:
#
#
EOF
			main_defaults_file_text = header + main_defaults_file_text
			File.open(defaults_file_name, 'w'){|file| file.puts main_defaults_file_text}
      if @runner.is_in_repo?
        repo = Repository.open_in_subfolder(Dir.pwd)
        repo.add(defaults_file_name)
        repo.autocommit("Added local defaults file #{defaults_file_name} in folder #{Dir.pwd}")
      end
                                                                                     #{defaults_file_name} in folder #{Dir.pwd
                                                                                     ##{defaults_file_name} in folder #{Dir.pwd
                                                                                     #
		end
		#FileUtils.cp("#{defaults_location}/#{defaults_file_name}", defaults_file_name) 
		
		evaluate_defaults_file(defaults_file_name)
	end
	return unless parameters
	@parameter_hash_string = parameters
	raise "parameters: #{parameters.inspect} must be a string which evaluates to a hash" unless parameters.class == String and parameters = eval(parameters) and parameters.class == Hash # parameters.class == String and parameters =~ /\S/
	@parameter_hash = parameters 
	parameters.each do |var, value|
		raise CRFatal.new('Cannot specify id as a parameter') if var.to_sym == :id
		set(var, value) unless value == :default
		next if [:comment, :extra_files].include? var
		@naming_pars.push var
	end
	@naming_pars.uniq!
	self
end

def execute_submission
	if @runner.test_submission
		log 'testing submission'
		eputs info_file
		File.delete(@runner.root_folder + "/submitting")
		exit
	else
		execute
	end
end

# def submit
# 	logf(:submit)
# 	logi(:@nprocs, @nprocs)
# 	
# 	raise "Test Submit Error Handling" if @run_test_flags and @run_test_flags[:test_submit_error_handling]
# 	
# 	eputs "System " + SYS 
# 	eputs "nprocs " + @nprocs
# # 		puts send(:q)
# 
# 	raise CRFatal.new ("Can't find executable: #{executable_location}/#{executable_name}") unless FileTest.exist? File.expand_path("#{executable_location}/#{executable_name}")
# 
# 	@naming_pars.each{|par| raise CRFatal.new("@naming_par #{par} is not listed in variables") unless rcp.variables.include? par}
# # 	@other_pars = []
# # 	@@variables.dup.each do |par, type_co|
# # 		@other_pars.push par unless @naming_pars.include? par
# # 	end
# 
# # 	@dir_name = %[v#@version] + @naming_pars.inject("") do |str, par|
# # 		str+="/#{par}_#{send(par)}"
# # 	end
# 
# 	@dir_name = %[v#@version]
# 
# 	@run_name = %[v#@version] + @naming_pars.inject("") do |str, par|
# 		str+="_#{par}_#{send(par)}"
# 	end
# 	@dir_name = @dir_name.gsub(/\s+/, "_") + "/id_#@id"
# 	@run_name = @run_name.gsub(/\s+/, "_") + "_id_#@id"
# 	@directory = File.expand_path(@dir_name)
# 
# 	@job_no = nil
# 	qstat = queue_status #|| ""
# #  	puts qstat;# gets
# # 	qstat = qstat =~ /\S/ ? qstat : nil 
# 	if qstat and qstat.class == String
# 		FileUtils.makedirs(@dir_name)
# 		Dir.chdir(@dir_name) do 
# 			generate_input_file
# 			job_nos = qstat.scan(/^\s*(\d+)/).map{|match| match[0].to_i} if qstat
# # 			logi(:job_nos, job_nos)
# 			##################
# 			execute_submission
# 			##################
# 			qstat = queue_status #|| ""
# # 			qstat = qstat=~/\S/ ? qstat : nil
# 			5.times do # job_no may not appear instantly
# 				new_job_nos = qstat.scan(/^\s*(\d+)/).map{|match| match[0].to_i}
# # 				puts new_job_nos
# 				logi(:new_minus_old, new_job_nos-job_nos)
# 				@job_no = (new_job_nos-job_nos).sort[-1]
# 				break if @job_no
# 				sleep 0.2
# 				qstat = queue_status
# 			end
# 			@job_no ||= -1 # some functions don't work if job_no couldn't be found, but most are ok
# 			eputs info_file
# 			@sys = SYS
# 			write_info
# 			File.open(".code_runner_version.txt", 'w'){|file| file.puts CODE_RUNNER_VERSION}
# 			File.open("code_runner_modlet.rb", 'w'){|file| file.puts rcp.modlet_source} if rcp.modlet_required
# 		end
# 		
# 
# 	else 
# 		File.delete("submitting")
# 		raise CRFatal.new("queue_status did not return a string; submission cancelled. Suggest editing system_modules/#{SYS}.rb")
# 	end
# 
# end

#   Generate the run name and the directory name, and check that the directory is empty. The run name, i.e. @run_name can be set beforehand, in which case it will not be changed. The directory name choice can be influenced by the variable @dir_name, which is not used outside this function.

def prepare_submission(options={})
	raise "Test Submit Error Handling" if @run_test_flags and @run_test_flags[:test_submit_error_handling]
	
	#p '@nprocs', @nprocs
	if @runner
		SUBMIT_OPTIONS.each do |option|
				set(option, @runner.send(option)) if @runner.send(option)
		end
	end
	#p '@nprocs', @nprocs
	
# 		puts send(:q)

	raise CRFatal.new ("Can't find executable: #{executable_location}/#{executable_name}") unless FileTest.exist? File.expand_path("#{executable_location}/#{executable_name}")

	@naming_pars.each{|par| raise CRFatal.new("@naming_par #{par} is not listed in variables or run_info") unless (rcp.variables + rcp.run_info).include? par}
	@naming_pars.delete(:g_exb_start_timestep)
	unless @dir_name # dir_name can be set in advance to change the default directory name
		@dir_name = %[v#@version]
		@dir_name = @dir_name.gsub(/\s+/, "_") + "/id_#@id"
	end
	generate_run_name unless @run_name
	
	@directory = File.expand_path(@dir_name)
	#@relative_directory = File.expand_path(Dir.pwd).sub(File.expand_path(@runner.root_folder) + '/', '')
	#@relative_directory = @directory.sub(File.expand_path(@runner.root_folder) + '/', '')
	@relative_directory = @dir_name

	raise "Directory #@dir_name contains code_runner_info" if FileTest.exist? @directory and Dir.entries(@directory).include? ["code_runner_info.rb"]

	@job_no = nil
	FileUtils.makedirs(@dir_name)
	Dir.chdir(@dir_name) do 
		generate_input_file
    copy_extra_files
		
		File.open(".code_runner_version.txt", 'w'){|file| file.puts CODE_RUNNER_VERSION}
		#File.open("code_runner_modlet.rb", 'w'){|file| file.puts rcp.modlet_source} if rcp.modlet_required
	end
	@dir_name = nil

end

#This function copies any files which are required at run time into the run folder.
#It takes the form of an input parameter 'extra_files' which takes in an array
#of file locations and copies them when the run folder is set up. It is called in prepare_submission. 
def copy_extra_files
  if @extra_files.kind_of?String
    @extra_files = [@extra_files]
  end
  if @extra_files.kind_of?Array
    @extra_files.each{|file| 
    FileUtils.cp(file, File.basename(file))}
  end
end

def generate_run_name
		@run_name = %[v#@version] + @naming_pars.inject("") do |str, par|
			str+="_#{par}_#{send(par).to_s[0...8]}"
		end
		@run_name = @run_name.gsub(/\s+/, "_").gsub(/\//, '') + "_id_#@id"
end

def write_info
	Dir.chdir(@directory){File.open("code_runner_info.rb", 'w'){|file| file.puts info_file}}
end

# private :write_info

def info_file
		@modlet = rcp.modlet if rcp.modlet?
		return <<EOF
# <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
# #{rcp.code_long} Input Parameters
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
# Code: 		#{rcp.code}
# System: 	#{@sys}
# Version:	#{@version}
# Nprocs: 	#{@nprocs}
# Directory:	#{Dir.pwd}
# Runname:	#{@run_name}
# ID:		#{@id}
# #{@modlet ? "Modlet:\t#@modlet" : ""} 
# Classname:	#{self.class.to_s}

# #{@job_no ? "Job_No:		#{@job_no}" : ""}

# Parameters:
#{(rcp.variables + rcp.run_info + [:version, :code, :modlet, :sys] - [:component_runs]).inject({}){|hash, var| hash[var] = send(var) unless (!send(var) and send(var) ==  nil); hash}.pretty_inspect}


# Actual Command:
# #{run_command.gsub(/\n/, "\n#")}
# <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
EOF

end

def set_modlet(modlet, folder=nil)
	logf(:set_modlet)
	rcp.modlet.sub!(/.*/, modlet)
	self.class.set_modlet(modlet, folder)
end
private :set_modlet

def self.set_modlet(modlet, folder = nil)
	raise 'old method -- needs to be debugged'
	Log.log("self.set_modlet", self.to_s)
	class_eval(File.read("#{folder ? folder + "/" : ""}#{modlet}"))
	check_and_update
end

# aliold :inspect
def inspect
	old, @runner = @runner, nil
	str = super
	@runner = old
	str
end


# aliold :pretty_inspect
def pretty_print(q)
	old, @runner = @runner, nil
	str = q.pp_object(self)
	@runner = old
	str

end

#    def pretty_print(q)
#       if /\(Kernel\)#/ !~ Kernel.instance_method(:method).bind(self).call(:inspect).inspect
#         q.text self.inspect
#       elsif /\(Kernel\)#/ !~ Kernel.instance_method(:method).bind(self).call(:to_s).inspect && instance_variables.empty?
#         q.text self.to_s
#       else
#         q.pp_object(self)
#       end
#     end

# A hook for module developers

def self.finish_setting_up_class
end

# ALL = []
# READOUT_LIST = []
# CODE = nil

def self.check_and_update
		Log.logf(:check_and_update)

# 	
		finish_setting_up_class
# 				ep self.to_s, constants, self.ancestors

# 		raise CRFatal.new("Code not defined (#{CODE.inspect}) in class #{self.to_s}") unless CODE and CODE.class == String and CODE =~ /\S/  


		NECESSARY_RUN_SYSTEM_METHODS.each do |method|
			raise CRFatal.new("#{method} not defined in #{SYS}_system_runner.rb") unless instance_methods.include?(method)
		end

		NECESSARY_RUN_CODE_METHODS.each do |method|
			raise CRFatal.new("#{method} not defined in #{self.class}_code_runner.rb") unless instance_methods.include?(method)
		end
	
		
		NECESSARY_RUN_CLASS_PROPERTIES.each do |v,class_list|
# 			raise CRFatal.new("#{v} not defined") unless rcp[v]
			raise CRFatal.new("#{v} not defined correctly: class is #{rcp[v].class} instead of one of #{class_list.to_s}") unless class_list.include? rcp[v].class
		end
		
		@readout_list = (rcp.variables+rcp.results) unless rcp.readout_list?

		raise "

Please add the line 

-----------------------------------------------------------
@code_module_folder = folder = File.dirname(File.expand_path(__FILE__)) # i.e. the directory this file is in
---------------------------------------------------------

to your code module.
		
		" unless rcp.code_module_folder?

# 		(variables+results).each{|v| const_get(:READOUT_LIST).push v} unless READOUT_LIST.size > 0

		#if rcp.variables_0_5_0
			#rcp.variables_0_5_0.dup.each do |par, info| #for backwards compatibility only
				#rcp.variables_0_5_0[par] = info[0] if info.class == Array
			#end
		#end





# 		Log.log(:@@variables0, @@variables[0])

		@run_info = rcp.run_info || [] # Run info can optionally be defined in the code module.
# 		ep @run_info
		@run_info = rcp.run_info + ([:preamble, :job_no, :running, :id, :status, :sys, :is_component, :naming_pars, :run_name, :resubmit_id, :real_id, :component_runs, :parameter_hash, :parameter_hash_string, :output_file, :error_file, :extra_files, :code_run_environment] + SUBMIT_OPTIONS) #.each{|v| RUN_INFO.push v} unless RUN_INFO.include? :job_no
		@all = (rcp.variables + rcp.results + rcp.run_info) #.each{|v| ALL.push v}
# 		ep "GOT HERE"
		(@all + [:directory, :run_name, :modlet, :relative_directory]).each{|var| send(:attr_accessor, var)}
		#eputs "Checking and updating"
    @user_defaults_location = ENV['HOME'] + "/.coderunner/#{rcp.code}crmod/defaults_files"
		#eputs ' user_defaults_location', rcp.user_defaults_location
		define_method(:output_file) do 
			return @output_file if @output_file
			@output_file = super()
		end
		define_method(:error_file) do 
			return @error_file if @error_file
			@error_file = super()
		end

		Dir.chdir(SCRIPT_FOLDER + "/system_modules") do 
		@system_run_classes ||= 	
			Dir.entries(Dir.pwd).find_all{|file| file =~ /^[^\.].+\.rb$/}.inject([]) do |arr, file|
				#p Dir.pwd
				#p 'required', file, Dir.pwd
				require Dir.pwd + '/' + file
# 				p CodeRunner.constants
				sys = file.sub(/\.rb$/, '')
				arr.push(add_a_child_class("#{sys.variable_to_class_name}Run"))
				arr[-1].send(:include, CodeRunner.const_get(sys.variable_to_class_name))
				arr
			end
		end

		
end

def dup
	return self.class.new(@runner).learn_from(self)
end

def create_component
	@component_runs ||= []
	new_run = dup
	new_run.is_component = true
	new_run.real_id = @id
	@runner.add_component_run(new_run)
	@component_runs.push new_run
	new_run
end

def learn_from(run)
	run.instance_variables.each do |var|	
#   		puts var
#  		puts run.instance_variable_get(var)
			instance_variable_set(var,run.instance_variable_get(var)) 
#  				puts instance_variable_get(var)

# 		rescue NoMethodError
# 			next
# 		end
	end
	self
end



		
def logiv
	instance_variables.each do |var|
		unless var == :@runner or var == :@system_triers
			log(var); logi(instance_variable_get(var))
		end
	end
end

def recheck
	logf(:recheck)
	Dir.chdir(@directory) do
# 		puts 'ackack'
		puts "Rechecking #@run_name"
		runner = @runner
		instance_variables.each{|var| instance_variable_set(var, nil) unless var == :@runner}
		begin File.delete("CODE_RUNNER_RUN_DATA") rescue Errno::ENOENT end
		begin File.delete("CODE_RUNNER_RESULTS") rescue Errno::ENOENT end
		process_directory
		save
	end
end

def generate_component_runs
end
	
def generate_combined_ids(type)
	raise CRFatal.new("Can't call generate_combined_ids from a run")
end

# @@maxes = {}
# @@cmaxes = {}

def max(variable, complete=false) #does this run have the maximum value of this variable
	raise ArgumentError.new("complete must be true or false") unless [TrueClass, FalseClass].include? complete.class
	@runner.generate_combined_ids
	ids = @runner.combined_ids 
	if complete
		ids = ids.find_all{|id| @runner.combined_run_list[id].status == :Complete}
		max_id = @runner.cmaxes[variable] ||= ids.sort_by{|id| @runner.combined_run_list[id].send(variable)}[-1]
	else
		max_id = @runner.maxes[variable] ||= ids.sort_by{|id| @runner.combined_run_list[id].send(variable)}[-1]
	end
	return @runner.combined_run_list[max_id].send(variable) == send(variable)
end

# # @@mins = {}
# @@cmins = {}


def min(variable, complete=false) #does this run have the minimum value of this variable
	raise ArgumentError.new("complete must be true or false") unless [TrueClass, FalseClass].include? complete.class
	@runner.generate_combined_ids
	ids = @runner.combined_ids 
	
	if complete
		ids = ids.find_all{|id| @runner.combined_run_list[id].status == :Complete}
		min_id = @runner.cmins[variable] ||= ids.sort_by{|id| @runner.combined_run_list[id].send(variable)}[0]
	else
		min_id = @runner.mins[variable] ||= ids.sort_by{|id| @runner.combined_run_list[id].send(variable)}[0]
	end
	return @runner.combined_run_list[min_id].send(variable) == send(variable)
end

# @@fmaxes = {}
# @@cfmaxes = {}

# # Does this run have the maximum value of this variable to be found amoung the filtered runs?
# 
# def fmax(variable, complete = false) 
# 	raise ArgumentError.new("complete must be true or false") unless [TrueClass, FalseClass].include complete.class
# 	@runner.generate_combined_ids
# 	ids = @runner.filtered_ids # o^o-¬
# 	if complete
# 		ids = ids.find_all{|id| @runner.combined_run_list[id].status == :Complete}
# 		max_id = @@cfmaxes[variable] ||= ids.sort_by{|id| @runner.combined_run_list[id].send(variable)}[-1]
# 	else
# 		max_id = @@fmaxes[variable] ||= ids.sort_by{|id| @runner.combined_run_list[id].send(variable)}[-1]
# 	end
# 	return @runner.combined_run_list[max_id].send(variable) == send(variable)
# end
# 

def smax(variable,sweep=nil, complete=nil)
	logf(:max)
 	sweep ||= variable
	if complete
		@csmaxes[variable] ||= {}
		max_id = @csmaxes[variable][sweep] = @runner.get_max(self, variable,sweep, complete)
	else
		@smaxes[variable] ||= {}
		max_id = @smaxes[variable][sweep] = @runner.get_max(self, variable,sweep, complete)
	end
	return @runner.combined_run_list[max_id].send(variable) == send(variable)
end

def smin(variable,sweep=nil, complete=nil)
	logf(:min)
 	sweep ||= variable
	@smins ||= {}
	@csmins ||= {}
	if complete
		@csmins[variable] ||= {}
		min_id = @csmins[variable][sweep] = @runner.get_min(self, variable,sweep, complete)
	else
		@smins[variable] ||= {}
		min_id = @smins[variable][sweep] = @runner.get_min(self, variable,sweep, complete)
	end
	return @runner.combined_run_list[min_id].send(variable) == send(variable)
end

# aliold :_dump
# def _dump(*args)
# 	@runner, runner = nil, @runner
# 	ans = super(*args)
# 	@runner = runner
# 	return ans
# end

def executable_name
	File.basename(@executable||=@runner.executable)
end

def executable_location
	@executable||=@runner.executable
	raise "No executable" unless @executable
	File.dirname(@executable)
end

def update_in_queue
	unless @status == :Queueing
		raise 'Can only updated runs whose status is :Queueing'
	end
	unless methods.include? :batch_script_file
		raise 'Can only update runs which have been submitted using a batch script file'
	end	
	old_run_name = @run_name
	generate_run_name
	new_run_name = @run_name
	#@run_name = old_run_name
	unless FileTest.exist?(filename = @directory + '/' + batch_script_file) or 
	 	FileTest.exist?(filename =  @runner.root_folder + '/' + batch_script_file)
			raise 'Could not find batch_script_file'
	end
	old_batch_script=File.read(filename)
	eputs old_batch_script
eputs old_batch_script.gsub(Regexp.new(Regexp.escape(old_run_name)), new_run_name)
	ep Regexp.new(Regexp.escape(old_run_name))
	File.open(filename, 'w'){|file| file.puts old_batch_script.gsub(Regexp.new(Regexp.escape(old_run_name)), new_run_name)}

	
	generate_input_file
	#throw(:done)
	write_info
end

	# A hook... default is to do nothing

	def self.modify_job_script(runner, runs, script)
		return script
	end	

	# A hook... a string which gets put into the job
	# script. Used to load modules, configure the run 
	# time environment for a given code. Default
	# is to return an empty string.

	def code_run_environment
		@code_run_environment
	end

# Prints a warning message, useful for pre-submit checks.
def warning(message)
	eputs "Warning: " + message; sleep 0.1
end

class SubmitError < StandardError
end

# Prints an error message and raises a SubmitError, useful for pre-submit checks.
def error(message)
	raise("Error: " + message)
end

# Returns the number of nodes times the number of cores, assuming the processor 
# layout is specified as either cores, nodesxcores, or nodesxcoresxthreads
def actual_number_of_processors
	  raise "Please specify the processor layout using the -n or (n:) option" unless @nprocs
		  @nprocs.split('x').slice(0..1).map{|n| n.to_i}.inject(1){|ntot, n| ntot*n}
end

def latex_report_header
#gsub is a hack which removes 14 spaces from the beginning of the file. This allows nice code indentation here.
<<-EOF.gsub(/^ {4}/, "")
    % Set up  
    \\documentclass[11pt, twocolumn]{report}
    \\usepackage{amsmath}
    \\usepackage{amsthm}
    \\usepackage{amssymb}
    \\usepackage{graphicx}
    \\usepackage{caption}
    \\usepackage{subcaption}
    \\usepackage{wrapfig}
    \\usepackage{epstopdf}
    \\usepackage{fullpage}

    \\newcommand{\\newfig}[1]{
    \\includegraphics[width=\\linewidth]{#1}
    }

    \\begin{document}

    % Title Page
    \\title{Run summary for run number #{id}}
    \\date{#{Time.now}}
    \\author{CodeRunner}
                  
    \\maketitle

EOF

end

end

end