openstudio-analysis 1.3.6 → 1.4.0

data/lib/openstudio/analysis/formulation.rb

@@ -1,857 +1,881 @@
-# *******************************************************************************
-# OpenStudio(R), Copyright (c) Alliance for Sustainable Energy, LLC.
-# See also https://openstudio.net/license
-# *******************************************************************************
-
-# OpenStudio formulation class handles the generation of the OpenStudio Analysis format.
-module OpenStudio
-  module Analysis
-    SeedModel = Struct.new(:file)
-    WeatherFile = Struct.new(:file)
-
-    @@measure_paths = ['./measures']
-    # List of paths to look for measures when adding them. This currently only is used when loading an
-    # analysis hash file. It looks in the order of the measure_paths. As soon as it finds one, it stops.
-    def self.measure_paths
-      @@measure_paths
-    end
-
-    def self.measure_paths=(new_array)
-      @@measure_paths = new_array
-    end
-
-    class Formulation
-      attr_reader :seed_model
-      attr_reader :weather_file
-      attr_reader :analysis_type
-      attr_reader :outputs
-      attr_accessor :display_name
-      attr_accessor :workflow
-      attr_accessor :algorithm
-      attr_accessor :osw_path
-      attr_accessor :download_zip
-      attr_accessor :download_reports
-      attr_accessor :download_osw
-      attr_accessor :download_osm
-      attr_accessor :cli_debug
-      attr_accessor :cli_verbose
-      attr_accessor :initialize_worker_timeout
-      attr_accessor :run_workflow_timeout
-      attr_accessor :upload_results_timeout
-
-      # the attributes below are used for packaging data into the analysis zip file
-      attr_reader :weather_files
-      attr_reader :seed_models
-      attr_reader :worker_inits
-      attr_reader :worker_finalizes
-      attr_reader :libraries
-      attr_reader :server_scripts
-
-      # Create an instance of the OpenStudio::Analysis::Formulation
-      #
-      # @param display_name [String] Display name of the project.
-      # @return [Object] An OpenStudio::Analysis::Formulation object
-      def initialize(display_name)
-        @display_name = display_name
-        @analysis_type = nil
-        @outputs = []
-        @workflow = OpenStudio::Analysis::Workflow.new
-        # Initialize child objects (expect workflow)
-        @weather_file = WeatherFile.new
-        @seed_model = SeedModel.new
-        @algorithm = OpenStudio::Analysis::AlgorithmAttributes.new
-        @download_zip = true
-        @download_reports = true
-        @download_osw = true
-        @download_osm = true
-        @cli_debug = "--debug"
-        @cli_verbose = "--verbose"
-        @initialize_worker_timeout = 28800
-        @run_workflow_timeout = 28800
-        @upload_results_timeout = 28800
-
-        # Analysis Zip attributes
-        @weather_files = SupportFiles.new
-        @seed_models = SupportFiles.new
-        @worker_inits = SupportFiles.new
-        @worker_finalizes = SupportFiles.new
-        @libraries = SupportFiles.new
-        @server_scripts = ServerScripts.new
-      end
-     
-      # Define the type of analysis which is going to be running
-      #
-      # @param name [String] Name of the algorithm/analysis. (e.g. rgenoud, lhs, single_run)
-      # allowed values are ANALYSIS_TYPES = ['spea_nrel', 'rgenoud', 'nsga_nrel', 'lhs', 'preflight', 
-      #                                      'morris', 'sobol', 'doe', 'fast99', 'ga', 'gaisl', 
-      #                                      'single_run', 'repeat_run', 'batch_run']
-      def analysis_type=(value)
-        if OpenStudio::Analysis::AlgorithmAttributes::ANALYSIS_TYPES.include?(value)
-          @analysis_type = value
-        else
-          raise "Invalid analysis type. Allowed types: #{OpenStudio::Analysis::AlgorithmAttributes::ANALYSIS_TYPES}"
-        end
-      end
-
-      # Path to the seed model
-      #
-      # @param path [String] Path to the seed model. This should be relative.
-      def seed_model=(file)
-        @seed_model[:file] = file
-      end
-
-      # Path to the weather file (or folder). If it is a folder, then the measures will look for the weather file
-      # by name in that folder.
-      #
-      # @param path [String] Path to the weather file or folder.
-      def weather_file=(file)
-        @weather_file[:file] = file
-      end
-
-      # Set the value for 'download_zip'
-      #
-      # @param value [Boolean] The value for 'download_zip'
-      def download_zip=(value)
-        if [true, false].include?(value)
-          @download_zip = value
-        else
-          raise ArgumentError, "Invalid value for 'download_zip'. Only true or false allowed."
-        end
-      end
-      
-      # Set the value for 'download_reports'
-      #
-      # @param value [Boolean] The value for 'download_reports'
-      def download_reports=(value)
-        if [true, false].include?(value)
-          @download_reports = value
-        else
-          raise ArgumentError, "Invalid value for 'download_reports'. Only true or false allowed."
-        end
-      end
-      
-      # Set the value for 'download_osw'
-      #
-      # @param value [Boolean] The value for 'download_osw'
-      def download_osw=(value)
-        if [true, false].include?(value)
-          @download_osw = value
-        else
-          raise ArgumentError, "Invalid value for 'download_osw'. Only true or false allowed."
-        end
-      end
-      
-      # Set the value for 'download_osm'
-      #
-      # @param value [Boolean] The value for 'download_osm'
-      def download_osm=(value)
-        if [true, false].include?(value)
-          @download_osm = value
-        else
-          raise ArgumentError, "Invalid value for 'download_osm'. Only true or false allowed."
-        end
-      end
-
-      # Set the value for 'cli_debug'
-      #
-      # @param value [Boolean] The value for 'cli_debug'
-      def cli_debug=(value)
-        @cli_debug = value
-      end
-
-      # Set the value for 'cli_verbose'
-      #
-      # @param value [Boolean] The value for 'cli_verbose'
-      def cli_verbose=(value)
-        @cli_verbose = value
-      end
-
-      # Set the value for 'run_workflow_timeout'
-      #
-      # @param value [Integer] The value for 'run_workflow_timeout'
-      def run_workflow_timeout=(value)
-        if value.is_a?(Integer)
-          @run_workflow_timeout = value
-        else
-          raise ArgumentError, "Invalid value for 'run_workflow_timeout'. Only integer values allowed."
-        end
-      end
-
-      # Set the value for 'initialize_worker_timeout'
-      #
-      # @param value [Integer] The value for 'initialize_worker_timeout'
-      def initialize_worker_timeout=(value)
-        if value.is_a?(Integer)
-          @initialize_worker_timeout = value
-        else
-          raise ArgumentError, "Invalid value for 'initialize_worker_timeout'. Only integer values allowed."
-        end
-      end
-
-      # Set the value for 'upload_results_timeout'
-      #
-      # @param value [Integer] The value for 'upload_results_timeout'
-      def upload_results_timeout=(value)
-        if value.is_a?(Integer)
-          @upload_results_timeout = value
-        else
-          raise ArgumentError, "Invalid value for 'upload_results_timeout'. Only integer values allowed."
-        end
-      end
-
-      # Add an output of interest to the problem formulation
-      #
-      # @param output_hash [Hash] Hash of the output variable in the legacy format
-      # @option output_hash [String] :display_name Name to display
-      # @option output_hash [String] :display_name_short A shorter display name
-      # @option output_hash [String] :metadata_id Link to DEnCity ID in which this output corresponds
-      # @option output_hash [String] :name Unique machine name of the variable. Typically this is measure.attribute
-      # @option output_hash [String] :export Export the variable to CSV and dataframes from OpenStudio-server
-      # @option output_hash [String] :visualize Visualize the variable in the plots on OpenStudio-server
-      # @option output_hash [String] :units Units of the variable as a string
-      # @option output_hash [String] :variable_type Data type of the variable
-      # @option output_hash [Boolean] :objective_function Whether or not this output is an objective function. Default: false
-      # @option output_hash [Integer] :objective_function_index Index of the objective function. Default: nil
-      # @option output_hash [Float] :objective_function_target Target for the objective function to reach (if defined). Default: nil
-      # @option output_hash [Float] :scaling_factor How to scale the objective function(s). Default: nil
-      # @option output_hash [Integer] :objective_function_group If grouping objective functions, then group ID. Default: nil
-      def add_output(output_hash)
-        # Check if the name is already been added.
-        exist = @outputs.find_index { |o| o[:name] == output_hash[:name] }
-        # if so, update the fields but keep objective_function_index the same
-        if exist
-          original = @outputs[exist]
-          if original[:objective_function] && !output_hash[:objective_function]
-            return @outputs
-          end
-          output = original.merge(output_hash)
-          output[:objective_function_index] = original[:objective_function_index]
-          @outputs[exist] = output
-        else
-          output = {
-            units: '',
-            objective_function: false,
-            objective_function_index: nil,
-            objective_function_target: nil,
-            #set default to nil or 1 if objective_function is true and this is not set
-            objective_function_group: (output_hash[:objective_function] ? 1 : nil),
-            scaling_factor: nil,
-            #set default to false or true if objective_function is true and this is not set
-            visualize: (output_hash[:objective_function] ? true : false),
-            metadata_id: nil,
-            export: true,
-          }.merge(output_hash)
-          #set display_name default to be name if its not set
-          output[:display_name] = output_hash[:display_name] ? output_hash[:display_name] : output_hash[:name]
-          #set display_name_short default to be display_name if its not set, this can be null if :display_name not set
-          output[:display_name_short] = output_hash[:display_name_short] ? output_hash[:display_name_short] : output_hash[:display_name]
-          # if the variable is an objective_function, then increment and
-          # assign and objective function index
-          if output[:objective_function]
-            values = @outputs.select { |o| o[:objective_function] }
-            output[:objective_function_index] = values.size
-          end
-
-          @outputs << output
-        end
-
-        @outputs
-      end
-
-      # return the machine name of the analysis
-      def name
-        @display_name.to_underscore
-      end
-
-      # return a hash.
-      #
-      # @param version [Integer] Version of the format to return
-      # @return [Hash]
-      def to_hash(version = 1)
-        # fail 'Must define an analysis type' unless @analysis_type
-        if version == 1
-          h = {
-            analysis: {
-              display_name: @display_name,
-              name: name,
-              output_variables: @outputs,
-              problem: {
-                analysis_type: @analysis_type,
-                algorithm: algorithm.to_hash(version),
-                workflow: workflow.to_hash(version)
-              }
-            }
-          }
-
-          if @seed_model[:file]
-            h[:analysis][:seed] = {
-              file_type: File.extname(@seed_model[:file]).delete('.').upcase,
-              path: "./seed/#{File.basename(@seed_model[:file])}"
-            }
-          else
-            h[:analysis][:seed] = nil
-          end
-
-          # silly catch for if weather_file is not set
-          wf = nil
-          if @weather_file[:file]
-            wf = @weather_file
-          elsif !@weather_files.empty?
-            # get the first EPW file (not the first file)
-            wf = @weather_files.find { |w| File.extname(w[:file]).casecmp('.epw').zero? }
-          end
-
-          if wf
-            h[:analysis][:weather_file] = {
-              file_type: File.extname(wf[:file]).delete('.').upcase,
-              path: "./weather/#{File.basename(wf[:file])}"
-            }
-          else
-            # log: could not find weather file
-            warn 'Could not resolve a valid weather file. Check paths to weather files'
-          end
-
-          h[:analysis][:file_format_version] = version
-          h[:analysis][:cli_debug] = @cli_debug
-          h[:analysis][:cli_verbose] = @cli_verbose
-          h[:analysis][:run_workflow_timeout] = @run_workflow_timeout
-          h[:analysis][:upload_results_timeout] = @upload_results_timeout
-          h[:analysis][:initialize_worker_timeout] = @initialize_worker_timeout
-          h[:analysis][:download_zip] = @download_zip
-          h[:analysis][:download_reports] = @download_reports
-          h[:analysis][:download_osw] = @download_osw
-          h[:analysis][:download_osm] = @download_osm
-
-          #-BLB I dont think this does anything. server_scripts are run if they are in 
-          #the /scripts/analysis or /scripts/data_point directories
-          #but nothing is ever checked in the OSA.
-          #
-          h[:analysis][:server_scripts] = {}
-
-          # This is a hack right now, but after the initial hash is created go back and add in the objective functions
-          # to the the algorithm as defined in the output_variables list
-          ofs = @outputs.map { |i| i[:name] if i[:objective_function] }.compact
-          if h[:analysis][:problem][:algorithm]
-            h[:analysis][:problem][:algorithm][:objective_functions] = ofs
-          end
-
-          h
-        else
-          raise "Version #{version} not defined for #{self.class} and #{__method__}"
-        end
-      end
-
-      # Load the analysis JSON from a hash (with symbolized keys)
-      def self.from_hash(h, seed_dir = nil, weather_dir = nil)
-        o = OpenStudio::Analysis::Formulation.new(h[:analysis][:display_name])
-
-        version = 1
-        if version == 1
-          h[:analysis][:output_variables].each do |ov|
-            o.add_output(ov)
-          end
-
-          o.workflow = OpenStudio::Analysis::Workflow.load(workflow: h[:analysis][:problem][:workflow])
-
-          if weather_dir
-            o.weather_file "#{weather_path}/#{File.basename(h[:analysis][:weather_file][:path])}"
-          else
-            o.weather_file = h[:analysis][:weather_file][:path]
-          end
-
-          if seed_dir
-            o.seed_model "#{weather_path}/#{File.basename(h[:analysis][:seed][:path])}"
-          else
-            o.seed_model = h[:analysis][:seed][:path]
-          end
-        else
-          raise "Version #{version} not defined for #{self.class} and #{__method__}"
-        end
-
-        o
-      end
-
-      # return a hash of the data point with the static variables set
-      #
-      # @param version [Integer] Version of the format to return
-      # @return [Hash]
-      def to_static_data_point_hash(version = 1)
-        if version == 1
-          static_hash = {}
-          # TODO: this method should be on the workflow step and bubbled up to this interface
-          @workflow.items.map do |item|
-            item.variables.map { |v| static_hash[v[:uuid]] = v[:static_value] }
-          end
-
-          h = {
-            data_point: {
-              set_variable_values: static_hash,
-              status: 'na',
-              uuid: SecureRandom.uuid
-            }
-          }
-          h
-        end
-      end
-
-      # save the file to JSON. Will overwrite the file if it already exists
-      #
-      # @param filename [String] Name of file to create. It will create the directory and override the file if it exists. If no file extension is given, then it will use .json.
-      # @param version [Integer] Version of the format to return
-      # @return [Boolean]
-      def save(filename, version = 1)
-        filename += '.json' if File.extname(filename) == ''
-
-        FileUtils.mkdir_p File.dirname(filename) unless Dir.exist? File.dirname(filename)
-        File.open(filename, 'w') { |f| f << JSON.pretty_generate(to_hash(version)) }
-
-        true
-      end
-
-      # save the data point JSON with the variables set to the static values. Will overwrite the file if it already exists
-      #
-      # @param filename [String] Name of file to create. It will create the directory and override the file if it exists. If no file extension is given, then it will use .json.
-      # @param version [Integer] Version of the format to return
-      # @return [Boolean]
-      def save_static_data_point(filename, version = 1)
-        filename += '.json' if File.extname(filename) == ''
-
-        FileUtils.mkdir_p File.dirname(filename) unless Dir.exist? File.dirname(filename)
-        File.open(filename, 'w') { |f| f << JSON.pretty_generate(to_static_data_point_hash(version)) }
-
-        true
-      end
-
-      # save the analysis zip file which contains the measures, seed model, weather file, and init/final scripts
-      #
-      # @param filename [String] Name of file to create. It will create the directory and override the file if it exists. If no file extension is given, then it will use .json.
-      # @return [Boolean]
-      def save_zip(filename)
-        filename += '.zip' if File.extname(filename) == ''
-
-        FileUtils.mkdir_p File.dirname(filename) unless Dir.exist? File.dirname(filename)
-
-        save_analysis_zip(filename)
-      end
-      
-      
-      def save_osa_zip(filename, all_weather_files = false, all_seed_files = false)
-        filename += '.zip' if File.extname(filename) == ''
-
-        FileUtils.mkdir_p File.dirname(filename) unless Dir.exist? File.dirname(filename)
-
-        save_analysis_zip_osa(filename, all_weather_files, all_seed_files)
-      end
-      
-      # convert an OSW to an OSA
-      # osw_filename is the full path to the OSW file
-      # assumes the associated files and directories are in the same location
-      #  /example.osw
-      #  /measures
-      #  /seeds
-      #  /weather
-      #
-      def convert_osw(osw_filename, *measure_paths)
-        # load OSW so we can loop over [:steps]
-        if File.exist? osw_filename  #will this work for both rel and abs paths?
-          osw = JSON.parse(File.read(osw_filename), symbolize_names: true)
-          @osw_path = File.expand_path(osw_filename)
-        else
-          raise "Could not find workflow file #{osw_filename}"
-        end
-        
-        # set the weather and seed files if set in OSW
-        # use :file_paths and look for files to set
-        if osw[:file_paths]        
-          # seed_model, check if in OSW and not found in path search already
-          if osw[:seed_file]
-            osw[:file_paths].each do |path|
-              puts "searching for seed at: #{File.join(File.expand_path(path), osw[:seed_file])}"
-              if File.exist?(File.join(File.expand_path(path), osw[:seed_file]))
-                puts "found seed_file: #{osw[:seed_file]}"
-                self.seed_model = File.join(File.expand_path(path), osw[:seed_file])
-                break
-              end
-            end  
-          else 
-            warn "osw[:seed_file] is not defined"            
-          end
-
-          # weather_file, check if in OSW and not found in path search already
-          if osw[:weather_file]
-            osw[:file_paths].each do |path|
-              puts "searching for weather at: #{File.join(File.expand_path(path), osw[:weather_file])}"
-              if File.exist?(File.join(File.expand_path(path), osw[:weather_file]))
-                puts "found weather_file: #{osw[:weather_file]}"
-                self.weather_file = File.join(File.expand_path(path), osw[:weather_file])
-                break
-              end 
-            end
-          else 
-            warn "osw[:weather_file] is not defined"            
-          end
-
-        # file_paths is not defined in OSW, so warn and try to set 
-        else
-          warn ":file_paths is not defined in the OSW."
-          self.weather_file = osw[:weather_file] ? osw[:weather_file] : nil
-          self.seed_model = osw[:seed_file] ? osw[:seed_file] : nil
-        end
-        
-        #set analysis_type default to Single_Run
-        self.analysis_type = 'single_run'
-
-        #loop over OSW 'steps' and map over measures
-        #there is no name/display name in the OSW. Just measure directory name
-        #read measure.XML from directory to get name / display name
-        #increment name by +_1 if there are duplicates
-        #add measure
-        #change default args to osw arg values 
-        
-        osw[:steps].each do |step|
-          #get measure directory
-          measure_dir = step[:measure_dir_name]
-          measure_name = measure_dir.split("measures/").last
-          puts "measure_dir_name: #{measure_name}"
-          #get XML
-          # Loop over possible user defined *measure_paths, including the dir of the osw_filename path and :measure_paths, to find the measure, 
-          # then set measure_dir_abs_path to that path
-          measure_dir_abs_path = ''
-          paths_to_parse = [File.dirname(osw_filename), osw[:measure_paths], *measure_paths].flatten.compact.map { |path| File.join(File.expand_path(path), measure_dir, 'measure.xml') }
-          puts "searching for xml's in: #{paths_to_parse}"
-          xml = {}
-          paths_to_parse.each do |path|
-            if File.exist?(path)
-              puts "found xml: #{path}"
-              xml = parse_measure_xml(path)
-              if !xml.empty?
-                measure_dir_abs_path = path
-                break
-              end
-            end          
-          end
-          raise "measure #{measure_name} not found" if xml.empty?
-          puts ""          
-          #add check for previous names _+1
-          count = 1
-          name = xml[:name]
-          display_name = xml[:display_name]
-          loop do
-            measure = @workflow.find_measure(name)
-            break if measure.nil?
-
-            count += 1
-            name = "#{xml[:name]}_#{count}"
-            display_name = "#{xml[:display_name]} #{count}"
-          end   
-          #Add Measure to workflow
-          @workflow.add_measure_from_path(name, display_name, measure_dir_abs_path)  #this forces to an absolute path which seems constent with PAT
-          #@workflow.add_measure_from_path(name, display_name, measure_dir)  #this uses the path in the OSW which could be relative          
-          
-          #Change the default argument values to the osw values
-          #1. find measure in @workflow
-          m = @workflow.find_measure(name)
-          #2. loop thru osw args
-          #check if the :argument is missing from the measure step, it shouldnt be but just in case give a clean message
-          if step[:arguments].nil?
-            raise "measure #{name} step has no arguments: #{step}"
-          else          
-            step[:arguments].each do |k,v|
-              #check if argument is in measure, otherwise setting argument_value will crash
-              raise "OSW arg: #{k} is not in Measure: #{name}" if m.arguments.find_all { |a| a[:name] == k.to_s }.empty?
-              #set measure arg to match osw arg
-              m.argument_value(k.to_s, v)
-            end
-          end
-        end
-      end
-
-      private
-
-      # New format for OSAs. Package up the seed, weather files, and measures
-      # filename is the name of the file to be saved. ex: analysis.zip
-      # it will parse the OSA and zip up all the files defined in the workflow
-      def save_analysis_zip_osa(filename, all_weather_files = false, all_seed_files = false)
-        def add_directory_to_zip_osa(zipfile, local_directory, relative_zip_directory)
-          puts "Add Directory #{local_directory}"
-          Dir[File.join(local_directory.to_s, '**', '**')].each do |file|
-            puts "Adding File #{file}"
-            zipfile.add(file.sub(local_directory, relative_zip_directory), file)
-          end
-          zipfile
-        end
-        #delete file if exists
-        FileUtils.rm_f(filename) if File.exist?(filename)
-        #get the full path to the OSW, since all Files/Dirs should be in same directory as the OSW
-        puts "osw_path: #{@osw_path}"
-        osw_full_path = File.dirname(File.expand_path(@osw_path))
-        puts "osw_full_path: #{osw_full_path}"
-
-        Zip::File.open(filename, create: true) do |zf|
-         ## Weather files
-          puts 'Adding Support Files: Weather'
-          # check if weather file exists.  use abs path.  remove leading ./ from @weather_file path if there.
-          # check if path is already absolute
-          if @weather_file[:file]
-            if File.exists?(@weather_file[:file])
-              puts "  Adding #{@weather_file[:file]}"
-              #zf.add("weather/#{File.basename(@weather_file[:file])}", @weather_file[:file])
-              base_name = File.basename(@weather_file[:file], ".*")
-              puts "base_name: #{base_name}"
-              # convert backslash on windows to forward slash so Dir.glob will work (in case user uses \)
-              weather_dirname = File.dirname(@weather_file[:file]).gsub("\\", "/")
-              puts "weather_dirname: #{weather_dirname}"
-              # If all_weather_files is true, add all files in the directory to the zip.
-              # Otherwise, add only files that match the base name.
-              file_pattern = all_weather_files ? "*" : "#{base_name}.*"
-              Dir.glob(File.join(weather_dirname, file_pattern)) do |file_path|
-               puts "file_path: #{file_path}"
-               puts "zip path: weather/#{File.basename(file_path)}"
-               zf.add("weather/#{File.basename(file_path)}", file_path)
-            end
-            # make absolute path and check for file  
-            elsif File.exists?(File.join(osw_full_path,@weather_file[:file].sub(/^\.\//, '')))
-              puts "  Adding: #{File.join(osw_full_path,@weather_file[:file].sub(/^\.\//, ''))}"
-              #zf.add("weather/#{File.basename(@weather_file[:file])}", File.join(osw_full_path,@weather_file[:file].sub(/^\.\//, '')))
-              base_name = File.basename(@weather_file[:file].sub(/^\.\//, ''), ".*")
-              puts "base_name2: #{base_name}"
-              weather_dirname = File.dirname(File.join(osw_full_path,@weather_file[:file].sub(/^\.\//, ''))).gsub("\\", "/")
-              puts "weather_dirname: #{weather_dirname}"
-              file_pattern = all_weather_files ? "*" : "#{base_name}.*"
-              Dir.glob(File.join(weather_dirname, file_pattern)) do |file_path|
-                puts "file_path2: #{file_path}"
-                puts "zip path2: weather/#{File.basename(file_path)}"
-                zf.add("weather/#{File.basename(file_path)}", file_path)
-              end
-            else
-              raise "weather_file[:file] does not exist at: #{File.join(osw_full_path,@weather_file[:file].sub(/^\.\//, ''))}"
-            end
-          else
-            warn "weather_file[:file] is not defined"
-          end
-
-          ## Seed files
-          puts 'Adding Support Files: Seed Models'
-          #check if seed file exists.  use abs path.  remove leading ./ from @seed_model path if there.
-          #check if path is already absolute
-          if @seed_model[:file]
-            if File.exists?(@seed_model[:file])
-              puts "  Adding #{@seed_model[:file]}"
-              zf.add("seeds/#{File.basename(@seed_model[:file])}", @seed_model[:file])
-              if all_seed_files
-                seed_dirname = File.dirname(@seed_model[:file]).gsub("\\", "/")
-                puts "seed_dirname: #{seed_dirname}"
-                Dir.glob(File.join(seed_dirname, '*')) do |file_path|
-                  next if file_path == @seed_model[:file] # Skip if the file is the same as @seed_model[:file] so not added twice
-                  puts "file_path: #{file_path}"
-                  puts "zip path: seeds/#{File.basename(file_path)}"
-                  zf.add("seeds/#{File.basename(file_path)}", file_path)
-                end              
-              end
-            #make absolute path and check for file  
-            elsif File.exists?(File.join(osw_full_path,@seed_model[:file].sub(/^\.\//, '')))
-              puts "  Adding #{File.join(osw_full_path,@seed_model[:file].sub(/^\.\//, ''))}"
-              zf.add("seeds/#{File.basename(@seed_model[:file])}", File.join(osw_full_path,@seed_model[:file].sub(/^\.\//, '')))
-              if all_seed_files
-                seed_dirname = File.dirname(File.join(osw_full_path,@seed_model[:file].sub(/^\.\//, ''))).gsub("\\", "/")
-                puts "seed_dirname: #{seed_dirname}"
-                Dir.glob(File.join(seed_dirname, '*')) do |file_path|
-                  next if file_path == File.join(osw_full_path,@seed_model[:file].sub(/^\.\//, '')) # Skip if the file is the same as @seed_model[:file] so not added twice
-                  puts "file_path: #{file_path}"
-                  puts "zip path: seeds/#{File.basename(file_path)}"
-                  zf.add("seeds/#{File.basename(file_path)}", file_path)
-                end              
-              end
-            else
-              raise "seed_file[:file] does not exist at: #{File.join(osw_full_path,@seed_model[:file].sub(/^\.\//, ''))}"
-            end        
-          else
-            warn "seed_file[:file] is not defined"
-          end
-          
-          puts 'Adding Support Files: Libraries'
-          @libraries.each do |lib|
-            raise "Libraries must specify their 'library_name' as metadata which becomes the directory upon zip" unless lib[:metadata][:library_name]
-
-            if File.directory? lib[:file]
-              Dir[File.join(lib[:file], '**', '**')].each do |file|
-                puts "  Adding #{file}"
-                zf.add(file.sub(lib[:file], "lib/#{lib[:metadata][:library_name]}"), file)
-              end
-            else
-              # just add the file to the zip
-              puts "  Adding #{lib[:file]}"
-              zf.add(lib[:file], "lib/#{File.basename(lib[:file])}", lib[:file])
-            end
-          end
-
-          puts 'Adding Support Files: Server Scripts'
-          @server_scripts.each_with_index do |f, index|
-            if f[:init_or_final] == 'finalization'
-              file_name = 'finalization.sh'
-            else
-              file_name = 'initialization.sh'
-            end
-            if f[:server_or_data_point] == 'analysis'
-              new_name = "scripts/analysis/#{file_name}"
-            else
-              new_name = "scripts/data_point/#{file_name}"
-            end
-            puts "  Adding #{f[:file]} as #{new_name}"
-            zf.add(new_name, f[:file])
-
-            if f[:arguments]
-              arg_file = "#{(new_name.sub(/\.sh\z/, ''))}.args"
-              puts "  Adding arguments as #{arg_file}"
-              file = Tempfile.new('arg')
-              file.write(f[:arguments])
-              zf.add(arg_file, file)
-              file.close
-            end
-          end
-
-          ## Measures
-          puts 'Adding Measures'
-          added_measures = []
-          # The list of the measures should always be there, but make sure they are uniq
-          @workflow.each do |measure|
-            measure_dir_to_add = measure.measure_definition_directory_local
-
-            next if added_measures.include? measure_dir_to_add
-
-            puts "  Adding #{File.basename(measure_dir_to_add)}"
-            Dir[File.join(measure_dir_to_add, '**')].each do |file|
-              if File.directory?(file)
-                if File.basename(file) == 'resources' || File.basename(file) == 'lib'
-                  #remove leading ./ from measure_definition_directory path if there.
-                  add_directory_to_zip_osa(zf, file, "#{measure.measure_definition_directory.sub(/^\.\//, '')}/#{File.basename(file)}")
-                end
-              else
-                puts "    Adding File #{file}"
-                #remove leading ./ from measure.measure_definition_directory string with regex .sub(/^\.\//, '')
-                zip_path_for_measures = file.sub(measure_dir_to_add, measure.measure_definition_directory.sub(/^\.\//, ''))
-                #puts "    zip_path_for_measures: #{zip_path_for_measures}"
-                zf.add(zip_path_for_measures, file)
-              end
-            end
-
-            added_measures << measure_dir_to_add
-          end
-        end
-      end
-      
-      #keep legacy function
-      # Package up the seed, weather files, and measures
-      def save_analysis_zip(filename)
-        def add_directory_to_zip(zipfile, local_directory, relative_zip_directory)
-          # puts "Add Directory #{local_directory}"
-          Dir[File.join(local_directory.to_s, '**', '**')].each do |file|
-            # puts "Adding File #{file}"
-            zipfile.add(file.sub(local_directory, relative_zip_directory), file)
-          end
-          zipfile
-        end
-
-        FileUtils.rm_f(filename) if File.exist?(filename)
-
-        Zip::File.open(filename, Zip::File::CREATE) do |zf|
-          ## Weather files
-          # TODO: eventually remove the @weather_file attribute and grab the weather file out
-          # of the @weather_files
-          puts 'Adding Support Files: Weather'
-          if @weather_file[:file] && !@weather_files.files.find { |f| @weather_file[:file] == f[:file] }
-            # manually add the weather file
-            puts "  Adding #{@weather_file[:file]}"
-            zf.add("./weather/#{File.basename(@weather_file[:file])}", @weather_file[:file])
-          end
-          @weather_files.each do |f|
-            puts "  Adding #{f[:file]}"
-            zf.add("./weather/#{File.basename(f[:file])}", f[:file])
-          end
-
-          ## Seed files
-          puts 'Adding Support Files: Seed Models'
-          if @seed_model[:file] && !@seed_models.files.find { |f| @seed_model[:file] == f[:file] }
-            # manually add the weather file
-            puts "  Adding #{@seed_model[:file]}"
-            zf.add("./seed/#{File.basename(@seed_model[:file])}", @seed_model[:file])
-          end
-          @seed_models.each do |f|
-            puts "  Adding #{f[:file]}"
-            zf.add("./seed/#{File.basename(f[:file])}", f[:file])
-          end
-
-          puts 'Adding Support Files: Libraries'
-          @libraries.each do |lib|
-            raise "Libraries must specify their 'library_name' as metadata which becomes the directory upon zip" unless lib[:metadata][:library_name]
-
-            if File.directory? lib[:file]
-              Dir[File.join(lib[:file], '**', '**')].each do |file|
-                puts "  Adding #{file}"
-                zf.add(file.sub(lib[:file], "./lib/#{lib[:metadata][:library_name]}/"), file)
-              end
-            else
-              # just add the file to the zip
-              puts "  Adding #{lib[:file]}"
-              zf.add(lib[:file], "./lib/#{File.basename(lib[:file])}", lib[:file])
-            end
-          end
-
-          puts 'Adding Support Files: Worker Initialization Scripts'
-          @worker_inits.each_with_index do |f, index|
-            ordered_file_name = "#{index.to_s.rjust(2, '0')}_#{File.basename(f[:file])}"
-            puts "  Adding #{f[:file]} as #{ordered_file_name}"
-            zf.add(f[:file].sub(f[:file], "./scripts/worker_initialization//#{ordered_file_name}"), f[:file])
-
-            if f[:metadata][:args]
-              arg_file = "#{File.basename(ordered_file_name, '.*')}.args"
-              file = Tempfile.new('arg')
-              file.write(f[:metadata][:args])
-              zf.add("./scripts/worker_initialization/#{arg_file}", file)
-              file.close
-            end
-          end
-
-          puts 'Adding Support Files: Worker Finalization Scripts'
-          @worker_finalizes.each_with_index do |f, index|
-            ordered_file_name = "#{index.to_s.rjust(2, '0')}_#{File.basename(f[:file])}"
-            puts "  Adding #{f[:file]} as #{ordered_file_name}"
-            zf.add(f[:file].sub(f[:file], "scripts/worker_finalization/#{ordered_file_name}"), f[:file])
-
-            if f[:metadata][:args]
-              arg_file = "#{File.basename(ordered_file_name, '.*')}.args"
-              file = Tempfile.new('arg')
-              file.write(f[:metadata][:args])
-              zf.add("scripts/worker_finalization/#{arg_file}", file)
-              file.close
-            end
-          end
-          
-          ## Measures
-          puts 'Adding Measures'
-          added_measures = []
-          # The list of the measures should always be there, but make sure they are uniq
-          @workflow.each do |measure|
-            measure_dir_to_add = measure.measure_definition_directory_local
-
-            next if added_measures.include? measure_dir_to_add
-
-            puts "  Adding #{File.basename(measure_dir_to_add)}"
-            Dir[File.join(measure_dir_to_add, '**')].each do |file|
-              if File.directory?(file)
-                if File.basename(file) == 'resources' || File.basename(file) == 'lib'
-                  add_directory_to_zip(zf, file, "#{measure.measure_definition_directory}/#{File.basename(file)}")
-                end
-              else
-                # puts "Adding File #{file}"
-                zf.add(file.sub(measure_dir_to_add, "#{measure.measure_definition_directory}/"), file)
-              end
-            end
-
-            added_measures << measure_dir_to_add
-          end
-        end
-      end
-    end
-  end
-end
+# *******************************************************************************
+# OpenStudio(R), Copyright (c) Alliance for Sustainable Energy, LLC.
+# See also https://openstudio.net/license
+# *******************************************************************************
+
+# OpenStudio formulation class handles the generation of the OpenStudio Analysis format.
+module OpenStudio
+  module Analysis
+    SeedModel = Struct.new(:file)
+    WeatherFile = Struct.new(:file)
+
+    @@measure_paths = ['./measures']
+    # List of paths to look for measures when adding them. This currently only is used when loading an
+    # analysis hash file. It looks in the order of the measure_paths. As soon as it finds one, it stops.
+    def self.measure_paths
+      @@measure_paths
+    end
+
+    def self.measure_paths=(new_array)
+      @@measure_paths = new_array
+    end
+
+    class Formulation
+      attr_reader :seed_model
+      attr_reader :weather_file
+      attr_reader :analysis_type
+      attr_reader :outputs
+      attr_accessor :display_name
+      attr_accessor :workflow
+      attr_accessor :algorithm
+      attr_accessor :osw_path
+      attr_accessor :download_zip
+      attr_accessor :download_reports
+      attr_accessor :download_osw
+      attr_accessor :download_osm
+      attr_accessor :cli_debug
+      attr_accessor :cli_verbose
+      attr_accessor :initialize_worker_timeout
+      attr_accessor :run_workflow_timeout
+      attr_accessor :upload_results_timeout
+      
+
+      # the attributes below are used for packaging data into the analysis zip file
+      attr_reader :weather_files
+      attr_reader :seed_models
+      attr_reader :worker_inits
+      attr_reader :worker_finalizes
+      attr_reader :libraries
+      attr_reader :server_scripts
+      attr_reader :gem_files
+
+      # Create an instance of the OpenStudio::Analysis::Formulation
+      #
+      # @param display_name [String] Display name of the project.
+      # @return [Object] An OpenStudio::Analysis::Formulation object
+      def initialize(display_name)
+        @display_name = display_name
+        @analysis_type = nil
+        @outputs = []
+        @workflow = OpenStudio::Analysis::Workflow.new
+        # Initialize child objects (expect workflow)
+        @weather_file = WeatherFile.new
+        @seed_model = SeedModel.new
+        @algorithm = OpenStudio::Analysis::AlgorithmAttributes.new
+        @download_zip = true
+        @download_reports = true
+        @download_osw = true
+        @download_osm = true
+        @cli_debug = "--debug"
+        @cli_verbose = "--verbose"
+        @initialize_worker_timeout = 28800
+        @run_workflow_timeout = 28800
+        @upload_results_timeout = 28800
+
+        # Analysis Zip attributes
+        @weather_files = SupportFiles.new
+        @gem_files = SupportFiles.new
+        @seed_models = SupportFiles.new
+        @worker_inits = SupportFiles.new
+        @worker_finalizes = SupportFiles.new
+        @libraries = SupportFiles.new
+        @server_scripts = ServerScripts.new
+      end
+     
+      # Define the type of analysis which is going to be running
+      #
+      # @param name [String] Name of the algorithm/analysis. (e.g. rgenoud, lhs, single_run)
+      # allowed values are ANALYSIS_TYPES = ['spea_nrel', 'rgenoud', 'nsga_nrel', 'lhs', 'preflight', 
+      #                                      'morris', 'sobol', 'doe', 'fast99', 'ga', 'gaisl', 
+      #                                      'single_run', 'repeat_run', 'batch_run']
+      def analysis_type=(value)
+        if OpenStudio::Analysis::AlgorithmAttributes::ANALYSIS_TYPES.include?(value)
+          @analysis_type = value
+        else
+          raise "Invalid analysis type. Allowed types: #{OpenStudio::Analysis::AlgorithmAttributes::ANALYSIS_TYPES}"
+        end
+      end
+
+      # Path to the seed model
+      #
+      # @param path [String] Path to the seed model. This should be relative.
+      def seed_model=(file)
+        @seed_model[:file] = file
+      end
+
+      # Path to the weather file (or folder). If it is a folder, then the measures will look for the weather file
+      # by name in that folder.
+      #
+      # @param path [String] Path to the weather file or folder.
+      def weather_file=(file)
+        @weather_file[:file] = file
+      end
+
+      # Set the value for 'download_zip'
+      #
+      # @param value [Boolean] The value for 'download_zip'
+      def download_zip=(value)
+        if [true, false].include?(value)
+          @download_zip = value
+        else
+          raise ArgumentError, "Invalid value for 'download_zip'. Only true or false allowed."
+        end
+      end
+      
+      # Set the value for 'download_reports'
+      #
+      # @param value [Boolean] The value for 'download_reports'
+      def download_reports=(value)
+        if [true, false].include?(value)
+          @download_reports = value
+        else
+          raise ArgumentError, "Invalid value for 'download_reports'. Only true or false allowed."
+        end
+      end
+      
+      # Set the value for 'download_osw'
+      #
+      # @param value [Boolean] The value for 'download_osw'
+      def download_osw=(value)
+        if [true, false].include?(value)
+          @download_osw = value
+        else
+          raise ArgumentError, "Invalid value for 'download_osw'. Only true or false allowed."
+        end
+      end
+      
+      # Set the value for 'download_osm'
+      #
+      # @param value [Boolean] The value for 'download_osm'
+      def download_osm=(value)
+        if [true, false].include?(value)
+          @download_osm = value
+        else
+          raise ArgumentError, "Invalid value for 'download_osm'. Only true or false allowed."
+        end
+      end
+
+      # Set the value for 'cli_debug'
+      #
+      # @param value [Boolean] The value for 'cli_debug'
+      def cli_debug=(value)
+        @cli_debug = value
+      end
+
+      # Set the value for 'cli_verbose'
+      #
+      # @param value [Boolean] The value for 'cli_verbose'
+      def cli_verbose=(value)
+        @cli_verbose = value
+      end
+
+      # Set the value for 'run_workflow_timeout'
+      #
+      # @param value [Integer] The value for 'run_workflow_timeout'
+      def run_workflow_timeout=(value)
+        if value.is_a?(Integer)
+          @run_workflow_timeout = value
+        else
+          raise ArgumentError, "Invalid value for 'run_workflow_timeout'. Only integer values allowed."
+        end
+      end
+
+      # Set the value for 'initialize_worker_timeout'
+      #
+      # @param value [Integer] The value for 'initialize_worker_timeout'
+      def initialize_worker_timeout=(value)
+        if value.is_a?(Integer)
+          @initialize_worker_timeout = value
+        else
+          raise ArgumentError, "Invalid value for 'initialize_worker_timeout'. Only integer values allowed."
+        end
+      end
+
+      # Set the value for 'upload_results_timeout'
+      #
+      # @param value [Integer] The value for 'upload_results_timeout'
+      def upload_results_timeout=(value)
+        if value.is_a?(Integer)
+          @upload_results_timeout = value
+        else
+          raise ArgumentError, "Invalid value for 'upload_results_timeout'. Only integer values allowed."
+        end
+      end
+
+      # Add an output of interest to the problem formulation
+      #
+      # @param output_hash [Hash] Hash of the output variable in the legacy format
+      # @option output_hash [String] :display_name Name to display
+      # @option output_hash [String] :display_name_short A shorter display name
+      # @option output_hash [String] :metadata_id Link to DEnCity ID in which this output corresponds
+      # @option output_hash [String] :name Unique machine name of the variable. Typically this is measure.attribute
+      # @option output_hash [String] :export Export the variable to CSV and dataframes from OpenStudio-server
+      # @option output_hash [String] :visualize Visualize the variable in the plots on OpenStudio-server
+      # @option output_hash [String] :units Units of the variable as a string
+      # @option output_hash [String] :variable_type Data type of the variable
+      # @option output_hash [Boolean] :objective_function Whether or not this output is an objective function. Default: false
+      # @option output_hash [Integer] :objective_function_index Index of the objective function. Default: nil
+      # @option output_hash [Float] :objective_function_target Target for the objective function to reach (if defined). Default: nil
+      # @option output_hash [Float] :scaling_factor How to scale the objective function(s). Default: nil
+      # @option output_hash [Integer] :objective_function_group If grouping objective functions, then group ID. Default: nil
+      def add_output(output_hash)
+        # Check if the name is already been added.
+        exist = @outputs.find_index { |o| o[:name] == output_hash[:name] }
+        # if so, update the fields but keep objective_function_index the same
+        if exist
+          original = @outputs[exist]
+          if original[:objective_function] && !output_hash[:objective_function]
+            return @outputs
+          end
+          output = original.merge(output_hash)
+          output[:objective_function_index] = original[:objective_function_index]
+          @outputs[exist] = output
+        else
+          output = {
+            units: '',
+            objective_function: false,
+            objective_function_index: nil,
+            objective_function_target: nil,
+            #set default to nil or 1 if objective_function is true and this is not set
+            objective_function_group: (output_hash[:objective_function] ? 1 : nil),
+            scaling_factor: nil,
+            #set default to false or true if objective_function is true and this is not set
+            visualize: (output_hash[:objective_function] ? true : false),
+            metadata_id: nil,
+            export: true,
+          }.merge(output_hash)
+          #set display_name default to be name if its not set
+          output[:display_name] = output_hash[:display_name] ? output_hash[:display_name] : output_hash[:name]
+          #set display_name_short default to be display_name if its not set, this can be null if :display_name not set
+          output[:display_name_short] = output_hash[:display_name_short] ? output_hash[:display_name_short] : output_hash[:display_name]
+          # if the variable is an objective_function, then increment and
+          # assign and objective function index
+          if output[:objective_function]
+            values = @outputs.select { |o| o[:objective_function] }
+            output[:objective_function_index] = values.size
+          end
+
+          @outputs << output
+        end
+
+        @outputs
+      end
+
+      # return the machine name of the analysis
+      def name
+        @display_name.to_underscore
+      end
+
+      # return a hash.
+      #
+      # @param version [Integer] Version of the format to return
+      # @return [Hash]
+      def to_hash(version = 1)
+        # fail 'Must define an analysis type' unless @analysis_type
+        if version == 1
+          h = {
+            analysis: {
+              display_name: @display_name,
+              name: name,
+              output_variables: @outputs,
+              problem: {
+                analysis_type: @analysis_type,
+                algorithm: algorithm.to_hash(version),
+                workflow: workflow.to_hash(version)
+              }
+            }
+          }
+
+          if @seed_model[:file]
+            h[:analysis][:seed] = {
+              file_type: File.extname(@seed_model[:file]).delete('.').upcase,
+              path: "./seed/#{File.basename(@seed_model[:file])}"
+            }
+          else
+            h[:analysis][:seed] = nil
+          end
+
+          # silly catch for if weather_file is not set
+          wf = nil
+          if @weather_file[:file]
+            wf = @weather_file
+          elsif !@weather_files.empty?
+            # get the first EPW file (not the first file)
+            wf = @weather_files.find { |w| File.extname(w[:file]).casecmp('.epw').zero? }
+          end
+
+          if wf
+            h[:analysis][:weather_file] = {
+              file_type: File.extname(wf[:file]).delete('.').upcase,
+              path: "./weather/#{File.basename(wf[:file])}"
+            }
+          else
+            # log: could not find weather file
+            warn 'Could not resolve a valid weather file. Check paths to weather files'
+          end
+
+          h[:analysis][:file_format_version] = version
+          h[:analysis][:cli_debug] = @cli_debug
+          h[:analysis][:cli_verbose] = @cli_verbose
+          h[:analysis][:run_workflow_timeout] = @run_workflow_timeout
+          h[:analysis][:upload_results_timeout] = @upload_results_timeout
+          h[:analysis][:initialize_worker_timeout] = @initialize_worker_timeout
+          h[:analysis][:download_zip] = @download_zip
+          h[:analysis][:download_reports] = @download_reports
+          h[:analysis][:download_osw] = @download_osw
+          h[:analysis][:download_osm] = @download_osm
+          
+          # If there are Gemfiles, then set the hash to use the :gemfile. The zip file method will
+          # add them to the root of the zip file.
+          if @gem_files.size.positive?
+            h[:analysis][:gemfile] = true
+          else
+            h[:analysis][:gemfile] = false
+          end
+          
+          #-BLB I dont think this does anything. server_scripts are run if they are in 
+          #the /scripts/analysis or /scripts/data_point directories
+          #but nothing is ever checked in the OSA.
+          h[:analysis][:server_scripts] = {}
+
+          # This is a hack right now, but after the initial hash is created go back and add in the objective functions
+          # to the the algorithm as defined in the output_variables list
+          ofs = @outputs.map { |i| i[:name] if i[:objective_function] }.compact
+          if h[:analysis][:problem][:algorithm]
+            h[:analysis][:problem][:algorithm][:objective_functions] = ofs
+          end
+
+          
+
+          h
+        else
+          raise "Version #{version} not defined for #{self.class} and #{__method__}"
+        end
+      end
+
+      # Load the analysis JSON from a hash (with symbolized keys)
+      def self.from_hash(h, seed_dir = nil, weather_dir = nil)
+        o = OpenStudio::Analysis::Formulation.new(h[:analysis][:display_name])
+
+        version = 1
+        if version == 1
+          h[:analysis][:output_variables].each do |ov|
+            o.add_output(ov)
+          end
+
+          o.workflow = OpenStudio::Analysis::Workflow.load(workflow: h[:analysis][:problem][:workflow])
+
+          if weather_dir
+            o.weather_file "#{weather_path}/#{File.basename(h[:analysis][:weather_file][:path])}"
+          else
+            o.weather_file = h[:analysis][:weather_file][:path]
+          end
+
+          if seed_dir
+            o.seed_model "#{weather_path}/#{File.basename(h[:analysis][:seed][:path])}"
+          else
+            o.seed_model = h[:analysis][:seed][:path]
+          end
+        else
+          raise "Version #{version} not defined for #{self.class} and #{__method__}"
+        end
+
+        o
+      end
+
+      # return a hash of the data point with the static variables set
+      #
+      # @param version [Integer] Version of the format to return
+      # @return [Hash]
+      def to_static_data_point_hash(version = 1)
+        if version == 1
+          static_hash = {}
+          # TODO: this method should be on the workflow step and bubbled up to this interface
+          @workflow.items.map do |item|
+            item.variables.map { |v| static_hash[v[:uuid]] = v[:static_value] }
+          end
+
+          h = {
+            data_point: {
+              set_variable_values: static_hash,
+              status: 'na',
+              uuid: SecureRandom.uuid
+            }
+          }
+          h
+        end
+      end
+
+      # save the file to JSON. Will overwrite the file if it already exists
+      #
+      # @param filename [String] Name of file to create. It will create the directory and override the file if it exists. If no file extension is given, then it will use .json.
+      # @param version [Integer] Version of the format to return
+      # @return [Boolean]
+      def save(filename, version = 1)
+        filename += '.json' if File.extname(filename) == ''
+
+        FileUtils.mkdir_p File.dirname(filename) unless Dir.exist? File.dirname(filename)
+        File.open(filename, 'w') { |f| f << JSON.pretty_generate(to_hash(version)) }
+
+        true
+      end
+
+      # save the data point JSON with the variables set to the static values. Will overwrite the file if it already exists
+      #
+      # @param filename [String] Name of file to create. It will create the directory and override the file if it exists. If no file extension is given, then it will use .json.
+      # @param version [Integer] Version of the format to return
+      # @return [Boolean]
+      def save_static_data_point(filename, version = 1)
+        filename += '.json' if File.extname(filename) == ''
+
+        FileUtils.mkdir_p File.dirname(filename) unless Dir.exist? File.dirname(filename)
+        File.open(filename, 'w') { |f| f << JSON.pretty_generate(to_static_data_point_hash(version)) }
+
+        true
+      end
+
+      # save the analysis zip file which contains the measures, seed model, weather file, and init/final scripts
+      #
+      # @param filename [String] Name of file to create. It will create the directory and override the file if it exists. If no file extension is given, then it will use .json.
+      # @return [Boolean]
+      def save_zip(filename)
+        filename += '.zip' if File.extname(filename) == ''
+
+        FileUtils.mkdir_p File.dirname(filename) unless Dir.exist? File.dirname(filename)
+
+        save_analysis_zip(filename)
+      end
+      
+      
+      def save_osa_zip(filename, all_weather_files = false, all_seed_files = false)
+        filename += '.zip' if File.extname(filename) == ''
+
+        FileUtils.mkdir_p File.dirname(filename) unless Dir.exist? File.dirname(filename)
+
+        save_analysis_zip_osa(filename, all_weather_files, all_seed_files)
+      end
+      
+      # convert an OSW to an OSA
+      # osw_filename is the full path to the OSW file
+      # assumes the associated files and directories are in the same location
+      #  /example.osw
+      #  /measures
+      #  /seeds
+      #  /weather
+      #
+      def convert_osw(osw_filename, *measure_paths)
+        # load OSW so we can loop over [:steps]
+        if File.exist? osw_filename  #will this work for both rel and abs paths?
+          osw = JSON.parse(File.read(osw_filename), symbolize_names: true)
+          @osw_path = File.expand_path(osw_filename)
+        else
+          raise "Could not find workflow file #{osw_filename}"
+        end
+        
+        # set the weather and seed files if set in OSW
+        # use :file_paths and look for files to set
+        if osw[:file_paths]        
+          # seed_model, check if in OSW and not found in path search already
+          if osw[:seed_file]
+            osw[:file_paths].each do |path|
+              puts "searching for seed at: #{File.join(File.expand_path(path), osw[:seed_file])}"
+              if File.exist?(File.join(File.expand_path(path), osw[:seed_file]))
+                puts "found seed_file: #{osw[:seed_file]}"
+                self.seed_model = File.join(File.expand_path(path), osw[:seed_file])
+                break
+              end
+            end  
+          else 
+            warn "osw[:seed_file] is not defined"            
+          end
+
+          # weather_file, check if in OSW and not found in path search already
+          if osw[:weather_file]
+            osw[:file_paths].each do |path|
+              puts "searching for weather at: #{File.join(File.expand_path(path), osw[:weather_file])}"
+              if File.exist?(File.join(File.expand_path(path), osw[:weather_file]))
+                puts "found weather_file: #{osw[:weather_file]}"
+                self.weather_file = File.join(File.expand_path(path), osw[:weather_file])
+                break
+              end 
+            end
+          else 
+            warn "osw[:weather_file] is not defined"            
+          end
+
+        # file_paths is not defined in OSW, so warn and try to set 
+        else
+          warn ":file_paths is not defined in the OSW."
+          self.weather_file = osw[:weather_file] ? osw[:weather_file] : nil
+          self.seed_model = osw[:seed_file] ? osw[:seed_file] : nil
+        end
+        
+        #set analysis_type default to Single_Run
+        self.analysis_type = 'single_run'
+
+        #loop over OSW 'steps' and map over measures
+        #there is no name/display name in the OSW. Just measure directory name
+        #read measure.XML from directory to get name / display name
+        #increment name by +_1 if there are duplicates
+        #add measure
+        #change default args to osw arg values 
+        
+        osw[:steps].each do |step|
+          #get measure directory
+          measure_dir = step[:measure_dir_name]
+          measure_name = measure_dir.split("measures/").last
+          puts "measure_dir_name: #{measure_name}"
+          #get XML
+          # Loop over possible user defined *measure_paths, including the dir of the osw_filename path and :measure_paths, to find the measure, 
+          # then set measure_dir_abs_path to that path
+          measure_dir_abs_path = ''
+          paths_to_parse = [File.dirname(osw_filename), osw[:measure_paths], *measure_paths].flatten.compact.map { |path| File.join(File.expand_path(path), measure_dir, 'measure.xml') }
+          puts "searching for xml's in: #{paths_to_parse}"
+          xml = {}
+          paths_to_parse.each do |path|
+            if File.exist?(path)
+              puts "found xml: #{path}"
+              xml = parse_measure_xml(path)
+              if !xml.empty?
+                measure_dir_abs_path = path
+                break
+              end
+            end          
+          end
+          raise "measure #{measure_name} not found" if xml.empty?
+          puts ""          
+          #add check for previous names _+1
+          count = 1
+          name = xml[:name]
+          display_name = xml[:display_name]
+          loop do
+            measure = @workflow.find_measure(name)
+            break if measure.nil?
+
+            count += 1
+            name = "#{xml[:name]}_#{count}"
+            display_name = "#{xml[:display_name]} #{count}"
+          end   
+          #Add Measure to workflow
+          @workflow.add_measure_from_path(name, display_name, measure_dir_abs_path)  #this forces to an absolute path which seems constent with PAT
+          #@workflow.add_measure_from_path(name, display_name, measure_dir)  #this uses the path in the OSW which could be relative          
+          
+          #Change the default argument values to the osw values
+          #1. find measure in @workflow
+          m = @workflow.find_measure(name)
+          #2. loop thru osw args
+          #check if the :argument is missing from the measure step, it shouldnt be but just in case give a clean message
+          if step[:arguments].nil?
+            raise "measure #{name} step has no arguments: #{step}"
+          else          
+            step[:arguments].each do |k,v|
+              #check if argument is in measure, otherwise setting argument_value will crash
+              raise "OSW arg: #{k} is not in Measure: #{name}" if m.arguments.find_all { |a| a[:name] == k.to_s }.empty?
+              #set measure arg to match osw arg
+              m.argument_value(k.to_s, v)
+            end
+          end
+        end
+      end
+
+      private
+
+      # New format for OSAs. Package up the seed, weather files, and measures
+      # filename is the name of the file to be saved. ex: analysis.zip
+      # it will parse the OSA and zip up all the files defined in the workflow
+      def save_analysis_zip_osa(filename, all_weather_files = false, all_seed_files = false)
+        def add_directory_to_zip_osa(zipfile, local_directory, relative_zip_directory)
+          puts "Add Directory #{local_directory}"
+          Dir[File.join(local_directory.to_s, '**', '**')].each do |file|
+            puts "Adding File #{file}"
+            zipfile.add(file.sub(local_directory, relative_zip_directory), file)
+          end
+          zipfile
+        end
+        #delete file if exists
+        FileUtils.rm_f(filename) if File.exist?(filename)
+        #get the full path to the OSW, since all Files/Dirs should be in same directory as the OSW
+        puts "osw_path: #{@osw_path}"
+        osw_full_path = File.dirname(File.expand_path(@osw_path))
+        puts "osw_full_path: #{osw_full_path}"
+
+        Zip::File.open(filename, create: true) do |zf|
+         ## Weather files
+          puts 'Adding Support Files: Weather'
+          # check if weather file exists.  use abs path.  remove leading ./ from @weather_file path if there.
+          # check if path is already absolute
+          if @weather_file[:file]
+            if File.exist?(@weather_file[:file])
+              puts "  Adding #{@weather_file[:file]}"
+              #zf.add("weather/#{File.basename(@weather_file[:file])}", @weather_file[:file])
+              base_name = File.basename(@weather_file[:file], ".*")
+              puts "base_name: #{base_name}"
+              # convert backslash on windows to forward slash so Dir.glob will work (in case user uses \)
+              weather_dirname = File.dirname(@weather_file[:file]).gsub("\\", "/")
+              puts "weather_dirname: #{weather_dirname}"
+              # If all_weather_files is true, add all files in the directory to the zip.
+              # Otherwise, add only files that match the base name.
+              file_pattern = all_weather_files ? "*" : "#{base_name}.*"
+              Dir.glob(File.join(weather_dirname, file_pattern)) do |file_path|
+               puts "file_path: #{file_path}"
+               puts "zip path: weather/#{File.basename(file_path)}"
+               zf.add("weather/#{File.basename(file_path)}", file_path)
+            end
+            # make absolute path and check for file  
+            elsif File.exist?(File.join(osw_full_path,@weather_file[:file].sub(/^\.\//, '')))
+              puts "  Adding: #{File.join(osw_full_path,@weather_file[:file].sub(/^\.\//, ''))}"
+              #zf.add("weather/#{File.basename(@weather_file[:file])}", File.join(osw_full_path,@weather_file[:file].sub(/^\.\//, '')))
+              base_name = File.basename(@weather_file[:file].sub(/^\.\//, ''), ".*")
+              puts "base_name2: #{base_name}"
+              weather_dirname = File.dirname(File.join(osw_full_path,@weather_file[:file].sub(/^\.\//, ''))).gsub("\\", "/")
+              puts "weather_dirname: #{weather_dirname}"
+              file_pattern = all_weather_files ? "*" : "#{base_name}.*"
+              Dir.glob(File.join(weather_dirname, file_pattern)) do |file_path|
+                puts "file_path2: #{file_path}"
+                puts "zip path2: weather/#{File.basename(file_path)}"
+                zf.add("weather/#{File.basename(file_path)}", file_path)
+              end
+            else
+              raise "weather_file[:file] does not exist at: #{File.join(osw_full_path,@weather_file[:file].sub(/^\.\//, ''))}"
+            end
+          else
+            warn "weather_file[:file] is not defined"
+          end
+
+          ## Seed files
+          puts 'Adding Support Files: Seed Models'
+          #check if seed file exists.  use abs path.  remove leading ./ from @seed_model path if there.
+          #check if path is already absolute
+          if @seed_model[:file]
+            if File.exist?(@seed_model[:file])
+              puts "  Adding #{@seed_model[:file]}"
+              zf.add("seeds/#{File.basename(@seed_model[:file])}", @seed_model[:file])
+              if all_seed_files
+                seed_dirname = File.dirname(@seed_model[:file]).gsub("\\", "/")
+                puts "seed_dirname: #{seed_dirname}"
+                Dir.glob(File.join(seed_dirname, '*')) do |file_path|
+                  next if file_path == @seed_model[:file] # Skip if the file is the same as @seed_model[:file] so not added twice
+                  puts "file_path: #{file_path}"
+                  puts "zip path: seeds/#{File.basename(file_path)}"
+                  zf.add("seeds/#{File.basename(file_path)}", file_path)
+                end              
+              end
+            #make absolute path and check for file  
+            elsif File.exist?(File.join(osw_full_path,@seed_model[:file].sub(/^\.\//, '')))
+              puts "  Adding #{File.join(osw_full_path,@seed_model[:file].sub(/^\.\//, ''))}"
+              zf.add("seeds/#{File.basename(@seed_model[:file])}", File.join(osw_full_path,@seed_model[:file].sub(/^\.\//, '')))
+              if all_seed_files
+                seed_dirname = File.dirname(File.join(osw_full_path,@seed_model[:file].sub(/^\.\//, ''))).gsub("\\", "/")
+                puts "seed_dirname: #{seed_dirname}"
+                Dir.glob(File.join(seed_dirname, '*')) do |file_path|
+                  next if file_path == File.join(osw_full_path,@seed_model[:file].sub(/^\.\//, '')) # Skip if the file is the same as @seed_model[:file] so not added twice
+                  puts "file_path: #{file_path}"
+                  puts "zip path: seeds/#{File.basename(file_path)}"
+                  zf.add("seeds/#{File.basename(file_path)}", file_path)
+                end              
+              end
+            else
+              raise "seed_file[:file] does not exist at: #{File.join(osw_full_path,@seed_model[:file].sub(/^\.\//, ''))}"
+            end        
+          else
+            warn "seed_file[:file] is not defined"
+          end
+          
+          puts 'Adding Support Files: Libraries'
+          @libraries.each do |lib|
+            raise "Libraries must specify their 'library_name' as metadata which becomes the directory upon zip" unless lib[:metadata][:library_name]
+
+            if File.directory? lib[:file]
+              Dir[File.join(lib[:file], '**', '**')].each do |file|
+                puts "  Adding #{file}"
+                zf.add(file.sub(lib[:file], "lib/#{lib[:metadata][:library_name]}"), file)
+              end
+            else
+              # just add the file to the zip
+              puts "  Adding #{lib[:file]}"
+              zf.add(lib[:file], "lib/#{File.basename(lib[:file])}", lib[:file])
+            end
+          end
+
+          puts 'Adding Support Files: Server Scripts'
+          @server_scripts.each_with_index do |f, index|
+            if f[:init_or_final] == 'finalization'
+              file_name = 'finalization.sh'
+            else
+              file_name = 'initialization.sh'
+            end
+            if f[:server_or_data_point] == 'analysis'
+              new_name = "scripts/analysis/#{file_name}"
+            else
+              new_name = "scripts/data_point/#{file_name}"
+            end
+            puts "  Adding #{f[:file]} as #{new_name}"
+            zf.add(new_name, f[:file])
+
+            if f[:arguments]
+              arg_file = "#{(new_name.sub(/\.sh\z/, ''))}.args"
+              puts "  Adding arguments as #{arg_file}"
+              file = Tempfile.new('arg')
+              file.write(f[:arguments])
+              zf.add(arg_file, file)
+              file.close
+            end
+          end
+
+          puts 'Adding Gemfiles'
+          @gem_files.each do |f| 
+            puts "  Adding #{f[:file]}"
+            zf.add(File.basename(f[:file]), f[:file])
+          end
+
+          ## Measures
+          puts 'Adding Measures'
+          added_measures = []
+          # The list of the measures should always be there, but make sure they are uniq
+          @workflow.each do |measure|
+            measure_dir_to_add = measure.measure_definition_directory_local
+
+            next if added_measures.include? measure_dir_to_add
+
+            puts "  Adding #{File.basename(measure_dir_to_add)}"
+            Dir[File.join(measure_dir_to_add, '**')].each do |file|
+              if File.directory?(file)
+                if File.basename(file) == 'resources' || File.basename(file) == 'lib'
+                  #remove leading ./ from measure_definition_directory path if there.
+                  add_directory_to_zip_osa(zf, file, "#{measure.measure_definition_directory.sub(/^\.\//, '')}/#{File.basename(file)}")
+                end
+              else
+                puts "    Adding File #{file}"
+                #remove leading ./ from measure.measure_definition_directory string with regex .sub(/^\.\//, '')
+                zip_path_for_measures = file.sub(measure_dir_to_add, measure.measure_definition_directory.sub(/^\.\//, ''))
+                #puts "    zip_path_for_measures: #{zip_path_for_measures}"
+                zf.add(zip_path_for_measures, file)
+              end
+            end
+
+            added_measures << measure_dir_to_add
+          end
+        end
+      end
+      
+      #keep legacy function
+      # Package up the seed, weather files, and measures
+      def save_analysis_zip(filename)
+        def add_directory_to_zip(zipfile, local_directory, relative_zip_directory)
+          # puts "Add Directory #{local_directory}"
+          Dir[File.join(local_directory.to_s, '**', '**')].each do |file|
+            # puts "Adding File #{file}"
+            zipfile.add(file.sub(local_directory, relative_zip_directory), file)
+          end
+          zipfile
+        end
+
+        FileUtils.rm_f(filename) if File.exist?(filename)
+
+        Zip::File.open(filename, Zip::File::CREATE) do |zf|
+          ## Weather files
+          # TODO: eventually remove the @weather_file attribute and grab the weather file out
+          # of the @weather_files
+          puts 'Adding Support Files: Weather'
+          if @weather_file[:file] && !@weather_files.files.find { |f| @weather_file[:file] == f[:file] }
+            # manually add the weather file
+            puts "  Adding #{@weather_file[:file]}"
+            zf.add("./weather/#{File.basename(@weather_file[:file])}", @weather_file[:file])
+          end
+          @weather_files.each do |f|
+            puts "  Adding #{f[:file]}"
+            zf.add("./weather/#{File.basename(f[:file])}", f[:file])
+          end
+
+          ## Seed files
+          puts 'Adding Support Files: Seed Models'
+          if @seed_model[:file] && !@seed_models.files.find { |f| @seed_model[:file] == f[:file] }
+            # manually add the weather file
+            puts "  Adding #{@seed_model[:file]}"
+            zf.add("./seed/#{File.basename(@seed_model[:file])}", @seed_model[:file])
+          end
+          @seed_models.each do |f|
+            puts "  Adding #{f[:file]}"
+            zf.add("./seed/#{File.basename(f[:file])}", f[:file])
+          end
+
+          puts 'Adding Support Files: Libraries'
+          @libraries.each do |lib|
+            raise "Libraries must specify their 'library_name' as metadata which becomes the directory upon zip" unless lib[:metadata][:library_name]
+
+            if File.directory? lib[:file]
+              Dir[File.join(lib[:file], '**', '**')].each do |file|
+                puts "  Adding #{file}"
+                zf.add(file.sub(lib[:file], "./lib/#{lib[:metadata][:library_name]}/"), file)
+              end
+            else
+              # just add the file to the zip
+              puts "  Adding #{lib[:file]}"
+              zf.add(lib[:file], "./lib/#{File.basename(lib[:file])}", lib[:file])
+            end
+          end
+
+          puts 'Adding Support Files: Worker Initialization Scripts'
+          @worker_inits.each_with_index do |f, index|
+            ordered_file_name = "#{index.to_s.rjust(2, '0')}_#{File.basename(f[:file])}"
+            puts "  Adding #{f[:file]} as #{ordered_file_name}"
+            zf.add(f[:file].sub(f[:file], "./scripts/worker_initialization//#{ordered_file_name}"), f[:file])
+
+            if f[:metadata][:args]
+              arg_file = "#{File.basename(ordered_file_name, '.*')}.args"
+              file = Tempfile.new('arg')
+              file.write(f[:metadata][:args])
+              zf.add("./scripts/worker_initialization/#{arg_file}", file)
+              file.close
+            end
+          end
+
+          puts 'Adding Support Files: Worker Finalization Scripts'
+          @worker_finalizes.each_with_index do |f, index|
+            ordered_file_name = "#{index.to_s.rjust(2, '0')}_#{File.basename(f[:file])}"
+            puts "  Adding #{f[:file]} as #{ordered_file_name}"
+            zf.add(f[:file].sub(f[:file], "scripts/worker_finalization/#{ordered_file_name}"), f[:file])
+
+            if f[:metadata][:args]
+              arg_file = "#{File.basename(ordered_file_name, '.*')}.args"
+              file = Tempfile.new('arg')
+              file.write(f[:metadata][:args])
+              zf.add("scripts/worker_finalization/#{arg_file}", file)
+              file.close
+            end
+          end
+
+          puts 'Adding Gemfiles'
+          @gem_files.each do |f| 
+            puts "  Adding #{f}"
+            zf.add(File.basename(f), f)
+          end
+          
+          ## Measures
+          puts 'Adding Measures'
+          added_measures = []
+          # The list of the measures should always be there, but make sure they are uniq
+          @workflow.each do |measure|
+            measure_dir_to_add = measure.measure_definition_directory_local
+
+            next if added_measures.include? measure_dir_to_add
+
+            puts "  Adding #{File.basename(measure_dir_to_add)}"
+            Dir[File.join(measure_dir_to_add, '**')].each do |file|
+              if File.directory?(file)
+                if File.basename(file) == 'resources' || File.basename(file) == 'lib'
+                  add_directory_to_zip(zf, file, "#{measure.measure_definition_directory}/#{File.basename(file)}")
+                end
+              else
+                # puts "Adding File #{file}"
+                zf.add(file.sub(measure_dir_to_add, "#{measure.measure_definition_directory}/"), file)
+              end
+            end
+
+            added_measures << measure_dir_to_add
+          end
+        end
+      end
+    end
+  end
+end