nera 0.0.1

data/History.txt

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+== 0.0.1 2009-03-25
+
+* 1 major enhancement:
+  * Initial release

data/Manifest.txt

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+History.txt
+Manifest.txt
+README.rdoc
+Rakefile
+bin/nera
+bin/nera_addsim
+lib/nera.rb
+lib/nera/nera_cui.rb
+lib/nera/nera_database.rb
+lib/nera/nera_db_folders.rb
+lib/nera/nera_dialog.rb
+lib/nera/nera_job_layer_controller.rb
+lib/nera/nera_job_records.rb
+lib/nera/nera_job_script.rb
+lib/nera/nera_parameter_layer_controller.rb
+lib/nera/nera_parameter_records.rb
+lib/nera/nera_run_layer_controller.rb
+lib/nera/nera_run_records.rb
+lib/nera/nera_simulator.rb
+lib/nera/nera_simulator_layer_controller.rb
+lib/nera/nera_simulator_records.rb
+lib/nera_addsim/make_simulator.rb
+scripts/make_manifest.rb
+test/runner.rb
+test/test_helper.rb
+test/test_nera_database.rb
+test/test_nera_db_folders.rb
+test/test_nera_dialog.rb
+test/test_nera_job_layer_controller.rb
+test/test_nera_job_records.rb
+test/test_nera_parameter_layer_controller.rb
+test/test_nera_parameter_records.rb
+test/test_nera_run_layer_controller.rb
+test/test_nera_run_records.rb
+test/test_nera_simulator.rb
+test/test_nera_simulator_layer_controller.rb
+test/test_nera_simulator_records.rb

data/README.rdoc

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+= nera
+
+* http://nera.rubyforge.com
+
+== DESCRIPTION:
+
+This is an application which helps you to manage a database for the Monte Carlo simulations. 
+For the dtailed usage, see http://nera.rubyforge.com
+
+== SYNOPSIS:
+
+If you want to start the program, spcify the name of the database (say, 'nera_db') as the first argument.
+
+  nera 'neradb'
+
+To add your own simulators,
+
+  nera_addsim 'neradb'
+
+== REQUIREMENTS:
+
+Ruby 1.8.0 or later
+
+== INSTALL:
+
+To install,
+
+  sudo gem install nera
+
+== LICENSE:
+
+NER_Analyzer : A database management application for Monte Carlo simulations
+Copyright (C) 2009 Yohsuke Murase and Shigenori Matsumoto 
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+

data/Rakefile

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+%w[rubygems rake rake/clean fileutils newgem rubigen].each { |f| require f }
+require File.dirname(__FILE__) + '/lib/nera'
+
+# Generate all the Rake tasks
+# Run 'rake -T' to see list of generated tasks (from gem root directory)
+$hoe = Hoe.new('nera', NERA::VERSION) do |p|
+  p.developer('Yohsuke Murase', 'murase@serow.t.u-tokyo.ac.jp')
+  p.changes              = p.paragraphs_of("History.txt", 0..1).join("\n\n")
+  p.rubyforge_name       = p.name # TODO this is default value
+  # p.extra_deps         = [
+  #   ['activesupport','>= 2.0.2'],
+  # ]
+  p.extra_dev_deps = [
+    ['newgem', ">= #{::Newgem::VERSION}"]
+  ]
+  
+  p.clean_globs |= %w[**/.DS_Store tmp *.log]
+  path = (p.rubyforge_name == p.name) ? p.rubyforge_name : "\#{p.rubyforge_name}/\#{p.name}"
+  p.remote_rdoc_dir = File.join(path.gsub(/^#{p.rubyforge_name}\/?/,''), 'rdoc')
+  p.rsync_args = '-av --delete --ignore-errors'
+end
+
+require 'newgem/tasks' # load /tasks/*.rake
+Dir['tasks/**/*.rake'].each { |t| load t }
+
+# TODO - want other tests/tasks run by default? Add them to the list
+# task :default => [:spec, :features]

data/bin/nera

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+#!/usr/bin/env ruby
+#
+#  Created by Yohsuke Murase on 2009-3-25.
+#  Copyright (c) 2009. All rights reserved.
+require 'optparse'
+require File.expand_path(File.dirname(__FILE__) + "/../lib/nera")
+
+parser = OptionParser.new do |opts|
+  opts.banner = <<-BANNER.gsub(/^    /,'')
+    
+    Usage: #{File.basename($0)} [options] 'nera_db_folder'
+    
+    BANNER
+  opts.separator ""
+  opts.on("-h", "--help",
+          "Show this help message.") { $stdout.puts opts; exit }
+  opts.on("-v", "--version", "Show version.") { $stdout.puts NERA::VERSION; exit}
+  opts.parse!(ARGV)
+end
+
+unless ARGV.size == 1
+  $stderr.puts "Usage :\t nera \"nera_db_folder\""
+  raise "\nSpecify the argument."
+end
+
+Dir.chdir( File.dirname( ARGV[0]) ) {
+  NERA::CUI_exec.new( File.basename(ARGV[0]) )
+}
+

data/bin/nera_addsim

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+#!/usr/bin/env ruby
+#
+#  Created by Yohsuke Murase on 2009-3-25.
+#  Copyright (c) 2009. All rights reserved.
+
+require 'optparse'
+require File.expand_path(File.dirname(__FILE__) + "/../lib/nera")
+
+parser = OptionParser.new do |opts|
+  opts.banner = <<-BANNER.gsub(/^    /,'')
+    
+    Usage: #{File.basename($0)} [options] 'nera_db_folder'
+    
+    BANNER
+  opts.separator ""
+  opts.on("-h", "--help",
+          "Show this help message.") { stdout.puts opts; exit }
+  opts.parse!(ARGV)
+end
+
+unless ARGV.size == 1
+  raise "\n\nUsage:\n nera_addsim 'nera_db_folder'"
+end
+folder_path = ARGV[0]+'/Simulator_classes/'
+unless FileTest.directory?( folder_path)
+  raise "Folder #{folder_path} does not exist."
+end
+
+require File.expand_path(File.dirname(__FILE__) + "/../lib/nera_addsim/make_simulator")
+test = NERA::CUI_Simulator_Adder.new('hoge')

data/lib/nera/nera_cui.rb

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+require 'nera_simulator_layer_controller'
+require 'nera_job_layer_controller'
+require 'nera_parameter_layer_controller'
+require 'nera_run_layer_controller'
+require 'nera_dialog'
+
+# --- start CUI based NER analyzer ---
+# - db_name : name of the database folder
+module NERA
+  class CUI_exec
+
+    # folder structure
+    @path_db_folder
+
+    # simulator layer controller
+    @sim_cont
+
+    # param layer controller
+    @param_cont
+
+    # run layer controller
+    @run_cont
+
+    # job layer controller
+    @job_cont
+    
+    # state [ :simulator_layer, :parameter_layer, :run_layer, :job_layer, :exit]
+    @state
+
+    # model which is currently selected
+    @simulator_class
+    
+    # parameter which is currently selected
+    @parameter_id
+
+  # --- main method
+    def initialize( path_db_folder)
+      @state = :simulator_layer
+      @path_db_folder = path_db_folder
+      unless FileTest.directory?(@path_db_folder)
+        NERA::DbFolders.create_db(@path_db_folder)
+      end
+      
+      while true
+        case @state
+        when :simulator_layer
+          @state = sim_layer_action
+        when :parameter_layer
+          @state = param_layer_action
+        when :run_layer
+          @state = run_layer_action
+        when :job_layer
+          @state = job_layer_action
+        when :exit
+          return 0
+        else
+          raise "Must not happen"
+        end
+      end
+    end
+    
+    # --- action at simulator layer
+    def sim_layer_action
+      $stdout.puts <<"HEADER"
+===============================================
+--- in simulator layer ------------------------
+  #{@path_db_folder} 
+===============================================
+HEADER
+      
+      slc = NERA::SimulatorLayerController.new(@path_db_folder)
+      list = slc.list
+      names = list.map do |r|
+        r[:name]
+      end
+      names.unshift("go to Jobs layer")
+      names += ["exit"]
+      selected = 0
+      Dir.chdir( slc.path_to_sim_layer) {
+        selected = Dialog::select_one_or_return_string( names, "Select a simulator.")
+        if selected.is_a?(String)
+          system( selected)
+          return :simulator_layer
+        end
+      }
+      if names[selected] == "go to Jobs layer"
+        return :job_layer
+      elsif names[selected] == "exit"
+        return :exit
+      else
+        @simulator_class = eval(names[selected])
+        return :parameter_layer
+      end
+    end
+
+    # --- selection of a parameter set
+    def param_layer_action
+      $stdout.puts <<"HEADER"
+===============================================
+--- in parameter layer ------------------------
+  #{@path_db_folder} / #{@simulator_class.to_s}
+===============================================
+HEADER
+
+      plc = NERA::ParameterLayerController.new( @path_db_folder, @simulator_class)
+      unless plc
+        Dialog::message("Specified simulator does not exist #{@path_db_folder}/#{@simulator_class.to_s}")
+        return :simulator_layer
+      end
+      
+      header,list = plc.parameters_list_in_csv
+      list.unshift( "Menu")
+      selected = 0
+      Dir.chdir( plc.path_to_param_layer) {
+        selected = Dialog::select_one_or_return_string( list, header)
+        if selected.is_a?(String)
+          system(selected)
+          return :parameter_layer
+        end
+      }
+      if selected == 0
+        layer = parameter_layer_menu_select
+        return layer
+      else
+        id = plc.get_id_from_csv_string( list[selected])
+        @parameter_id = id
+        return :run_layer
+      end
+    end
+    
+    # --- menu at a parameter layer
+    def parameter_layer_menu_select
+      menu = ["return to simulator layer",
+              "create a new parameter set",
+              "move a parameter set into the trashbox",
+              "revert a parameter set in the trashbox",
+              "delete a parameter set completely",
+              "exit"]
+      s = Dialog::select_one( menu, "Select one from the following")
+      plc = NERA::ParameterLayerController.new( @path_db_folder, @simulator_class)
+      case menu[s]
+      when "return to simulator layer"
+        return :simulator_layer
+      when "create a new parameter set"
+        plist = plc.list_of_parameters
+        new_param_hash = Dialog::set_multiple_values( plist, "Input the new parameter set")
+        f = plc.create_a_new_parameter_set( new_param_hash)
+        if f
+          Dialog::message("A new parameter is successfully added to the table.")
+        else
+          Dialog::message("This parameter already exists in the database.")
+        end
+        return :parameter_layer
+      when "move a parameter set into the trashbox"
+        header,list = plc.parameters_list_in_csv
+        list.unshift("Cancel")
+        s = Dialog::select_one( list, header)
+        if s == 0
+          return :parameter_layer
+        else
+          id = plc.get_id_from_csv_string( list[s])
+          f = plc.move_a_parameter_set_into_trashbox(id)
+          if f
+            Dialog::message("Parameter #{id} was successfully moved into the trashbox")
+          else
+            Dialog::message("Couldn't move the parameter #{id} to the trashbox.\nYou have to cancel all the jobs that are not finished.")
+          end
+          return :parameter_layer
+        end
+      when "revert a parameter set in the trashbox"
+        header,list = plc.trashbox_parameter_list_in_csv
+        list.unshift("Cancel")
+        s = Dialog::select_one( list, header)
+        if s == 0
+          return :parameter_layer
+        else
+          id = plc.get_id_from_csv_string( list[s])
+          f = plc.revert_a_parameter_set_in_trashbox(id)
+          if f
+            Dialog::message("Parameter #{id} was successfully reverted.")
+          else
+            Dialog::message("Couldn't revert the parameter #{id}")
+          end
+          return :parameter_layer
+        end
+      when "delete a parameter set completely"
+        header,list = plc.trashbox_parameter_list_in_csv
+        list.unshift("Cancel")
+        s = Dialog::select_one( list, header)
+        if s == 0
+          return :parameter_layer
+        else
+          id = plc.get_id_from_csv_string( list[s])
+          f = plc.delete_a_parameter_set( id)
+          if f
+            Dialog::message("Parameter #{id} was successfully deleted.")
+          else
+            Dialog::message("Couldn't delete the parameter #{id}")
+          end
+          return :parameter_layer
+        end
+      when "exit"
+        return :exit
+      else
+        raise "must not happen"
+      end
+    end
+    
+    # --- action at run layer
+    def run_layer_action
+      $stdout.puts <<"HEADER"
+===============================================
+--- in run layer ------------------------------
+  #{@path_db_folder} / #{@simulator_class.to_s} / #{@parameter_id}
+===============================================
+HEADER
+
+      action_list = ["Back to parameter layer",
+                     "Show run infos",
+                     "Create jobs",
+                     #"Execute created jobs",
+                     #"Submit created jobs to remote host",
+                     "Cancel jobs",
+                     "Analyze data",
+                     "Exit"]
+      rlc = NERA::RunLayerController.new( @path_db_folder, @simulator_class, @parameter_id)
+      unless rlc
+        Dialog::message("Table #{@path_db_folder}/#{@simulator_class.to_s}/#{@parameter_id} is not found.")
+        return :parameter_layer
+      end
+
+      selected = 0
+      Dir.chdir( rlc.path_to_run_layer) {
+        selected = Dialog::select_one_or_return_string( action_list, "Select one")
+        if selected.is_a?(String)
+          system( selected)
+          return :run_layer
+        end
+      }
+      
+      case action_list[selected]
+      when "Back to parameter layer"
+        return :parameter_layer
+      when "Show run infos"
+        Dir.chdir( rlc.path_to_run_layer) {
+          system("less runs.yml")
+        }
+        return :run_layer
+      when "Create jobs"
+        num_job = Dialog::get_integer( "Input the number of jobs (must be equal or larget than zero)") { |i| i >= 0 }
+        return :run_layer if num_job == 0
+        num_run_per_job = Dialog::get_integer( "Input the number of runs per job (must be larger than zero)") { |i| i > 0 }
+        jobids = rlc.create_jobs( num_job, num_run_per_job)
+        str = jobids.join(", ")
+        Dialog::message( "The following jobs are newly created.\n#{str}")
+        return :run_layer
+      when "Execute created jobs"
+=begin        
+        header,list = rlc.not_finished_runs_list_in_csv
+      list = RunLayerController::get_created_runs_list( @db_folder, @model_id, @parameter_id)
+      selected = select_one( list, "Select a job to execute")
+      job_id = list[selected][:job_id]
+      stat = JobLayerController::execute_one( @db_folder, job_id)
+      if stat
+        $stderr.puts "Simulation finished successfully"
+      else
+        $stderr.puts "Simulation failed"
+      end
+=end
+        return :run_layer
+      when "Submit created jobs to remote host"
+=begin        
+        header,list = rlc.not_finished_runs_list_in_csv
+        list.unshift("Cancel")
+        selected_jobs = Dialog::select_many( list, header)
+        unless selected_jobs.include?(0)
+          rc = RemoteConnector.new( @db_folder)
+          hosts = rc.hostnames
+          hosts.unshift("Cancel")
+          s = Dialog::select_one( hosts, "Select a host")
+          return :run_layer if s == 0
+          if rc.connect( hosts[s])
+            Dialog::message( rc.get_status)
+            action = Dialog::select_one( ["Transfer", "Transfer and Submit", "Cancel"], "Select action")
+            stat = nil
+            case action
+            when 0
+              stat = rc.transfer( selected_jobs)
+              Dialog::message("File transfer to #{hosts[s]} failed") unless stat
+            when 1
+              stat = rc.submit( selected_jobs)
+              Dialog::message("Submission to #{hosts[s]} failed") unless stat
+            when 2
+            end
+            Dialog::message("Completed successfully.") if stat
+          else
+            Dialog::message("Connection to #{hosts[s]} failed.")
+          end
+        end
+=end
+        return :run_layer
+      when "Cancel jobs"
+        header,list = rlc.not_finished_jobs_list_in_csv
+        list.unshift("Cancel")
+        selected_jobs = Dialog::select_many( list, header).map do |num|
+          list[num].split(',')[0].to_i
+        end
+        unless selected_jobs.include?(0)
+          stat = rlc.cancel_jobs( selected_jobs)
+          if stat
+            str = selected_jobs.join(", ")
+            Dialog::message("The following jobs are successfully cancelled.\n#{str}")
+          else
+            Dialog::message("Cancellation failed.")
+          end
+        end
+        return :run_layer
+      when "Analyze data"
+        list = rlc.analysis_methods
+        list = [ "Cancel", "All"] + list
+        sel = Dialog.select_many( list, "Select numbers.")
+        if sel.include?(0)
+          return :run_layer
+        elsif sel.include?(1)
+          rlc.analyze_all
+          return :run_layer
+        else
+          sel.each do |i|
+            rlc.analyze( list[i])
+          end
+          return :run_layer
+        end
+      when "Exit"
+        return :exit
+      else
+        raise "Must not happen"
+      end
+    end
+
+  # --- action at job layer
+    def job_layer_action
+      $stdout.puts <<"HEADER"
+===============================================
+--- in job layer ------------------------------
+  #{@path_db_folder} / Jobs
+===============================================
+HEADER
+
+      action_list = ["Back to simulator layer",
+                     "Show job infos",
+                     "Cancel jobs",
+                     "Include data",
+                     "Exit"]
+      jlc = NERA::JobLayerController.new( @path_db_folder)
+
+      selected = 0
+      Dir.chdir( jlc.path_to_job_layer) {
+        selected = Dialog.select_one_or_return_string( action_list, "Select one")
+        if selected.is_a?(String)
+          system( selected)
+          return :job_layer
+        end
+      }
+      
+      case action_list[selected]
+      when "Back to simulator layer"
+        return :simulator_layer
+      when "Show job infos"
+        Dir.chdir( jlc.path_to_job_layer) {
+          system("less jobs.yml")
+        }
+        return :job_layer
+      when "Cancel jobs"
+        header,list = jlc.not_finished_list_in_csv
+        list.unshift("Cancel")
+        selected_jobs = Dialog::select_many( list, header).map do |num|
+          list[num].split(',')[0].to_i
+        end
+        unless selected_jobs.include?(0)
+          stat = jlc.cancel_jobs( selected_jobs)
+          if stat
+            str = selected_jobs.join(", ")
+            Dialog::message("The following jobs are successfully cancelled.\n#{str}")
+          else
+            Dialog::message("Cancellation failed.")
+          end
+        end
+        return :job_layer
+      when "Include data"
+        list = jlc.include_list
+        list = ["Cancel","All"] + list
+        sel = Dialog::select_many( list)
+        status = nil
+        if sel.include?(0)
+          return :job_layer
+        elsif sel.include?(1)
+          status = jlc.include_all
+        else
+          sel.each do |num|
+            status = jlc.include( list[num])
+          end
+        end
+        if status
+          Dialog::message("Inclusion successfully completed.")
+        else
+          Dialog::message("Inclusion failed.")
+        end
+        return :job_layer
+      when "Exit"
+        return :exit
+      end
+    end
+
+    
+  end
+end
+