workflow_manager 0.0.5

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in workflow_manager.gemspec
+gemspec

data/LICENSE.txt

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+Copyright (c) 2013 Function Genomics Center Zurich
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# WorkflowManager
+
+TODO: Write a gem description
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'workflow_manager'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install workflow_manager
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Contributing
+
+1. Fork it
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request

data/Rakefile

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+require "bundler/gem_tasks"

data/bin/wfm_get_log

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+#!/usr/bin/env ruby
+# encoding: utf-8
+# 20121112 masa workflow manager client
+Version = '20130307-094928'
+
+require 'drb/drb' 
+
+unless job_id = ARGV[0]
+	puts "Usage:\n #{__FILE__} [job_id] [with_err] [server]"
+  puts
+  puts "  job_id: required"
+  puts "  with_err: if you want also standard errors"
+  puts "  server: workflow_manager sever URI (default: druby://localhost:12345)"
+	exit
+end
+with_err = ARGV[1]
+uri = ARGV[2]||'druby://localhost:12345'
+
+wfmrc = if File.exist?(".wfmrc")
+          ".wfmrc"
+        elsif File.exist?(File.expand_path("~/.wfmrc"))
+          File.expand_path("~/.wfmrc")
+        end
+if wfmrc
+  File.readlines(wfmrc).each do |line|
+    if line =~ /server:\s*(druby.+)/
+      uri = $1
+    end
+  end
+end
+workflow_manager = DRbObject.new_with_uri(uri)
+puts workflow_manager.get_log(job_id, with_err)

data/bin/wfm_get_script

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+#!/usr/bin/env ruby
+# encoding: utf-8
+# 20121112 masa workflow manager client
+Version = '20130307-094955'
+
+require 'drb/drb' 
+
+unless job_id = ARGV[0]
+	puts "Usage:\n #{__FILE__} [job_id] [server]"
+  puts
+  puts "  job_id: required"
+  puts "  server: workflow_manager URI (default: druby://localhost:12345)"
+	exit
+end
+uri = ARGV[1]||'druby://localhost:12345'
+wfmrc = if File.exist?(".wfmrc")
+          ".wfmrc"
+        elsif File.exist?(File.expand_path("~/.wfmrc"))
+          File.expand_path("~/.wfmrc")
+        end
+if wfmrc
+  File.readlines(wfmrc).each do |line|
+    if line =~ /server:\s*(druby.+)/
+      uri = $1
+    end
+  end
+end
+workflow_manager = DRbObject.new_with_uri(uri)
+puts workflow_manager.get_script(job_id)

data/bin/wfm_hello

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+#!/usr/bin/env ruby
+# encoding: utf-8
+# 20121112 masa workflow manager client
+Version = '20130517-111334'
+
+require 'drb/drb' 
+
+if ARGV[0]=='-h' or ARGV[0]=='--help'
+  puts "Usage:\n #{__FILE__}"
+  exit
+end
+
+uri = ARGV[0]||'druby://localhost:12345'
+wfmrc = if File.exist?(".wfmrc")
+          ".wfmrc"
+        elsif File.exist?(File.expand_path("~/.wfmrc"))
+          File.expand_path("~/.wfmrc")
+        end
+if wfmrc
+  File.readlines(wfmrc).each do |line|
+    if line =~ /server:\s*(druby.+)/
+      uri = $1
+    end
+    if line =~ /project:\s*(\d+)/
+      project_number = $1
+    end
+  end
+end
+workflow_manager = DRbObject.new_with_uri(uri)
+puts workflow_manager.hello

data/bin/wfm_job_list

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+#!/usr/bin/env ruby
+# encoding: utf-8
+# 20121112 masa workflow manager client
+Version = '20131104-192211'
+
+require 'drb/drb' 
+require 'workflow_manager/optparse_ex'
+#require File.join((File.expand_path('../../lib',__FILE__)), 'optparse_ex.rb')
+
+opt = OptionParser.new do |o|
+  o.banner = "Usage:\n #{File.basename(__FILE__)} [options]"
+#  o.on(:user, 'sushi lover', '-u user', '--user', 'who submitted?')
+  o.on(:project, nil, '-p project', '--project', 'project number')
+  o.on(:server, 'druby://localhost:12345', '-d server', '--server', 'workflow manager URI (default: druby://localhost:12345)')
+  o.parse!(ARGV)
+end
+
+with_result = false
+uri = opt.server||'druby://localhost:12345'
+project_number = opt.project
+wfmrc = if File.exist?(".wfmrc")
+          ".wfmrc"
+        elsif File.exist?(File.expand_path("~/.wfmrc"))
+          File.expand_path("~/.wfmrc")
+        end
+if wfmrc
+  File.readlines(wfmrc).each do |line|
+    if line =~ /server:\s*(druby.+)/
+      uri = $1
+    end
+    if line =~ /project:\s*(\d+)/
+      project_number = $1
+    end
+  end
+end
+workflow_manager = DRbObject.new_with_uri(uri)
+puts workflow_manager.job_list(with_result, project_number)

data/bin/wfm_monitoring

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+#!/usr/bin/env ruby
+# encoding: utf-8
+# 20121112 masa workflow manager client
+Version = '20131104-192323'
+
+require 'drb/drb' 
+require 'workflow_manager/optparse_ex'
+
+opt = OptionParser.new do |o|
+  o.banner = "Usage:\n #{File.basename(__FILE__)} [options] [job_script.sh]"
+  o.on(:user, 'sushi lover', '-u user', '--user', 'who submitted? (default: sushi lover)')
+  o.on(:project, 1001, '-p project', '--project', 'project number (default: 1001)')
+  o.on(:server, 'druby://localhost:12345', '-d server', '--server', 'workflow manager URI (default: druby://localhost:12345)')
+  o.on(:log, '-o logdir', '--logdir', 'directory of standard output and standard error file outputted after the job')
+  o.on(:cores, '-c cores', '--cores', 'Number of cores to request for g-sub')
+  o.on(:nodes, '-n nodes', '--nodes', 'Comma separated list of nodes to submit to for g-sub')
+  o.on(:ram, '-r RAM', '--RAM', 'Amount of RAM to request in Gigs for g-sub')
+  o.on(:scratch, '-s scratch', '--scratch', 'Amount of scratch space to request in Gigs for g-sub')
+  o.parse!(ARGV)
+end
+unless script_file = ARGV[0] and script_file =~ /\.sh/
+  print opt.help
+  exit
+end
+
+project_number = opt.project
+uri = opt.server
+user = opt.user
+wfmrc = if File.exist?(".wfmrc")
+          ".wfmrc"
+        elsif File.exist?(File.expand_path("~/.wfmrc"))
+          File.expand_path("~/.wfmrc")
+        end
+if wfmrc
+  File.readlines(wfmrc).each do |line|
+    if line =~ /user:\s*(.+)/
+      user = $1
+    end
+    if line =~ /server:\s*(druby.+)/
+      uri = $1
+    end
+    if line =~ /project:\s*(\d+)/
+      project_number = $1
+    end
+  end
+end
+sge_options = []
+sge_options << "-c #{opt.cores}" if opt.cores
+sge_options << "-r #{opt.ram}" if opt.ram
+sge_options << "-s #{opt.scratch}" if opt.scratch
+sge_options << "-n #{opt.nodes}" if opt.nodes
+
+script_content = File.read(script_file)
+workflow_manager = DRbObject.new_with_uri(uri)
+puts workflow_manager.start_monitoring(script_file, user, 0, script_content, project_number, sge_options.join(' '), opt.log)

data/bin/wfm_status

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+#!/usr/bin/env ruby
+# encoding: utf-8
+# 20121112 masa workflow manager client
+Version = '20130307-095018'
+
+require 'drb/drb' 
+
+unless job_id = ARGV[0]
+	puts "Usage:\n #{__FILE__} [job_id] [server]"
+  puts
+  puts "  job_id: required"
+  puts "  server: workflow_manager URI (default: druby://localhost:12345)"
+	exit
+end
+uri = ARGV[1]||'druby://localhost:12345'
+wfmrc = if File.exist?(".wfmrc")
+          ".wfmrc"
+        elsif File.exist?(File.expand_path("~/.wfmrc"))
+          File.expand_path("~/.wfmrc")
+        end
+if wfmrc
+  File.readlines(wfmrc).each do |line|
+    if line =~ /server:\s*(druby.+)/
+      uri = $1
+    end
+  end
+end
+workflow_manager = DRbObject.new_with_uri(uri)
+puts workflow_manager.status(job_id)

data/bin/workflow_manager

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+#!/usr/bin/env ruby
+# encoding: utf-8
+# 20121109 masa workflow manager druby server
+Version = '20131104-192005'
+
+require 'drb/drb' 
+require 'fileutils'
+require 'kyotocabinet'
+require_relative '../lib/workflow_manager'
+
+
+# default parameters
+#LOG_DIR  = '/srv/GT/analysis/workflow_manager_logs'
+LOG_DIR  = 'logs'
+DB_DIR   = 'dbs'
+INTERVAL = 30
+RESUBMIT = 0
+
+class WorkflowManager
+  @@config = nil
+  class Config
+    attr_accessor :log_dir
+    attr_accessor :db_dir
+    attr_accessor :interval
+    attr_accessor :resubmit
+    attr_accessor :cluster
+  end
+  def self.config=(config)
+    @@config = config
+  end
+  def self.config
+    @@config
+  end
+  def config
+    @@config ||= WorkflowManager.configure{}
+  end
+  def self.configure
+    @@config = Config.new
+    # default values
+    @@config.log_dir  = LOG_DIR
+    @@config.db_dir   = DB_DIR
+    @@config.interval = INTERVAL  # interval to check jobs, [s]
+    @@config.resubmit = RESUBMIT  # how many times at maximum to resubmit when job fails
+    yield(@@config)
+    if @@config.cluster
+      @@config.cluster.log_dir = File.expand_path(@@config.log_dir)
+    end
+    @@config
+  end
+end
+
+class WorkflowManager
+  def initialize
+		@interval = config.interval
+		@resubmit = config.resubmit
+    @db_stat = File.join(config.db_dir, 'statuses.kch')
+    @db_logs  = File.join(config.db_dir, 'logs.kch')
+
+		@log_dir = File.expand_path(config.log_dir)
+    @db_dir  = File.expand_path(config.db_dir)
+		FileUtils.mkdir_p @log_dir unless File.exist?(@log_dir)
+		FileUtils.mkdir_p @db_dir unless File.exist?(@db_dir)
+    @statuses = KyotoCabinet::DB.new
+		@logs = KyotoCabinet::DB.new 
+		@system_log = File.join(@log_dir, "system.log")
+		@mutex = Mutex.new
+    @cluster = config.cluster
+		log_puts("Server starts")
+  end
+  def hello
+    'hello, '+ @cluster.name
+  end
+  def copy_commands(org_dir, dest_parent_dir)
+    @cluster.copy_commands(org_dir, dest_parent_dir)
+  end
+	def log_puts(str)
+		time = Time.now.strftime("[%Y.%m.%d %H:%M:%S]")
+		@mutex.synchronize do
+			open(@system_log, "a") do |out|
+				out.print time + " " + str + "\n"
+			end
+		end
+	end
+	def start_monitoring(submit_command, user = 'sushi lover', resubmit = 0, script = '', project_number = 0, sge_options='', log_dir = '')
+		log_puts("monitoring: script=" + submit_command + " user=" + user + " resubmit=" + resubmit.to_s + " project=" + project_number.to_s + " sge option=" + sge_options + " log dir=" + log_dir.to_s)
+
+		#warn submit_command
+		#
+		# TODO: analyze arguments
+		#
+		job_id, log_file, command = @cluster.submit_job(submit_command, script, sge_options)
+    log_puts("submit: " + job_id + " " + command)
+
+		#
+		# monitor worker
+		#
+		if job_id and log_file
+			monitor_worker = Thread.new(job_id, log_file, submit_command, user, resubmit, script, project_number, sge_options, log_dir) do |t_job_id, t_log_file, t_submit_command, t_user, t_resubmit, t_script, t_project_number, t_sge_options, t_log_dir|
+				loop do
+					status = success_or_fail(t_job_id, t_log_file) 
+          script_name = File.basename(submit_command).split(/-/).first
+          @statuses.open(@db_stat)
+          start_time = if stat = @statuses[t_job_id] and stat = stat.split(/,/) and time = stat[2]
+                         time
+                       end
+          time = if start_time 
+                   if status == 'success' or status == 'fail'
+                     start_time + '/' + Time.now.strftime("%Y-%m-%d %H:%M:%S")
+                   else
+                     start_time
+                   end
+                 else
+                   Time.now.strftime("%Y-%m-%d %H:%M:%S")
+                 end
+			    @statuses[t_job_id] = [status, script_name, time, user, project_number].join(',')
+          @statuses.close
+          @logs.open(@db_logs)
+					@logs[t_job_id] = t_log_file
+          @logs.close
+					#warn t_job_id + " " + status
+					if status == 'success'
+						log_puts(status + ": " + t_job_id)
+            unless t_log_dir.empty?
+              copy_commands(t_log_file, t_log_dir).each do |command|
+                log_puts(command)
+                system command
+              end
+              err_file = t_log_file.gsub('_o.log','_e.log')
+              copy_commands(err_file, t_log_dir).each do |command|
+                log_puts(command)
+                system command
+              end
+            end
+						Thread.current.kill
+					elsif status == 'fail'
+						log_puts(status + ": " + t_job_id)
+						#
+						# TODO: re-submit
+						#
+						if t_resubmit < RESUBMIT
+							log_puts("resubmit: " + t_job_id)
+							resubmit_job_id = start_monitoring(t_submit_command, t_user, t_resubmit + 1, t_script, t_project_number, t_sge_options)
+              script_name = File.basename(submit_command).split(/-/).first
+              @statuses.open(@db_stat)
+							@statuses[t_job_id] = ["resubmit: " + resubmit_job_id.to_s, script_name, Time.now.strftime("%Y-%m-%d %H:%M:%S"), t_user, t_project_number].join(',')
+              @statuses.close
+						else
+							log_puts("fail: " + t_job_id)
+						end
+            unless t_log_dir.empty?
+              copy_commands(t_log_file, t_log_dir).each do |command|
+                log_puts(command)
+                system command
+              end
+              err_file = t_log_file.gsub('_o.log','_e.log')
+              copy_commands(err_file, t_log_dir).each do |command|
+                log_puts(command)
+                system command
+              end
+            end
+						Thread.current.kill
+					end
+					sleep @interval
+				end	
+			end
+			job_id.to_i
+		end
+	end
+	def status(job_id)
+    stat = nil
+    @statuses.open(@db_stat)
+		stat = @statuses[job_id.to_s]
+    @statuses.close
+    stat
+	end
+  def job_list(with_results=false, project_number=nil)
+    s = []
+    @statuses.open(@db_stat)
+    @statuses.each do |key, value|
+      if project_number 
+        if x = value.split(/,/)[4].to_i==project_number.to_i
+          s << [key, value]
+        end
+      else
+        s << [key, value]
+      end
+    end
+    @statuses.close
+    s.sort.reverse.map{|v| v.join(',')}.join("\n")
+  end
+	def get_log(job_id, with_err=false)
+    @logs.open(@db_logs)
+		log_file = @logs[job_id.to_s]
+    @logs.close
+		log_data = if log_file and File.exist?(log_file)
+			"__STDOUT LOG__\n\n" + File.read(log_file)
+		else
+			'no log file'
+		end
+    if with_err
+      err_file = log_file.gsub(/_o\.log/,'_e.log')
+     if err_file and File.exist?(err_file)
+        log_data << "\n\n__STDERR LOG__\n\n"
+        log_data << File.read(err_file)
+      end
+    end
+		log_data
+	end
+	def get_script(job_id)
+    @logs.open(@db_logs)
+		script_file = @logs[job_id.to_s]
+    @logs.close
+    if script_file
+      script_file = script_file.gsub(/_o\.log/,'')
+    end
+		script = if script_file and File.exist?(script_file)
+			File.read(script_file)
+		else
+			'no script file'
+		end
+		script
+	end
+	def success_or_fail(job_id, log_file)
+    job_running = @cluster.job_running?(job_id)
+    job_ends = @cluster.job_ends?(log_file)
+		msg = if job_running
+			'running'
+		elsif job_ends
+			'success'
+		else
+			'fail'
+		end
+		msg
+	end
+end
+
+#
+# main
+#
+#if __FILE__ == $0
+
+  opt = OptionParser.new do |o|
+    o.banner = "Usage:\n #{File.basename(__FILE__)} -d [druby://host:port] -m [development|production]"
+    o.on(:server, 'druby://localhost:12345', '-d server', '--server', 'workflow manager URI (default: druby://localhost:12345)')
+    o.on(:mode, 'development', '-m mode', '--mode', 'development|production (default: development)')
+    o.parse!(ARGV)
+  end
+
+	uri = opt.server
+  if opt.mode =~ /[development|production]/
+    config = File.join(File.dirname(File.expand_path(__FILE__)), "../config/environments/#{opt.mode}.rb")
+    opt.mode = nil unless File.exist?(config)
+  end
+  print "mode = #{opt.mode}\n"
+  if opt.mode
+    require_relative "../config/environments/#{opt.mode}"
+  end
+	DRb.start_service(uri, WorkflowManager.new) 
+	puts DRb.uri
+	DRb.thread.join
+	#sleep
+#end

data/config/environments/development.rb

@@ -0,0 +1,11 @@
+#!/usr/bin/env ruby
+# encoding: utf-8
+
+WorkflowManager.configure do |config|
+  config.log_dir = 'logs'
+  config.db_dir = 'dbs'
+  config.interval = 30
+  config.resubmit = 0
+  config.cluster = LocalComputer.new('local_computer')
+end
+

data/config/environments/production.rb

@@ -0,0 +1,11 @@
+#!/usr/bin/env ruby
+# encoding: utf-8
+
+WorkflowManager.configure do |config|
+  config.log_dir = 'logs'
+  config.db_dir = 'dbs'
+  config.interval = 30
+  config.resubmit = 0
+  config.cluster = LocalComputer.new('local_computer')
+end
+

data/lib/workflow_manager.rb

@@ -0,0 +1,5 @@
+
+require_relative "workflow_manager/version"
+
+require_relative "workflow_manager/optparse_ex"
+require_relative "workflow_manager/cluster"

data/lib/workflow_manager/cluster.rb

@@ -0,0 +1,113 @@
+#!/usr/bin/env ruby
+# encoding: utf-8
+
+class Cluster
+  attr_accessor :name
+  attr_reader :options
+  attr_accessor :log_dir
+  def initialize(name='', log_dir='')
+    @name = name
+    @options = {}
+    @log_dir = log_dir
+  end
+  def generate_new_job_script(script_name, script_content)
+    new_job_script = File.basename(script_name) + "_" + Time.now.strftime("%Y%m%d%H%M%S")
+    new_job_script = File.join(@log_dir, new_job_script)
+    open(new_job_script, 'w') do |out|
+      out.print script_content
+      out.print "\necho __SCRIPT END__\n"
+    end
+    new_job_script
+  end
+  def submit_job(script_file, script_content, option='')
+  end
+  def job_running?(job_id)
+  end
+  def job_ends?(log_file)
+  end
+  def copy_commands(org_dir, dest_parent_dir)
+  end
+end
+
+class LocalComputer < Cluster
+  def submit_job(script_file, script_content, option='')
+    if script_name = File.basename(script_file) and script_name =~ /\.sh$/
+      new_job_script = generate_new_job_script(script_name, script_content)
+      new_job_script_base = File.basename(new_job_script)
+      log_file = File.join(@log_dir, new_job_script_base + "_o.log")
+      err_file = File.join(@log_dir, new_job_script_base + "_e.log")
+      command = "bash #{new_job_script} 1> #{log_file} 2> #{err_file}"
+      pid = spawn(command)
+      Process.detach(pid)
+      [pid.to_s, log_file, command]
+    end
+  end
+  def job_running?(pid)
+    command = "ps aux"
+    result = IO.popen(command) do |io|
+      flag = false
+      while line=io.gets
+        x = line.split
+        if x[1].to_i == pid.to_i
+          flag = true
+          break
+        end
+      end
+      flag
+    end
+    result
+  end
+  def job_ends?(log_file)
+    command = "tail -n 20 #{log_file}|grep '__SCRIPT END__'"
+    result = `#{command}`
+    result.to_s.empty? ? false : true
+  end
+  def copy_commands(org_dir, dest_parent_dir)
+    commands = []
+    commands << "mkdir -p #{dest_parent_dir}"
+    commands << "cp -r #{org_dir} #{dest_parent_dir}"
+    commands
+  end
+end
+
+class FGCZCluster < Cluster
+  def submit_job(script_file, script_content, option='')
+    if script_name = File.basename(script_file) and script_name =~ /\.sh$/
+      new_job_script = generate_new_job_script(script_name, script_content)
+      new_job_script_base = File.basename(new_job_script)
+      log_file = File.join(@log_dir, new_job_script_base + "_o.log")
+      err_file = File.join(@log_dir, new_job_script_base + "_e.log")
+      command = "g-sub -o #{log_file} -e #{err_file} #{option} #{new_job_script}"
+      job_id = `#{command}`
+      job_id = job_id.match(/Your job (\d+) \(/)[1]
+      [job_id, log_file, command]
+    end
+  end
+  def job_running?(job_id)
+   qstat_flag = false
+    IO.popen('qstat -u "*"') do |io|
+      while line=io.gets
+        if line =~ /#{job_id}/
+          qstat_flag = true
+          break
+        end
+      end
+    end
+    qstat_flag
+  end
+  def job_ends?(log_file)
+    log_flag = false
+    IO.popen("tail -n 10 #{log_file}") do |io|
+      while line=io.gets
+        if line =~ /__SCRIPT END__/
+          log_flag = true
+          break
+        end
+      end
+    end
+    log_flag
+  end
+  def copy_commands(org_dir, dest_parent_dir)
+    commands = ["g-req -w copy #{org_dir} #{dest_parent_dir}"]
+  end
+end

data/lib/workflow_manager/optparse_ex.rb

@@ -0,0 +1,52 @@
+#!/usr/bin/env ruby
+# encoding: utf-8
+
+require 'optparse'
+# Version = '20130517-120455'
+
+class OptionParser
+  attr_reader :p
+  alias :_on :on
+  def on(attr, *args, &block)
+    if attr.is_a?(Symbol)
+      self.class.class_eval do
+        unless method_defined?(attr)
+          attr_accessor attr 
+        else
+          raise "Method #{attr.to_s} is already defined in OptionParser class"
+        end
+      end
+      unless args[0] =~ /\-/
+        default = args.shift
+        self.send(attr.to_s+"=", default)
+      end
+      _on(*args) do |i|
+        self.send(attr.to_s+"=", i)
+        block.call(i) if block
+      end
+    else
+      args.unshift attr
+      _on(*args, block)
+    end
+  end
+end
+
+if __FILE__ == $0
+  opt = OptionParser.new do |o|
+    o.banner = "Last update: #{o.version}\nUsage: ruby #{__FILE__} [options]"
+    o.on(:size, 100, '-N N', '--pop_size', Integer, 'population size (default: 100)'){|i| p i}
+    o.on(:seed, '-R R', '--rseed', 'random seed')
+    o.on(:flag, '-f', 'flag')
+    o.on('-M M', '--hoge', Integer, 'hoge'){|i| p i}
+    o.parse!(ARGV)
+  end
+
+  print "opt.flag = "
+  p opt.flag
+  print "opt.size = "
+  p opt.size
+  print "opt.seed = "
+  p opt.seed
+  puts
+  puts opt.help
+end

data/lib/workflow_manager/version.rb

@@ -0,0 +1,3 @@
+class WorkflowManager
+  VERSION = "0.0.5"
+end

data/workflow_manager.gemspec

@@ -0,0 +1,24 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'workflow_manager/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "workflow_manager"
+  spec.version       = WorkflowManager::VERSION
+  spec.authors       = ["Functional Genomics Center Zurich"]
+  spec.email         = ["masaomi.hatakeyama@fgcz.uzh.ch"]
+  spec.description   = %q{Workflow Manager manages job submissions using dRuby.}
+  spec.summary       = %q{Workflow Manager manages job submissions using dRuby.}
+  spec.homepage      = ""
+  spec.license       = "MIT"
+
+  #spec.files         = `git ls-files`.split($/)
+  spec.files         = `bzr ls --versioned --recursive`.split($/).select{|file| !File.directory?(file)}
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.3"
+  spec.add_development_dependency "rake"
+end

metadata

@@ -0,0 +1,103 @@
+--- !ruby/object:Gem::Specification
+name: workflow_manager
+version: !ruby/object:Gem::Version
+  version: 0.0.5
+  prerelease: 
+platform: ruby
+authors:
+- Functional Genomics Center Zurich
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-11-07 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+description: Workflow Manager manages job submissions using dRuby.
+email:
+- masaomi.hatakeyama@fgcz.uzh.ch
+executables:
+- wfm_get_log
+- wfm_get_script
+- wfm_hello
+- wfm_job_list
+- wfm_monitoring
+- wfm_status
+- workflow_manager
+extensions: []
+extra_rdoc_files: []
+files:
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/wfm_get_log
+- bin/wfm_get_script
+- bin/wfm_hello
+- bin/wfm_job_list
+- bin/wfm_monitoring
+- bin/wfm_status
+- bin/workflow_manager
+- config/environments/development.rb
+- config/environments/production.rb
+- lib/workflow_manager/cluster.rb
+- lib/workflow_manager/optparse_ex.rb
+- lib/workflow_manager/version.rb
+- lib/workflow_manager.rb
+- workflow_manager.gemspec
+homepage: ''
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.24
+signing_key: 
+specification_version: 3
+summary: Workflow Manager manages job submissions using dRuby.
+test_files: []