workflow_manager 0.0.5 → 0.0.6

data/.bzrignore

@@ -0,0 +1,17 @@
+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp

data/bin/workflow_manager

@@ -1,262 +1,39 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# 20121109 masa workflow manager druby server
-Version = '20131104-192005'
 
-require 'drb/drb' 
+require 'workflow_manager'
 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
+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
 
-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
+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
+  config_dir = "./config/environments/"
+  FileUtils.mkdir_p config_dir
+  config_file = File.join(config_dir, opt.mode+".rb")
+  unless File.exist?(config_file)
+    app_dir = File.expand_path('..', __FILE__)
+    default_config_dir = File.join(app_dir, "../config/environments")
+    p default_config_dir
+    default_config_file = File.join(default_config_dir, opt.mode+".rb")
+    if File.exist?(default_config_file)
+      FileUtils.cp(default_config_file, config_file)
+    else
+      raise "Configure file does not exist: #{config_file}"
     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
+  require config_file
 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
+DRb.start_service(uri, WorkflowManager::Server.new) 
+puts DRb.uri
+DRb.thread.join

data/config/environments/development.rb

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

data/lib/workflow_manager.rb

@@ -1,5 +1,6 @@
 
-require_relative "workflow_manager/version"
+require 'workflow_manager/version'
 
-require_relative "workflow_manager/optparse_ex"
-require_relative "workflow_manager/cluster"
+require 'workflow_manager/optparse_ex'
+require 'workflow_manager/cluster'
+require 'workflow_manager/server'

data/lib/workflow_manager/cluster.rb

@@ -1,113 +1,115 @@
 #!/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"
+module WorkflowManager
+  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
-    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$/
-      new_job_script = generate_new_job_script(script_name, script_content)
-      new_job_script_base = File.basename(new_job_script)
-      log_file = File.join(@log_dir, new_job_script_base + "_o.log")
-      err_file = File.join(@log_dir, new_job_script_base + "_e.log")
-      command = "bash #{new_job_script} 1> #{log_file} 2> #{err_file}"
-      pid = spawn(command)
-      Process.detach(pid)
-      [pid.to_s, log_file, command]
+  class LocalComputer < Cluster
+    def submit_job(script_file, script_content, option='')
+      if script_name = File.basename(script_file) and script_name =~ /\.sh$/
+        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
-  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
+    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
-      flag
+      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
-    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]
+  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
-  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
+    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
-    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
+    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
-    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/server.rb

@@ -0,0 +1,236 @@
+#!/usr/bin/env ruby
+# encoding: utf-8
+
+require 'drb/drb' 
+require 'fileutils'
+require 'kyotocabinet'
+
+module WorkflowManager
+  # default parameters
+  #LOG_DIR  = '/srv/GT/analysis/workflow_manager_logs'
+  LOG_DIR  = 'logs'
+  DB_DIR   = 'dbs'
+  INTERVAL = 30
+  RESUBMIT = 0
+
+  #class WorkflowManager
+  class Server
+    @@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
+#  class Server
+    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
+end
+

data/lib/workflow_manager/version.rb

@@ -1,3 +1,3 @@
-class WorkflowManager
-  VERSION = "0.0.5"
+module WorkflowManager
+  VERSION = "0.0.6"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: workflow_manager
 version: !ruby/object:Gem::Version
-  version: 0.0.5
+  version: 0.0.6
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-11-07 00:00:00.000000000 Z
+date: 2013-11-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -57,6 +57,7 @@ executables:
 extensions: []
 extra_rdoc_files: []
 files:
+- .bzrignore
 - Gemfile
 - LICENSE.txt
 - README.md
@@ -72,6 +73,7 @@ files:
 - config/environments/production.rb
 - lib/workflow_manager/cluster.rb
 - lib/workflow_manager/optparse_ex.rb
+- lib/workflow_manager/server.rb
 - lib/workflow_manager/version.rb
 - lib/workflow_manager.rb
 - workflow_manager.gemspec