Class: WorkflowManager::Server

Inherits:
Object
  • Object
show all
Defined in:
lib/workflow_manager/server.rb

Defined Under Namespace

Classes: Config, KyotoDB, PStoreDB, RedisDB

Constant Summary collapse

@@config = 
nil

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Server

Returns a new instance of Server.



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# File 'lib/workflow_manager/server.rb', line 130

def initialize
  @interval = config.interval
  @resubmit = config.resubmit
  extension = case DB_MODE
                when "PStore"
                  '.pstore'
                when "KyotoCabinet"
                  '.kch'
                when "Redis"
                  @redis_conf = config.redis_conf
                  '.rdb'
                end
  @db_stat = File.join(config.db_dir, 'statuses'+extension)
  @db_logs  = File.join(config.db_dir, 'logs'+extension)

  @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 = case DB_MODE
                when "PStore"
                  PStoreDB.new(@db_stat)
                when "KyotoCabinet"
                  KyotoDB.new(@db_stat)
                when "Redis"
                  RedisDB.new(0, @redis_conf)
              end
  @logs = case DB_MODE
              when "PStore"
                PStoreDB.new(@db_logs)
              when "KyotoCabinet"
                KyotoDB.new(@db_logs)
              when "Redis"
                RedisDB.new(1, @redis_conf)
            end
  @jobs = RedisDB.new(2, @redis_conf)
  @trees = RedisDB.new(4, @redis_conf)

  @system_log = File.join(@log_dir, "system.log")
  @mutex = Mutex.new
  @cluster = config.cluster
  puts("DB = #{DB_MODE}")
  if DB_MODE == "Redis"
    puts("Redis conf = #{config.redis_conf}")
    puts("Redis port = #{@logs.port}")
  end
  puts("Cluster = #{@cluster.name}")
  log_puts("DB = #{DB_MODE}")
  log_puts("Cluster = #{@cluster.name}")
  log_puts("Server starts")
  log_puts("Recovery check")
  sleep 2
  recovery_job_checker
end

Class Method Details

.config ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 64

def self.config
  @@config
end

.config=(config) ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 61

def self.config=(config)
  @@config = config
end

.configure {|@@config| ... } ⇒ Object

Yields:



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# File 'lib/workflow_manager/server.rb', line 70

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

Instance Method Details

#cluster_node_list ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 556

def cluster_node_list
  @cluster.node_list
end

#cluster_nodes ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 214

def cluster_nodes
  @cluster.cluster_nodes
end

#config ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 67

def config
  @@config ||= WorkflowManager.configure{}
end

#copy_commands(org_dir, dest_parent_dir, now = nil) ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 204

def copy_commands(org_dir, dest_parent_dir, now=nil)
  @cluster.copy_commands(org_dir, dest_parent_dir, now)
end

#default_node ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 217

def default_node
  @cluster.default_node.to_s
end

#delete_command(target) ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 211

def delete_command(target)
  @cluster.delete_command(target)
end

#finalize_monitoring(current_status, log_file, log_dir) ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 284

def finalize_monitoring(current_status, log_file, log_dir)
  if current_status == 'success' or current_status == 'fail'
    unless log_dir.empty?
      copy_commands(log_file, log_dir).each do |command|
        log_puts(command)
        system command
      end
      err_file = log_file.gsub('_o.log','_e.log')
      copy_commands(err_file, log_dir).each do |command|
        log_puts(command)
        system command
      end
    end
    Thread.current.kill
  end
end

#get_log(job_id, with_err = false) ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 501

def get_log(job_id, with_err=false)
  log_file = nil
  @logs.transaction do |logs|
    log_file = logs[job_id.to_s]
  end
  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

#get_script(job_id) ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 520

def get_script(job_id)
  script_file = nil
  @logs.transaction do |logs|
    script_file = logs[job_id.to_s]
  end
  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

#get_script_path(job_id) ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 535

def get_script_path(job_id)
  script_file = nil
  @logs.transaction do |logs|
    script_file = logs[job_id.to_s]
  end
  script_path = if script_file and File.exist?(script_file)
                  script_file.gsub(/_o\.log/,'')
                end
end

#hello ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 201

def hello
  'hello hoge hoge bar boo bundle, '+ @cluster.name
end

#input_dataset_exist?(file_list) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/workflow_manager/server.rb', line 252

def input_dataset_exist?(file_list)
  flag = true
  file_list.each do |file|
    unless File.exist?(file)
      flag = false
      break
    end
  end
  flag
end

#input_dataset_file_list(dataset_tsv_path) ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 241

def input_dataset_file_list(dataset_tsv_path)
  file_list = []
  CSV.foreach(dataset_tsv_path, :headers=>true, :col_sep=>"\t") do |row|
    row.each do |header, value|
      if header =~ /\[File\]/
        file_list << value
      end
    end
  end
  file_list
end

#input_dataset_tsv_path(script_content) ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 228

def input_dataset_tsv_path(script_content)
  gstore_dir = nil
  input_dataset_path = nil
  script_content.split(/\n/).each do |line|
    if line =~ /GSTORE_DIR=(.+)/
      gstore_dir = $1.chomp
    elsif line =~ /INPUT_DATASET=(.+)/
      input_dataset_path = $1.chomp
      break
    end
  end
  [gstore_dir, input_dataset_path]
end

#job_list(with_results = false, project_number = nil, job_ids: nil) ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 472

def job_list(with_results=false, project_number=nil, job_ids:nil)
  s = []
  job_idsh = if job_ids
               Hash[*(job_ids.split(',')).map{|job_id| [job_id, true]}.flatten]
             end
  if project_number
    s_ = {}
    @jobs.transaction do |jobs|
      if project_jobs = jobs[project_number]
        s_ = Hash[*eval(project_jobs)]
      end
    end
    @statuses.transaction do |statuses|
      s_.each do |job_id, stat|
        s << [job_id, statuses[job_id]]
      end
    end
  else
    @statuses.transaction do |statuses|
      statuses.each do |key, value|
        s << [key, value]
      end
    end
  end
  if job_ids
    s = s.select{|job_id, stat| job_idsh[job_id]}
  end
  s.sort_by{|key, value| value.split(',')[2]}.reverse.map{|v| v.join(',')}.join("\n")
end

#kill_job(job_id) ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 207

def kill_job(job_id)
  status(job_id, 'FAIL')
  status = `#{@cluster.kill_command(job_id)}`
end

#load_dataset_tree(project_number) ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 565

def load_dataset_tree(project_number)
  json = nil
  @trees.transaction do |trees|
    json = trees[project_number]
  end
  json
end

#log_puts(str) ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 220

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

#recovery_job_checker ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 184

def recovery_job_checker
  @logs.transaction do |logs|
  @statuses.transaction do |statuses|
    statuses.each do |job_id, status|
      # puts [job_id, status].join(",")
      # 120249,RUNNING,QC_ventricles_100k.sh,2021-07-30 09:47:04/2021-07-30 09:47:04,masaomi,1535
      stat, script_basename, time, user, project_number, next_dataset_id = status.split(",")
      if stat == "RUNNING" or stat == "PENDING"
        log_file = logs[job_id]
        log_puts("JobID (in recovery check): #{job_id}")
        puts "JobID (in recovery check): #{job_id}"
        JobChecker.perform_async(job_id, script_basename, log_file, user, project_number, next_dataset_id)
      end
    end
  end
  end
end

#save_dataset_tree(project_number, json) ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 559

def save_dataset_tree(project_number, json)
  @trees.transaction do |trees|
    trees[project_number] = json
  end
  json
end

#start_monitoring(submit_command, user = 'sushi lover', resubmit = 0, script = '', project_number = 0, sge_options = '', log_dir = '') ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 361

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)
        @statuses.transaction do |statuses|
        #start_time = if stat = @statuses[t_job_id] and stat = stat.split(/,/) and time = stat[2]
          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[t_job_id] = [status, script_name, time, user, project_number].join(',')
        #@statuses.close
        end
        @logs.transaction do |logs|
          logs[t_job_id] = t_log_file
        end
        #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.transaction do |statuses|
              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
            end
          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

#start_monitoring2(script_path, script_content, user = 'sushi_lover', project_number = 0, sge_options = '', log_dir = '') ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 311

def start_monitoring2(script_path, script_content, user='sushi_lover', project_number=0, sge_options='', log_dir='')
  # script_path is only used to generate a log file name
  # It is not used to read the script contents
  go_submit = false
  waiting_time = 0
  gstore_dir, input_dataset_path = input_dataset_tsv_path(script_content)
  if gstore_dir and input_dataset_path
    waiting_max = 60*60*8 # 8h
    # wait until the files come
    until waiting_time > waiting_max or 
      File.exist?(input_dataset_path) and
      file_list = input_dataset_file_list(input_dataset_path) and
      file_list.map!{|file| File.join(gstore_dir, file)} and
      go_submit = input_dataset_exist?(file_list)
      sleep @interval
      waiting_time += @interval
    end
  end 

  job_id, log_file, command = if go_submit 
                                @cluster.submit_job(script_path, script_content, sge_options)
                              else
                                raise "stop submitting #{File.basename(script_path)}, since waiting_time #{waiting_time} > #{waiting_max}"
                              end

  if job_id and log_file 
    # save log_file in logs
    @logs.transaction do |logs|
      logs[job_id] = log_file
    end

    # job status check until it finishes with success or fail 
    worker = Thread.new(log_dir, script_path, script_content, sge_options) do |log_dir, script_path, script_content, sge_options|
      loop do
        # check status
        current_status = check_status(job_id, log_file)

        # save time and status
        update_time_status(job_id, current_status, script_path, user, project_number)

        # finalize (kill current thred) in case of success or fail 
        finalize_monitoring(current_status, log_file, log_dir)

        # wait
        sleep @interval
      end # loop
    end
    job_id
  end
end

#start_monitoring3(script_path, script_content, user = 'sushi_lover', project_number = 0, sge_options = '', log_dir = '', next_dataset_id = '') ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 300

def start_monitoring3(script_path, script_content, user='sushi_lover', project_number=0, sge_options='', log_dir='', next_dataset_id='')
  script_basename = File.basename(script_path)
  job_id, log_file, command = @cluster.submit_job(script_path, script_content, sge_options)
  #p command
  #p log_file
  #p job_id
  puts "JobID (in WorkflowManager): #{job_id}"
  sleep 1
  JobChecker.perform_async(job_id, script_basename, log_file, user, project_number, next_dataset_id)
  job_id
end

#status(job_id, new_status = nil) ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 452

def status(job_id, new_status=nil)
  stat = nil
  #@statuses.open(@db_stat)
  @statuses.transaction do |statuses|
    if new_status and stat = statuses[job_id.to_s]
      status_list = ['CONPLETED', 'RUNNING', 'PENDING', 'FAIL']
      if status_list.include?(new_status)
        items = stat.split(/,/)
        items.shift
        items.unshift(new_status)
        stat = items.join(',')
        statuses[job_id.to_s] = stat
      end
    else
      stat = statuses[job_id.to_s]
    end
  end
  #@statuses.close
  stat
end

#success_or_fail(job_id, log_file) ⇒ Object Also known as: check_status 



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# File 'lib/workflow_manager/server.rb', line 544

def success_or_fail(job_id, log_file)
  msg = if @cluster.job_running?(job_id)
          'running'
        elsif @cluster.job_ends?(log_file)
          'success'
        elsif @cluster.job_pending?(job_id)
          'pending'
        else
          'fail'
        end
end

#update_time_status(job_id, current_status, script_name, user, project_number) ⇒ Object 



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# File 'lib/workflow_manager/server.rb', line 262

def update_time_status(job_id, current_status, script_name, user, project_number)
  # if the current status changed from last time, then save, otherwise do nothing
  # once status changes into success or fail, then the thread is expected to be killed in later process
  @statuses.transaction do |statuses|
    start_time = nil
    if stat = statuses[job_id] 
      last_status, script_name, start_time, user, project_number = stat.split(/,/)
    end
    time = if start_time 
             if current_status == 'success' or current_status == 'fail'
               start_time + '/' + Time.now.strftime("%Y-%m-%d %H:%M:%S")
             elsif current_status != last_status
               Time.now.strftime("%Y-%m-%d %H:%M:%S")
             end
           else
             Time.now.strftime("%Y-%m-%d %H:%M:%S")
           end
    if time
      statuses[job_id] = [current_status, script_name, time, user, project_number].join(',')
    end
  end
end