Class: SushiFabric::SushiApp

Inherits:
Object
  • Object
show all
Defined in:
lib/sushi_fabric/sushiApp.rb

Overview

module_function :save_data_set

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ SushiApp

Returns a new instance of SushiApp.



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# File 'lib/sushi_fabric/sushiApp.rb', line 229

def initialize
  @gstore_dir = GSTORE_DIR
  @project = nil
  @name = nil
  @params = {}
  @params['cores'] = nil
  @params['ram'] = nil
  @params['scratch'] = nil
  @params['partition'] = ''
  @params['process_mode'] = 'SAMPLE'
  @params['samples'] = ''
  @job_ids = []
  @required_columns = []
  @module_source = MODULE_SOURCE
  @modules = []
  #@workflow_manager = workflow_manager_instance||DRbObject.new_with_uri(WORKFLOW_MANAGER)
  @last_job = true
end

Instance Attribute Details

#analysis_category ⇒ Object (readonly)

Returns the value of attribute analysis_category.



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# File 'lib/sushi_fabric/sushiApp.rb', line 205

def analysis_category
  @analysis_category
end

#current_user ⇒ Object

Returns the value of attribute current_user.



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# File 'lib/sushi_fabric/sushiApp.rb', line 219

def current_user
  @current_user
end

#data_set ⇒ Object

Returns the value of attribute data_set.



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# File 'lib/sushi_fabric/sushiApp.rb', line 212

def data_set
  @data_set
end

#dataset_hash ⇒ Object (readonly)

Returns the value of attribute dataset_hash.



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# File 'lib/sushi_fabric/sushiApp.rb', line 204

def dataset_hash
  @dataset_hash
end

#dataset_name ⇒ Object

Returns the value of attribute dataset_name.



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# File 'lib/sushi_fabric/sushiApp.rb', line 216

def dataset_name
  @dataset_name
end

#dataset_sushi_id ⇒ Object

Returns the value of attribute dataset_sushi_id.



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# File 'lib/sushi_fabric/sushiApp.rb', line 211

def dataset_sushi_id
  @dataset_sushi_id
end

#dataset_tsv_file ⇒ Object

Returns the value of attribute dataset_tsv_file.



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# File 'lib/sushi_fabric/sushiApp.rb', line 209

def dataset_tsv_file
  @dataset_tsv_file
end

#description ⇒ Object (readonly)

Returns the value of attribute description.



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# File 'lib/sushi_fabric/sushiApp.rb', line 206

def description
  @description
end

#employee ⇒ Object (readonly)

Returns the value of attribute employee.



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# File 'lib/sushi_fabric/sushiApp.rb', line 226

def employee
  @employee
end

#inactivate_nodes ⇒ Object (readonly)

Returns the value of attribute inactivate_nodes.



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# File 'lib/sushi_fabric/sushiApp.rb', line 225

def inactivate_nodes
  @inactivate_nodes
end

#input_dataset_bfabric_application_number ⇒ Object

Returns the value of attribute input_dataset_bfabric_application_number.



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# File 'lib/sushi_fabric/sushiApp.rb', line 223

def input_dataset_bfabric_application_number
  @input_dataset_bfabric_application_number
end

#job_ids ⇒ Object (readonly)

Returns the value of attribute job_ids.



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# File 'lib/sushi_fabric/sushiApp.rb', line 200

def job_ids
  @job_ids
end

#logger ⇒ Object

Returns the value of attribute logger.



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# File 'lib/sushi_fabric/sushiApp.rb', line 220

def logger
  @logger
end

#mango_run_name ⇒ Object

Returns the value of attribute mango_run_name.



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# File 'lib/sushi_fabric/sushiApp.rb', line 222

def mango_run_name
  @mango_run_name
end

#modules ⇒ Object (readonly)

Returns the value of attribute modules.



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# File 'lib/sushi_fabric/sushiApp.rb', line 208

def modules
  @modules
end

#name ⇒ Object (readonly)

Returns the value of attribute name.



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# File 'lib/sushi_fabric/sushiApp.rb', line 207

def name
  @name
end

#next_dataset_bfabric_application_number ⇒ Object

Returns the value of attribute next_dataset_bfabric_application_number.



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# File 'lib/sushi_fabric/sushiApp.rb', line 224

def next_dataset_bfabric_application_number
  @next_dataset_bfabric_application_number
end

#next_dataset_comment ⇒ Object

Returns the value of attribute next_dataset_comment.



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# File 'lib/sushi_fabric/sushiApp.rb', line 217

def next_dataset_comment
  @next_dataset_comment
end

#next_dataset_id ⇒ Object (readonly)

Returns the value of attribute next_dataset_id.



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# File 'lib/sushi_fabric/sushiApp.rb', line 201

def next_dataset_id
  @next_dataset_id
end

#next_dataset_name ⇒ Object

Returns the value of attribute next_dataset_name.



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# File 'lib/sushi_fabric/sushiApp.rb', line 215

def next_dataset_name
  @next_dataset_name
end

#off_bfabric_registration ⇒ Object

Returns the value of attribute off_bfabric_registration.



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# File 'lib/sushi_fabric/sushiApp.rb', line 221

def off_bfabric_registration
  @off_bfabric_registration
end

#parameterset_tsv_file ⇒ Object

Returns the value of attribute parameterset_tsv_file.



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# File 'lib/sushi_fabric/sushiApp.rb', line 210

def parameterset_tsv_file
  @parameterset_tsv_file
end

#params ⇒ Object (readonly)

Returns the value of attribute params.



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# File 'lib/sushi_fabric/sushiApp.rb', line 199

def params
  @params
end

#project ⇒ Object

Returns the value of attribute project.



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# File 'lib/sushi_fabric/sushiApp.rb', line 213

def project
  @project
end

#queue ⇒ Object

Returns the value of attribute queue.



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# File 'lib/sushi_fabric/sushiApp.rb', line 227

def queue
  @queue
end

#required_columns ⇒ Object (readonly)

Returns the value of attribute required_columns.



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# File 'lib/sushi_fabric/sushiApp.rb', line 202

def required_columns
  @required_columns
end

#required_params ⇒ Object (readonly)

Returns the value of attribute required_params.



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# File 'lib/sushi_fabric/sushiApp.rb', line 203

def required_params
  @required_params
end

#user ⇒ Object

Returns the value of attribute user.



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# File 'lib/sushi_fabric/sushiApp.rb', line 214

def user
  @user
end

#workflow_manager ⇒ Object

Returns the value of attribute workflow_manager.



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# File 'lib/sushi_fabric/sushiApp.rb', line 218

def workflow_manager
  @workflow_manager
end

Instance Method Details

#batch_mode ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 748

def batch_mode
  @job_script = if @dataset_sushi_id and dataset = DataSet.find_by_id(@dataset_sushi_id.to_i)
                  File.join(@job_script_dir, dataset.name.gsub(/\s+/,'_') + '.sh')
                else 
                  File.join(@job_script_dir, 'job_script.sh')
                end
  @dataset_hash.each do |row|
    @dataset = Hash[*row.map{|key,value| [key.gsub(/\[.+\]/,'').strip, value]}.flatten]
    make_job_script('append')
    @result_dataset << next_dataset
  end
  @job_scripts << @job_script
end

#check_application_parameters ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 342

def check_application_parameters
  if @required_params and (@required_params - @params.keys).empty?
    # PD, 20230623, the following fix changed parameters.tsv info, and reverted
    #@output_params = {"sushi_app" => self.class.name}.merge(@params.clone)
    @output_params = @params.clone
  end
end

#check_latest_modules_version(modules) ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 403

def check_latest_modules_version(modules)
  command_out =  %x[ bash -lc "source #{@module_source}; module whatis #{modules.join(" ")} 2>&1" | cut -f 1 -d " " | uniq ]
  latest_modules = []
  command_out.split("\n").each do |line_|
    line = line_.chomp
    unless line.empty?
      if line =~ /#{modules.join("|")}/
        latest_modules << line
      end
    end
  end
  latest_modules
end

#check_required_columns ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 335

def check_required_columns
  if @dataset_hash and @required_columns and (@required_columns-@dataset_hash.map{|row| row.keys}.flatten.uniq.map{|colname| colname.gsub(/\[.+\]/,'').strip}).empty?
    true
  else
    false
  end
end

#cluster_nodes ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 684

def cluster_nodes
  @workflow_manager||=DRbObject.new_with_uri(WORKFLOW_MANAGER)
  @workflow_manager.cluster_nodes
end

#commands ⇒ Object

 this should be overwritten in a subclass



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# File 'lib/sushi_fabric/sushiApp.rb', line 515

def commands
  # this should be overwritten in a subclass
end

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



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# File 'lib/sushi_fabric/sushiApp.rb', line 627

def copy_commands(org_dir, dest_parent_dir, now=nil, queue="light")
  @workflow_manager||=DRbObject.new_with_uri(WORKFLOW_MANAGER)
  com = ''
  cnt_retry = 0
  begin
    com = @workflow_manager.copy_commands(org_dir, dest_parent_dir, now, queue)
  rescue => e
    time = Time.now.strftime("[%Y.%m.%d %H:%M:%S]")
    @logger.error("*"*50)
    @logger.error("copy_command error #{time}")
    @logger.error("error: #{e}")
    @logger.error("org_dir: #{org_dir}, dest_parent_dir: #{dest_parent_dir}, now: #{now}")
    @logger.error("*"*50)
    sleep 1
    cnt_retry += 1
    retry if cnt_retry < 3
  end
  com
end

#copy_inputdataset_parameter_jobscripts ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 658

def copy_inputdataset_parameter_jobscripts
  org = @scratch_result_dir
  dest = @gstore_project_dir
  copy_commands(org, dest, 'now').each do |command|
    puts `which python`
    puts command
    unless system command
      raise "fails in copying input_dataset, parameters and jobscript files from /scratch to /gstore"
    end
  end
  #sleep 1
end

#copy_nextdataset ⇒ Object

sleep 1



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# File 'lib/sushi_fabric/sushiApp.rb', line 670

def copy_nextdataset
  org = @next_dataset_tsv_path
  dest = File.join(@gstore_project_dir, @result_dir_base)
  copy_commands(org, dest, 'now').each do |command|
    puts `which python`
    puts command
    unless system command
      raise "fails in copying next_dataset files from /scratch to /gstore"
    end
  end
  sleep 1
  command = "rm -rf #{@scratch_result_dir}"
  `#{command}`
end

#copy_uploaded_files ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 646

def copy_uploaded_files
  if not @uploaded_files.empty?
    @uploaded_files.compact.select{|file| !file.empty?}.each do |file|
      FileUtils.cp(file, @uploaded_files_dir)
      command = "cp #{file} #{@uploaded_files_dir}"
      puts command
      FileUtils.rm_r(File.dirname(file))
      command = "rm -rf #{File.dirname(file)}"
      puts command
    end
  end
end

#dataset_has_column?(colname) ⇒ Boolean

 this should be overwritten in a subclass

Returns:

  • (Boolean) 


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# File 'lib/sushi_fabric/sushiApp.rb', line 308

def dataset_has_column?(colname)
  flag = false
  if @dataset_hash
    @dataset_hash.map{|sample| 
      sample.each do |key, value|
        if key =~ /#{colname}/
          flag = true
        end
      end
      break
    }
  end
  flag
end

#dataset_mode ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 726

def dataset_mode
  selected_samples = unless @params['samples'].empty?
                       Hash[*@params['samples'].split(',').map{|sample_name| [sample_name, true]}.flatten]
                     else
                       Hash[*@dataset_hash.map{|row| row['Name']}.map{|sample_name| [sample_name, true]}.flatten]
                     end
  # for a case of @dataset is used in def next_datast in SUSHIApp
  @dataset = []
  @dataset_hash.each do |row|
    if selected_samples[row['Name']]
      @dataset << row
    end
  end
  @job_script = if @dataset_sushi_id and dataset = DataSet.find_by_id(@dataset_sushi_id.to_i)
                  File.join(@job_script_dir, @analysis_category + '_' + dataset.name.gsub(/[\s+,\/]/,'_') + '.sh')
                else 
                  File.join(@job_script_dir, @analysis_category + '_' + 'job_script.sh')
                end
  make_job_script
  @job_scripts << @job_script
  @result_dataset << next_dataset
end

#default_node ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 688

def default_node
  @workflow_manager||=DRbObject.new_with_uri(WORKFLOW_MANAGER)
  @workflow_manager.default_node
end

#get_columns_with_tag(tag) ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 299

def get_columns_with_tag(tag)
  #@factor_cols = @dataset_hash.first.keys.select{|header| header =~ /\[#{tag}\]/}.map{|header| header.gsub(/\[.+\]/,'').strip}
  @dataset_hash.map{|row| 
    Hash[*row.select{|k,v| k=~/\[#{tag}\]/}.map{|k,v| [k.gsub(/\[.+\]/,'').strip,v]}.flatten]
  }
end

#job_footer ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 469

def job_footer
  @out.print "#### JOB IS DONE WE PUT THINGS IN PLACE AND CLEAN AUP\n"
  if File.exist?("/usr/local/ngseq/miniconda3/etc/profile.d/conda.sh")
    @out.print <<-EOS
. "/usr/local/ngseq/miniconda3/etc/profile.d/conda.sh"
conda activate sushi
    EOS
  end

  src_files = []
  dest_dirs = []
  greq = (copy_commands("AAA", "BBB").join =~ /g-req/)
  if @output_files
    @output_files.map{|header| next_dataset[header]}.each do |file|
      src_file = File.basename(file)
      dest_dir = File.dirname(File.join(@gstore_dir, file))
      src_files << src_file
      dest_dirs << dest_dir
    end
    if dest_dirs.uniq.length == 1 and greq
      src_file = src_files.join(" ")
      dest_dir = dest_dirs.first
      @out.print copy_commands(src_file, dest_dir, nil, @queue).join("\n"), "\n"
    else
      @output_files.map{|header| next_dataset[header]}.each do |file|
        # in actual case, to save under /srv/gstore/
        src_file = File.basename(file)
        dest_dir = File.dirname(File.join(@gstore_dir, file))
        @out.print copy_commands(src_file, dest_dir, nil, @queue).join("\n"), "\n"
      end
    end
  end
  @out.print <<-EOF
cd #{SCRATCH_DIR}
rm -rf #{@scratch_dir} || exit 1

  EOF

end

#job_header ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 416

def job_header
  @scratch_dir = if @params['process_mode'] == 'SAMPLE'
                   @scratch_result_dir + "_" + @dataset['Name'] + '_temp$$'
                 else
                   @scratch_result_dir + '_temp$$'
                 end
  hold_jid_option = if @dataset_sushi_id and parent_data_set = DataSet.find_by_id(@dataset_sushi_id.to_i) and !parent_data_set.jobs.empty? and parent_data_set_job_ids = parent_data_set.jobs.map{|job| job.submit_job_id} and !parent_data_set_job_ids.join.empty?
                      "#SBATCH --dependency=afterany:#{parent_data_set_job_ids.join(":")}"
                    else
                      ''
                    end
  module_src_command = if @module_source and @modules and !@modules.empty?
                     "source #{@module_source}"
                   else
                     ""
                   end
  module_add_commands = if @modules and !@modules.empty?
                          modules_with_version = check_latest_modules_version(@modules)
                          if @modules.length == modules_with_version.length
                            modules_with_version.compact!
                            "module add #{modules_with_version.join(' ')}"
                          else
                            @logger.error("#"*100)
                            @logger.error("# Error in checking modules ")
                            @logger.error("# Please check if all modules are correctly installed, searched #{@modules.join(",")} but only detected #{modules_with_version.join(",")}")
                            @logger.error("#"*100)
                            # "exit # Please check if all modules are correctly installed, searched #{@modules.join(",")} but only detected #{modules_with_version.join(",")}"
                            ""
                          end
                        else
                          ""
                        end
  @out.print <<-EOF
#!/bin/bash
#{hold_jid_option}
set -e
set -o pipefail
umask 0002

#### SET THE STAGE
SCRATCH_DIR=#{@scratch_dir}
GSTORE_DIR=#{@gstore_dir}
INPUT_DATASET=#{@input_dataset_tsv_path}
LAST_JOB=#{@last_job.to_s.upcase}
echo "Job runs on `hostname`"
echo "at $SCRATCH_DIR"
mkdir $SCRATCH_DIR || exit 1
cd $SCRATCH_DIR || exit 1
#{module_src_command}
#{module_add_commands}

  EOF
end

#job_main ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 508

def job_main
  @out.print "#### NOW THE ACTUAL JOBS STARTS\n"
  @out.print commands, "\n\n"
end

#main(mock = false) ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 818

def main(mock=false)
  ## sushi writes creates the job scripts and builds the result data set that is to be generated
  @result_dataset = []
  @job_scripts = []
  if @params['process_mode'] == 'SAMPLE'
    sample_mode
  elsif @params['process_mode'] == 'DATASET'
    dataset_mode
  elsif @params['process_mode'] == 'BATCH'
    batch_mode
  else 
    #stop
    warn "the process mode (#{@params['process_mode']}) is not defined"
    raise "stop job submitting"
  end
  if mock
    make_dummy_files
  end

  print 'result dataset: '
  p @result_dataset

  # copy application data to gstore 
  @next_dataset_tsv_path = save_next_dataset_as_tsv

  if @dataset_sushi_id and dataset = DataSet.find_by_id(@dataset_sushi_id.to_i)
    data_set_arr = []
    headers = []
    rows = []
    next_dataset_name = if name = @next_dataset_name
                          name.to_s
                        else
                          "#{@name.gsub(/\s/,'').gsub(/_/,'')}_#{dataset.id}"
                        end
    data_set_arr = if @params['next_dataset_root']
                     {'DataSetName'=>next_dataset_name, 'ProjectNumber'=>@project.gsub(/p/,''), 'Comment'=>@next_dataset_comment.to_s}
                   else
                     {'DataSetName'=>next_dataset_name, 'ProjectNumber'=>@project.gsub(/p/,''), 'ParentID'=>@dataset_sushi_id, 'Comment'=>@next_dataset_comment.to_s}
                   end

    csv = CSV.readlines(@next_dataset_tsv_path, :col_sep=>"\t")
    csv.each do |row|
      if headers.empty?
        headers = row
      else
        rows << row
      end
    end
    unless NO_ROR
      @current_user ||= nil
      @next_dataset_id = save_data_set(data_set_arr.to_a.flatten, headers, rows, @current_user, @child)
      save_parameters_in_sushi_db
    end
  end
  copy_uploaded_files
  copy_inputdataset_parameter_jobscripts

  # job submittion
  gstore_job_script_paths = []
  @job_scripts.each_with_index do |job_script, i|
    if job_id = submit(job_script, mock)
      @job_ids << job_id
      print "Submit job #{File.basename(job_script)} job_id=#{job_id}"
      gstore_job_script_paths << File.join(@gstore_script_dir, File.basename(job_script))
    end
  end

  puts
  print 'job scripts: '
  p @job_scripts


  unless @job_ids.empty? or NO_ROR
    # save job and dataset relation in Sushi DB
    job_ids.each_with_index do |job_id, i|
      new_job = Job.new
      new_job.submit_job_id = job_id.to_i
      new_job.script_path = gstore_job_script_paths[i]
      new_job.next_dataset_id = @next_dataset_id
      new_job.save
      new_job.data_set.jobs << new_job
      new_job.data_set.save
    end
  end
  copy_nextdataset
end

#make_dummy_files ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 916

def make_dummy_files
  dummy_files_header = []
  headers = @result_dataset.map{|row| row.keys}.flatten.uniq
  headers.select{|header| header.tag?('File')||header.tag?('Link')}.each do |header|
    dummy_files_header << header
  end
  dummy_files_ = []
  @result_dataset.each do |row|
    dummy_files_.concat(dummy_files_header.map{|header| row[header]})
  end
  dummy_files = []
  dummy_files_.each do |file|
    dummy_files << file.gsub(@result_dir, '')
  end
  dummy_files.uniq!

  dirs = []
  dummy_files.permutation(2).each do |a,b|
    if a.include?(b) and b !~ /\./
      dirs << b
    end
  end
  dirs.each do |dir|
    dummy_files.delete(dir)
  end
  dirs.each do |dir|
    command = "mkdir -p #{File.join(@scratch_result_dir, dir)}"
    puts command
    `#{command}`
  end
  dummy_files.each do |file|
    command = if file =~ /.html/
                "echo 'Hello, SUSHI world!' > #{File.join(@scratch_result_dir, file)}"
              else
                "touch #{File.join(@scratch_result_dir, file)}"
              end
    puts command
    `#{command}`
  end
end

#make_job_script(append = false) ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 693

def make_job_script(append = false)
  @out = if append
           open(@job_script, 'a')
         else
           open(@job_script, 'w')
         end
  job_header
  job_main
  job_footer
  @out.close
end

#mock_run ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 956

def mock_run
  test_run
  prepare_result_dir
  save_parameters_as_tsv
  save_input_dataset_as_tsv
  main(true)
end

#next_dataset ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 512

def next_dataset
  # this should be overwritten in a subclass
end

#prepare_result_dir ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 392

def prepare_result_dir
  FileUtils.mkdir_p(@scratch_result_dir)
  FileUtils.mkdir_p(@job_script_dir)
  @uploaded_files = []
  @params.each do |key, value|
    if @params[key, 'file_upload']
      FileUtils.mkdir_p(@uploaded_files_dir)
      @uploaded_files << value
    end
  end
end

#preprocess ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 571

def preprocess
  # this should be overwritten in a subclass
end

#run ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 904

def run
  test_run

  ## the user presses RUN
  prepare_result_dir

  ## copy application data to gstore 
  save_parameters_as_tsv
  save_input_dataset_as_tsv

  main
end

#sample_mode ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 704

def sample_mode
  selected_samples = unless @params['samples'].empty?
                       Hash[*@params['samples'].split(',').map{|sample_name| [sample_name, true]}.flatten]
                     else
                       Hash[*@dataset_hash.map{|row| row['Name']}.map{|sample_name| [sample_name, true]}.flatten]
                     end
  @dataset_hash.each_with_index do |row, i|
    @dataset = Hash[*row.map{|key,value| [key.gsub(/\[.+\]/,'').strip, value]}.flatten]
    if selected_samples[@dataset['Name']]
      sample_name = @dataset['Name']||@dataset.first
      @job_script = if @dataset_sushi_id and dataset = DataSet.find_by_id(@dataset_sushi_id.to_i)
                      File.join(@job_script_dir, @analysis_category + '_' + sample_name) + '_' + dataset.name.gsub(/\s+/,'_') + '.sh'
                    else
                      File.join(@job_script_dir, @analysis_category + '_' + sample_name) + '.sh'
                    end
      @last_job = (i == @dataset_hash.length - 1)
      make_job_script
      @job_scripts << @job_script
      @result_dataset << next_dataset
    end
  end
end

#save_data_set(data_set_arr, headers, rows, user = nil, child = nil) ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 761

def save_data_set(data_set_arr, headers, rows, user=nil, child=nil)
  data_set_hash = Hash[*data_set_arr]
  unless project = Project.find_by_number(data_set_hash['ProjectNumber'].to_i)
    project = Project.new
    project.number = data_set_hash['ProjectNumber'].to_i
    project.save
  end
  if project = Project.find_by_number(data_set_hash['ProjectNumber'].to_i)
    data_set = DataSet.new
    if user
      data_set.user = user
    end
    data_set.name = data_set_hash['DataSetName']
    data_set.project = project
    if parent_id = data_set_hash['ParentID'] and parent_data_set = DataSet.find_by_id(parent_id.to_i)
      data_set.data_set = parent_data_set
      data_set.sushi_app_name = self.class.name
    end
    if comment = data_set_hash['Comment'] and !comment.to_s.empty?
      data_set.comment = comment
    end
    if @mango_run_name
      data_set.run_name_order_id = @mango_run_name
    end

    sample_hash = {}
    rows.each do |row|
      headers.each_with_index do |header, i|
       sample_hash[header]=row[i]
      end
      sample = Sample.new
      sample.key_value = sample_hash.to_s
      sample.save # skip exact-match search
      data_set.samples << sample
    end

    if child
      data_set.child = true
    end

    data_set.md5 = data_set.md5hexdigest
    project.data_sets << data_set
    parent_data_set.data_sets << data_set if parent_data_set
    data_set.save
    if user
      user.data_sets << data_set
      user.save
    end
    data_set.id
  end
end

#save_input_dataset_as_tsv ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 599

def save_input_dataset_as_tsv
  file_path = File.join(@scratch_result_dir, @input_dataset_file)
  CSV.open(file_path, 'w', :col_sep=>"\t") do |out|
    headers = @dataset_hash.map{|row| row.keys}.flatten.uniq
    out << headers
    @dataset_hash.each do |row|
      out << headers.map{|header| 
        val = row[header]
        val.to_s.empty? ? nil:val
      }
    end
  end
  file_path
end

#save_next_dataset_as_tsv ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 613

def save_next_dataset_as_tsv
  headers = @result_dataset.map{|row| row.keys}.flatten.uniq
  file_path = File.join(@scratch_result_dir, @next_dataset_file)
  CSV.open(file_path, 'w', :col_sep=>"\t") do |out|
    out << headers
    @result_dataset.each do |row_hash|
      out << headers.map{|header| 
        val = row_hash[header]
        val.to_s.empty? ? nil:val
      }
    end
  end
  file_path
end

#save_parameters_as_tsv ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 582

def save_parameters_as_tsv
  file_path = File.join(@scratch_result_dir, @parameter_file)
  CSV.open(file_path, 'w', :col_sep=>"\t") do |out|
    out << ["sushi_app", self.class.name]
    @output_params.each do |key, value|
      if @output_params[key, 'file_upload'] and !value.to_s.empty?
        uploaded_file_path = File.join(@result_dir, "uploaded", File.basename(value))
        out << [key, uploaded_file_path]
        @params[key] = uploaded_file_path
        @output_params[key] = uploaded_file_path
      else
        out << [key, value]
      end
    end
  end
  file_path
end

#save_parameters_in_sushi_db ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 812

def save_parameters_in_sushi_db
  if @next_dataset_id and next_dataset = DataSet.find_by_id(@next_dataset_id)
    next_dataset.job_parameters = @output_params
    next_dataset.save
  end
end

#set_default_parameters ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 305

def set_default_parameters
  # this should be overwritten in a subclass
end

#set_dir_paths ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 371

def set_dir_paths
  ## sushi figures out where to put the resulting dataset
  unless @name and @project
    raise "should set #name and #project"
  end
  @name.gsub!(/\s/,'_')
  @result_dir_base = if @next_dataset_name
                      [@next_dataset_name, Time.now.strftime("%Y-%m-%d--%H-%M-%S")].join("_")
                    else
                      [@name, @dataset_sushi_id.to_s, Time.now.strftime("%Y-%m-%d--%H-%M-%S")].join("_")
                    end
  @result_dir = File.join(@project, @result_dir_base)
  @scratch_result_dir = File.join(SCRATCH_DIR, @result_dir_base)
  @job_script_dir = File.join(@scratch_result_dir, 'scripts')
  @uploaded_files_dir = File.join(@scratch_result_dir, 'uploaded')
  @gstore_result_dir = File.join(@gstore_dir, @result_dir)
  @gstore_script_dir = File.join(@gstore_result_dir, 'scripts')
  @gstore_project_dir = File.join(@gstore_dir, @project)
  @gstore_uploaded_dir = File.join(@gstore_result_dir, 'uploaded')
  set_file_paths
end

#set_file_paths ⇒ Object

 this should be overwritten in a subclass



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# File 'lib/sushi_fabric/sushiApp.rb', line 574

def set_file_paths
  @parameter_file = 'parameters.tsv'
  @input_dataset_file = 'input_dataset.tsv'
  @next_dataset_file = 'dataset.tsv'
  @input_dataset_tsv_path = File.join(@gstore_result_dir, @input_dataset_file)
  @parameters_tsv_path = File.join(@gstore_result_dir, @parameter_file)
  @next_dataset_tsv_path = File.join(@gstore_result_dir, @next_dataset_file)
end

#set_input_dataset ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 247

def set_input_dataset
  if @dataset_tsv_file
    dataset_tsv = CSV.readlines(@dataset_tsv_file, :headers=>true, :col_sep=>"\t")
    @dataset_hash = []
    @dataset = []
    dataset_tsv.each do |row|
      @dataset_hash << row.to_hash
      @dataset << row.to_hash
    end

    # save in sushi db unless it is saved in sushi db
    data_set_arr = []
    headers = []
    rows = []
    dataset_name = if @dataset_name
                     @dataset_name
                   else
                     File.basename(@dataset_tsv_file).gsub(/.tsv/, '')
                   end
    data_set_arr = {'DataSetName'=>dataset_name, 'ProjectNumber'=>@project.gsub(/p/,'')}
    csv = CSV.readlines(@dataset_tsv_file, :col_sep=>"\t")
    csv.each do |row|
      if headers.empty?
        headers = row
      else
        rows << row
      end
    end
    unless NO_ROR
      @current_user ||= nil
      if @dataset_sushi_id = save_data_set(data_set_arr.to_a.flatten, headers, rows, @current_user)
        unless @off_bfabric_registration
          if dataset = DataSet.find_by_id(@dataset_sushi_id.to_i)
            dataset.register_bfabric(bfabric_application_number: @input_dataset_bfabric_application_number)
          end
        end
      elsif data_set = headers[0] and data_set.instance_of?(DataSet)
        @dataset_sushi_id = data_set.id
      end
    end
  elsif @dataset_sushi_id
    @dataset_hash = []
    @dataset = []
    if dataset = DataSet.find_by_id(@dataset_sushi_id.to_i)
      dataset.samples.each do |sample|
        @dataset_hash << sample.to_hash
        @dataset << sample.to_hash
      end
    end
  end
  @dataset_hash
end

#set_output_files ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 323

def set_output_files
  if @params['process_mode'] == 'SAMPLE'
    @dataset = {}
  end
  next_dataset.keys.select{|header| header.tag?('File')}.each do |header|
    @output_files ||= []
    @output_files << header
  end
  if @output_files
    @output_files = @output_files.uniq
  end
end

#set_user_parameters ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 349

def set_user_parameters
  # this should be done in an instance of applicaiton subclass
  if @parameterset_tsv_file
    parameterset_tsv = CSV.readlines(@parameterset_tsv_file, :col_sep=>"\t")
    headers = []
    parameterset_tsv.each do |row|
      header, value = row
      headers << header
      @params[header] = if @params.data_type(header) == String or value == nil
                          value
                        else
                          eval(value)
                        end
    end
    (@params.keys - headers).each do |key|
      unless @params[key]
        @params[key] = @params.default_value(key)
      end
    end
  end
  @params
end

#submit(job_script, mock = false) ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 546

def submit(job_script, mock=false)
  begin
    job_id = unless mock
               i = submit_command(job_script)
               i.to_i
             else
               #Time.now.to_f.to_s.gsub('.', '')
               1234
             end
    unless job_id.to_i > 1
      @logger.error("#"*50)
      time = Time.now.strftime("[%Y.%m.%d %H:%M:%S]")
      @logger.error("error happened in job submitting, but maybe fine. #{time}")
      @logger.error("#"*50)
      job_id = nil
    end
  rescue
    @logger.error("@"*50)
    time = Time.now.strftime("[%Y.%m.%d %H:%M:%S]")
    @logger.error("error happened in job submitting, but maybe fine. #{time}")
    @logger.error("@"*50)
    job_id = nil
  end
  job_id
end

#submit_command(job_script) ⇒ Object

 this should be overwritten in a subclass



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# File 'lib/sushi_fabric/sushiApp.rb', line 518

def submit_command(job_script)
  gsub_options = []
  gsub_options << "-c #{@params['cores']}" unless @params['cores'].to_s.empty?
  gsub_options << "-n #{@params['node']}" unless @params['node'].to_s.empty?
  gsub_options << "-p #{@params['partition']}" unless @params['partition'].to_s.empty?
  gsub_options << "-r #{@params['ram']}" unless @params['ram'].to_s.empty?
  gsub_options << "-s #{@params['scratch']}" unless @params['scratch'].to_s.empty?
  gsub_options << "-i #{@params['nice']}" unless @params['nice'].to_s.empty?
  command = "wfm_monitoring --server #{WORKFLOW_MANAGER} --user #{@user} --project #{@project.gsub(/p/,'')} --logdir #{@gstore_script_dir} #{job_script} #{gsub_options.join(' ')}"
  puts "submit: #{command}"

  project_number = @project.gsub(/p/, '')
  @workflow_manager||=DRbObject.new_with_uri(WORKFLOW_MANAGER)
  script_content = File.read(job_script)
  job_id = 0
  begin
    #job_id = @workflow_manager.start_monitoring(job_script, @user, 0, script_content, project_number, gsub_options.join(' '), @gstore_script_dir)
    job_id = @workflow_manager.start_monitoring3(job_script, script_content, @user, project_number, gsub_options.join(' '), @gstore_script_dir, @next_dataset_id, RAILS_HOST)
  rescue => e
    time = Time.now.strftime("[%Y.%m.%d %H:%M:%S]")
    @logger.error("*"*50)
    @logger.error("submit_command error #{time}")
    @logger.error("error: #{e}")
    @logger.error("job_script: #{job_script}, @user: #{@user}, script_content: #{script_content.class} #{script_content.to_s.length} chrs, project_number: #{project_number}, gsub_options: #{gsub_options}, job_id: #{job_id}")
    @logger.error("*"*50)
  end
  job_id
end

#test_run ⇒ Object 



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# File 'lib/sushi_fabric/sushiApp.rb', line 963

def test_run
  set_input_dataset
  set_dir_paths
  preprocess
  set_output_files
  set_user_parameters

  failures = 0
  err_msgs = []
  print 'check project name: '
  unless @project
    err_msg = []
    err_msg << "\e[31mFAILURE\e[0m: project number is required but not found. you should set it in usecase."
    err_msg << "\tex.)"
    err_msg << "\tapp = #{self.class}.new"
    err_msg << "\tapp.project = 'p1001'"
    puts err_msg.join("\n")
    err_msgs.concat(err_msg)
    failures += 1
  else
    puts "\e[32mPASSED\e[0m:\n\t@project=#{@project}"
  end

  print 'check user name: '
  unless @user
    err_msg = []
    err_msg << "\e[31mWARNING\e[0m: user number is ought to be added but not found. you should set it in usecase. Default will be 'sushi lover'"
    err_msg << "\tex.)"
    err_msg << "\tapp = #{self.class}.new"
    err_msg << "\tapp.user = 'masa'"
    puts err_msg.join("\n")
    err_msgs.concat(err_msg)
  else
    puts "\e[32mPASSED\e[0m:\n\t@user=#{@user}"
  end

  print 'check application name: '
  if @name.to_s.empty?
    err_msg = []
    err_msg << "\e[31mFAILURE\e[0m: application name is required but not found. you should set it in application class."
    err_msg << "\tex.)"
    err_msg << "\tclass #{self.class}"
    err_msg << "\t def initialize"
    err_msg << "\t  @name = '#{self.class}'"
    err_msg << "\t end"
    err_msg << "\tend"
    puts err_msg.join("\n")
    err_msgs.concat(err_msg)
    failures += 1
  else
    puts "\e[32mPASSED\e[0m:\n\t@name=#{@name}"
  end

  print 'check analysis_category: '
  if @analysis_category.to_s.empty?
    err_msg = []
    err_msg << "\e[31mFAILURE\e[0m: analysis_category is required but not found. you should set it in application class."
    err_msg << "\tex.)"
    err_msg << "\tclass #{self.class}"
    err_msg << "\t def initialize"
    err_msg << "\t  @analysis_category = 'Mapping'"
    err_msg << "\t end"
    err_msg << "\tend"
    puts err_msg.join("\n")
    err_msgs.concat(err_msg)
    failures += 1
  else
    puts "\e[32mPASSED\e[0m:\n\t@analysis_category=#{@analysis_category}"
  end

  print 'check dataset: '
  if !@dataset_hash or @dataset_hash.empty?
    err_msg = []
    err_msg << "\e[31mFAILURE\e[0m: dataset is not found. you should set it by using #{self.class}#dataset_sushi_id or #{self.class}#dataset_tsv_file properties"
    err_msg << "\tex.)"
    err_msg << "\tusecase = #{self.class}.new"
    err_msg << "\tusecase.dataset_tsv_file = \"dataset.tsv\""
    puts err_msg.join("\n")
    err_msgs.concat(err_msg)
    failures += 1
  else
    puts "\e[32mPASSED\e[0m:\n\t@dataset_hash.length = #{@dataset_hash.length}"
  end

  print 'check required columns: '
  unless check_required_columns
    err_msg = []
    err_msg << "\e[31mFAILURE\e[0m: required_column(s) is not found in dataset. you should set it in application class."
    err_msg << "\tex.)"
    err_msg << "\tdef initialize"
    err_msg << "\t  @required_columns = ['Name', 'Read1']"
    puts err_msg.join("\n")
    err_msgs.concat(err_msg)
    failures += 1
  else
    puts "\e[32mPASSED\e[0m:"
  end
  puts "\trequired columns: #{@required_columns}"
  puts "\tdataset  columns: #{@dataset_hash.map{|row| row.keys}.flatten.uniq}" if @dataset_hash

  print 'check required parameters: '
  unless check_application_parameters
    err_msg = []
    err_msg << "\e[31mFAILURE\e[0m: required_param(s) is not set yet. you should set it in usecase"
    err_msg << "\tmissing params: #{@required_params-@params.keys}" if @required_params
    err_msg << "\tex.)"
    err_msg << "\tusecase = #{self.class}.new"
    if @required_params
      err_msg << "\tusecase.params['#{(@required_params-@params.keys)[0]}'] = parameter"
    else
      err_msg << "\tusecase.params['parameter name'] = default_parameter"
    end
    puts err_msg.join("\n")
    err_msgs.concat(err_msg)
    failures += 1
  else
    puts "\e[32mPASSED\e[0m:"
  end
  puts "\tparameters: #{@params.keys}"
  puts "\trequired  : #{@required_params}"

  print 'check next dataset: '
  if @params['process_mode'] == 'SAMPLE'
    @dataset={}
  end
  unless self.next_dataset
    err_msg = []
    err_msg << "\e[31mFAILURE\e[0m: next dataset is not set yet. you should overwrite SushiApp#next_dataset method in #{self.class}"
    err_msg << "\tnote: the return value should be Hash (key: column title, value: value in a tsv table)"
    puts err_msg.join("\n")
    err_msgs.concat(err_msg)
    failures += 1
  else
    puts "\e[32mPASSED\e[0m:"
  end

  print 'check output files: '
  if !@output_files or @output_files.empty?
    err_msg = []
    err_msg << "\e[31mWARNING\e[0m: no output files. you will not get any output files after the job running. you can set @output_files (array) in #{self.class}"
    err_msg << "\tnote: usually it should be define in initialize method"
    err_msg << "\t      the elements of @output_files should be chosen from #{self.class}#next_dataset.keys"
    err_msg << "\t      #{self.class}#next_dataset.keys: #{self.next_dataset.keys}" if self.next_dataset
    puts err_msg.join("\n")
    err_msgs.concat(err_msg)
  else
    puts "\e[32mPASSED\e[0m:"
  end

  print 'check commands: '
  if @params['process_mode'] == 'SAMPLE'
    @dataset_hash.each do |row|
      @dataset = Hash[*row.map{|key,value| [key.gsub(/\[.+\]/,'').strip, value]}.flatten]
      unless com = commands
        err_msg = []
        err_msg << "\e[31mFAILURE\e[0m: any commands is not defined yet. you should overwrite SushiApp#commands method in #{self.class}"
        err_msg << "\tnote: the return value should be String (this will be in the main body of submitted job script)"
        puts err_msg.join("\n")
        err_msgs.concat(err_msg)
        failures += 1
      else
        puts "\e[32mPASSED\e[0m:"
        puts "generated command will be:"
        puts "\t"+com.split(/\n/).join("\n\t")+"\n"
      end
    end
  elsif @params['process_mode'] == 'DATASET'
    unless com = commands
      err_msg = []
      err_msg << "\e[31mFAILURE\e[0m: any commands is not defined yet. you should overwrite SushiApp#commands method in #{self.class}"
      err_msg << "\tnote: the return value should be String (this will be in the main body of submitted job script)"
      puts err_msg.join("\n")
      err_msgs.concat(err_msg)
      failures += 1
    else
      puts "\e[32mPASSED\e[0m:"
      puts "generated command will be:"
      puts "\t"+com.split(/\n/).join("\n\t")+"\n"
    end
  end

  print 'check workflow manager: '
  begin
    @workflow_manager||=DRbObject.new_with_uri(WORKFLOW_MANAGER)
    hello = @workflow_manager.hello
  rescue
  end
  unless hello =~ /hello/
    err_msg = "\e[31mFAILURE\e[0m: workflow_manager does not reply. check if workflow_manager is working"
    puts err_msg
    err_msgs.concat([err_msg])
    failures += 1
  else
    puts "\e[32mPASSED\e[0m: #{WORKFLOW_MANAGER}"
  end

  if failures > 0
    puts
    err_msg = "\e[31mFailures (#{failures})\e[0m: All failures should be solved"
    puts err_msg
    err_msgs.unshift(err_msg)
    raise "\n"+err_msgs.join("\n")+"\n\n"
  else
    puts "All checks \e[32mPASSED\e[0m"
  end
end