sushiApp.rb in sushi_fabric-0.2.8

- old
+ new

@@ -1,8 +1,8 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20141009-103900'
+# Version = '20141009-135300'
 
 require 'csv'
 require 'fileutils'
 require 'yaml'
 require 'drb/drb'
@@ -516,82 +516,86 @@
 
     ## copy application data to gstore 
     save_parameters_as_tsv
     save_input_dataset_as_tsv
 
-    t = Thread.new do
+#    t = Thread.new do
+    pid = Process.fork do
+      Process.fork do
 
-      ## 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
-      else 
-        #stop
-        warn "the process mode (#{@params['process_mode']}) is not defined"
-        raise "stop job submitting"
-      end
-      copy_inputdataset_parameter_jobscripts
+        ## 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
+        else 
+          #stop
+          warn "the process mode (#{@params['process_mode']}) is not defined"
+          raise "stop job submitting"
+        end
+        copy_inputdataset_parameter_jobscripts
 
-      # job submittion
-      @job_scripts.each_with_index do |job_script, i|
-        job_id = submit(job_script)
-        @job_ids << job_id
-        print "Submit job #{File.basename(job_script)} job_id=#{job_id}"
-      end
+        # job submittion
+        @job_scripts.each_with_index do |job_script, i|
+          job_id = submit(job_script)
+          @job_ids << job_id
+          print "Submit job #{File.basename(job_script)} job_id=#{job_id}"
+        end
 
-      puts
-      print 'job scripts: '
-      p @job_scripts
-      print 'result dataset: '
-      p @result_dataset
+        puts
+        print 'job scripts: '
+        p @job_scripts
+        print 'result dataset: '
+        p @result_dataset
 
-      # copy application data to gstore 
-      @next_dataset_tsv_path = save_next_dataset_as_tsv
+        # copy application data to gstore 
+        @next_dataset_tsv_path = save_next_dataset_as_tsv
 
-      if !@job_ids.empty? and @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
-                              "#{@analysis_category}_#{@name.gsub(/\s/,'').gsub(/_/,'')}_#{dataset.id}"
-                            end
-        data_set_arr = {'DataSetName'=>next_dataset_name, 'ProjectNumber'=>@project.gsub(/p/,''), 'ParentID'=>@dataset_sushi_id, 'Comment'=>@next_dataset_comment.to_s}
-        csv = CSV.readlines(@next_dataset_tsv_path, :col_sep=>"\t")
-        csv.each do |row|
-          if headers.empty?
-            headers = row
-          else
-            rows << row
+        if !@job_ids.empty? and @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
+                                "#{@analysis_category}_#{@name.gsub(/\s/,'').gsub(/_/,'')}_#{dataset.id}"
+                              end
+          data_set_arr = {'DataSetName'=>next_dataset_name, 'ProjectNumber'=>@project.gsub(/p/,''), 'ParentID'=>@dataset_sushi_id, 'Comment'=>@next_dataset_comment.to_s}
+          csv = CSV.readlines(@next_dataset_tsv_path, :col_sep=>"\t")
+          csv.each do |row|
+            if headers.empty?
+              headers = row
+            else
+              rows << row
+            end
           end
-        end
-        unless NO_ROR
-          #@next_dataset_id = save_data_set(data_set_arr.to_a.flatten, headers, rows, current_user)
-          @next_dataset_id = save_data_set(data_set_arr.to_a.flatten, headers, rows)
+          unless NO_ROR
+            #@next_dataset_id = save_data_set(data_set_arr.to_a.flatten, headers, rows, current_user)
+            @next_dataset_id = save_data_set(data_set_arr.to_a.flatten, headers, rows)
 
-          # save job and dataset relation in Sushi DB
-          job_ids.each do |job_id|
-            new_job = Job.new
-            new_job.submit_job_id = job_id.to_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
+            # save job and dataset relation in Sushi DB
+            job_ids.each do |job_id|
+              new_job = Job.new
+              new_job.submit_job_id = job_id.to_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
         end
-      end
-      copy_nextdataset
-    end
-    if Thread.main == Thread.current # in case of running script directly on terminal
-      warn "copy next dataset..."
-      t.join
-      warn "copy finish."
-    end
+        copy_nextdataset
+      end # grand-child process
+    end # child process
+    Process.waitpid pid
+#    if Thread.main == Thread.current # in case of running script directly on terminal
+#      warn "copy next dataset..."
+#      t.join
+#      warn "copy finish."
+#    end
   end
   def test_run
     set_dir_paths
     set_input_dataset
     preprocess