lib/sushi_fabric/sushiApp.rb in sushi_fabric-0.8.9 vs lib/sushi_fabric/sushiApp.rb in sushi_fabric-0.9.0

@@ -1,8 +1,8 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20181012-131954'
+# Version = '20190104-191156'
 
 require 'csv'
 require 'fileutils'
 require 'yaml'
 require 'drb/drb'
@@ -317,11 +317,13 @@
     end
     flag
   end
 
   def set_output_files
-    @dataset = {}
+    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
@@ -518,11 +520,11 @@
   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, @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
   def save_parameters_as_tsv
     file_path = File.join(@scratch_result_dir, @parameter_file)
     CSV.open(file_path, 'w', :col_sep=>"\t") do |out|
@@ -992,10 +994,12 @@
     end
     puts "\tparameters: #{@params.keys}"
     puts "\trequired  : #{@required_params}"
 
     print 'check next dataset: '
-    @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")