sushiApp.rb in sushi_fabric-1.2.1

- old
+ new

@@ -1,8 +1,8 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20230404-145037'
+# Version = '20230622-143640'
 
 require 'csv'
 require 'fileutils'
 require 'yaml'
 require 'drb/drb'
@@ -347,11 +347,11 @@
       false
     end
   end
   def check_application_parameters
     if @required_params and (@required_params - @params.keys).empty?
-      @output_params = @params.clone
+      @output_params = {"sushi_app" => self.class}.merge(@params.clone)
     end
   end
   def set_user_parameters
     # this should be done in an instance of applicaiton subclass
     if @parameterset_tsv_file
@@ -586,13 +586,12 @@
     @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|
-      out << ["sushi_app", self.class.name]
       @output_params.each do |key, value|
-        if @output_params[key, 'file_upload']
+        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
@@ -649,10 +648,10 @@
     end
     com
   end
   def copy_uploaded_files
     if not @uploaded_files.empty?
-      @uploaded_files.each do |file|
+      @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)}"