sushi_fabric 1.2.2 → 1.2.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 18274b38a1b2b7a5c044435c9fb66406f865690b2807b01413d3fe349d1cdb90
-  data.tar.gz: 82d53f12e77604cc72b334103c0330e08b458ea4220579cd1f6284a4ee918bea
+  metadata.gz: 28252c62a5ac77892808193b02a694e48bf56c5f28cbe11ad8c26eb3076fd5d4
+  data.tar.gz: 9c15be2d98e78916fac71ebd653761e50b0b0f6ace6698ee15a277d73e28aea8
 SHA512:
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-  data.tar.gz: 534f1f1ea9e36c750255affed0925db10389fd9f27aacb13660e4638dc127c64f63f1b70b4fa15012c28514e46570c1488cc73efc0a9d4bdce9acd726f07a230
+  metadata.gz: 67e11563c751c2c2905f8109046d376c24fd16418707d7e39be79fae7b6c93a01a300cbed6d5fdcf97984af1e613510602a44add4358528affb58fe3b0de0994
+  data.tar.gz: 368bebe991f06642d8202eb7f65a97cb2dd6e762e01c712a1841e16350513dd45b59ef8b822a049163c383f5a00698057740faac540584158b71f97885e9b069

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20230623-165238'
+# Version = '20231208-144616'
 
 require 'csv'
 require 'fileutils'
@@ -233,6 +233,7 @@ class SushiApp
   attr_accessor :next_dataset_bfabric_application_number
   attr_reader :inactivate_nodes
   attr_reader :employee
+  attr_accessor :queue
 
   def initialize
     @gstore_dir = GSTORE_DIR
@@ -349,7 +350,9 @@ class SushiApp
   end
   def check_application_parameters
     if @required_params and (@required_params - @params.keys).empty?
-      @output_params = {"sushi_app" => self.class.name}.merge(@params.clone)
+      # 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
   def set_user_parameters
@@ -494,13 +497,13 @@ conda activate sushi
       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).join("\n"), "\n"
+        @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).join("\n"), "\n"
+          @out.print copy_commands(src_file, dest_dir, nil, @queue).join("\n"), "\n"
         end
       end
     end
@@ -588,6 +591,7 @@ rm -rf #{@scratch_dir} || exit 1
   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))
@@ -629,12 +633,12 @@ rm -rf #{@scratch_dir} || exit 1
     end
     file_path
   end
-  def copy_commands(org_dir, dest_parent_dir, now=nil)
+  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)
+      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)

data/lib/sushi_fabric/version.rb

@@ -1,3 +1,3 @@
 module SushiFabric
-  VERSION = "1.2.2"
+  VERSION = "1.2.4"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 1.2.2
+  version: 1.2.4
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2023-06-23 00:00:00.000000000 Z
+date: 2023-12-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler