sushi_fabric 1.2.3 → 1.2.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 4330f4843df678b5bd74f9c43ac7abcf036dc2b47284c7301d1b93b2e386bf40
-  data.tar.gz: 7f1d59a9197e1c545fd8d3fdf9d98002fc05fd89ecd1651f62e6b238b43038e9
+  metadata.gz: 68c7143037755247fc850a7c574aa720ab8aa4f39412f8e449d6236fd5d89d90
+  data.tar.gz: f0bd2e3063d60ce06367eb46df75a4af63fa9c5c7d8629c7d59e2190ea0a444b
 SHA512:
-  metadata.gz: 9f410544c24ec5ea2e8aa0815764cd1543d86ecc710aa514b224c724d698888acd4a2dc317889eeed02f36e300d66d9ed553641078aa5cb4b3eca193d8a838d8
-  data.tar.gz: b7eb98af2294187665b83c5d5594f988f9495b9831cc7d9da0d5513dfd4c9abd838080d9b33ca76d7a00d40923f0075458019ea1fae721008934540be6829883
+  metadata.gz: ebb89970779ede7d176f38bd6cad8de240b027cfca028eae28d0fc1c75793d1c2293f881040ddb8733bfd351f111e772d20eb7e8c833229366f557e0eb4beee6
+  data.tar.gz: c385481e909ce0e60a41d208dcb2271e5240cb94f3205b4e51990d038c939734200d5b3fa879c14f1b9831d3a35f34ff48eb1d9ce35b8524b14e00bab48c46fa

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20230623-175030'
+# Version = '20240723-154553'
 
 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
@@ -496,13 +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
@@ -632,12 +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)
@@ -871,20 +872,6 @@ rm -rf #{@scratch_dir} || exit 1
         @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
-
-        unless @off_bfabric_registration
-          if next_dataset = DataSet.find_by_id(@next_dataset_id)
-            next_dataset.register_bfabric(bfabric_application_number: @next_dataset_bfabric_application_number)
-            if next_dataset.workunit_id
-              @job_scripts.each do |job_script|
-                open(job_script, "a") do |out|
-                  out.puts "WORKUNIT_ID=#{next_dataset.workunit_id}"
-                  out.puts "update_resource_size -w $WORKUNIT_ID"
-                end
-              end
-            end
-          end
-        end
       end
     end
     copy_uploaded_files

data/lib/sushi_fabric/version.rb

@@ -1,3 +1,3 @@
 module SushiFabric
-  VERSION = "1.2.3"
+  VERSION = "1.2.5"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 1.2.3
+  version: 1.2.5
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
-autorequire:
+autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-06-23 00:00:00.000000000 Z
+date: 2024-07-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -69,7 +69,7 @@ homepage: ''
 licenses:
 - MIT
 metadata: {}
-post_install_message:
+post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
@@ -84,8 +84,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.3.26
-signing_key:
+rubygems_version: 3.5.5
+signing_key: 
 specification_version: 4
 summary: workflow manager client.
 test_files: