sushi_fabric 1.0.3 → 1.0.8

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 2630d702479d4eac533f737e226c80cbe115598d891eb526ec1f8e7004fc9481
+  metadata.gz: be295ca72915f5b15f5d1b06c062eedd66c2ebbf392f3e3263483d5b803249a4
+  data.tar.gz: d40e4224538f01ac25adf99eb3c701daf04d22a0a1be0f1a935173f798b23007
 SHA512:
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+  data.tar.gz: d16896e1fabc9c4bb683c0268fbb6908c3b9a8f2fe037b669ce5f7aad89b5c982c21f66f73561be787025d48667fed09f2a4d402a3de5ed7ba4110fd39dea122

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20201218-155451'
+# Version = '20210304-164250'
 
 require 'csv'
 require 'fileutils'
@@ -228,6 +228,8 @@ class SushiApp
   attr_accessor :input_dataset_bfabric_application_number
   attr_accessor :next_dataset_bfabric_application_number
   attr_reader :inactivate_nodes
+  attr_reader :employee
+
   def initialize
     @gstore_dir = GSTORE_DIR
     @project = nil
@@ -410,12 +412,11 @@ class SushiApp
                    else
                      @scratch_result_dir + '_temp$$'
                    end
-    hold_jid_option = if @dataset_sushi_id and parent_data_set = DataSet.find_by_id(@dataset_sushi_id.to_i) and !parent_data_set.jobs.empty?
-                                parent_data_set_job_ids = parent_data_set.jobs.map{|job| job.submit_job_id}.join(",")
-                                "#\$ -hold_jid #{parent_data_set_job_ids}"
-                              else
-                                ''
-                              end
+    hold_jid_option = if @dataset_sushi_id and parent_data_set = DataSet.find_by_id(@dataset_sushi_id.to_i) and !parent_data_set.jobs.empty? and parent_data_set_job_ids = parent_data_set.jobs.map{|job| job.submit_job_id} and !parent_data_set_job_ids.join.empty?
+                        "#SBATCH --dependency=afterany:#{parent_data_set_job_ids.join(":")}"
+                      else
+                        ''
+                      end
     module_src_command = if @module_source and @modules and !@modules.empty?
                        "source #{@module_source}"
                      else
@@ -466,12 +467,27 @@ conda activate sushi
       EOS
     end
 
+    src_files = []
+    dest_dirs = []
+    greq = (copy_commands("AAA", "BBB").join =~ /g-req/)
     if @output_files
       @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))
+        src_files << src_file
+        dest_dirs << dest_dir
+      end
+      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"
+      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"
+        end
       end
     end
     @out.print <<-EOF
@@ -864,17 +880,7 @@ rm -rf #{@scratch_dir} || exit 1
     save_parameters_as_tsv
     save_input_dataset_as_tsv
 
-    if SushiFabric::Application.config.fgcz?
-      # this causes sqlite3 IO error in Mac OSX (Yosemite)
-      pid = Process.fork do
-        Process.fork do
-          main
-        end # grand-child process
-      end # child process
-      Process.waitpid pid
-    else
-      main
-    end
+    main
   end
   def make_dummy_files
     dummy_files_header = []

data/lib/sushi_fabric/version.rb

@@ -1,3 +1,3 @@
 module SushiFabric
-  VERSION = "1.0.3"
+  VERSION = "1.0.8"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 1.0.3
+  version: 1.0.8
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-12-18 00:00:00.000000000 Z
+date: 2021-03-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler