sushi_fabric 1.0.4 → 1.0.9

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 4d14ca10808dbee2401088cc885d77ac2c4040ca73a984993f833b42d049ade8
+  metadata.gz: 35b2e022d1f18333d99515a5032500f8c9737cdeb924bf8af1fc23167a85847a
+  data.tar.gz: 7610de543b92274995a7e5ef0cfaa17cc12686106003da9e9e095d58727757de
 SHA512:
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-  data.tar.gz: 0d2f463786f8397c73cba8026cd2b1ac0f4a1fbda5252ca598c39f4aaf81d25c1d6d6c9020739f2c31ecee59857ee5d09ace1f4f9a1aa675694c4cf932273b59
+  metadata.gz: 57c7a0d1834299762b01d2e192aa855d07fbb04c3a304c24968a637f3ebab3e64ad0775ad465b9002156303c91551b28b0126a5412f1f2dbf9871ad71ea4a3aa
+  data.tar.gz: 003d07dbbbe71b0a02535b17d7e3f7cb2166141708575cde12d66aa9bdb50df19c977459e63a0ba0fbff73a2fa251c8929852cd38f7c6acf4c5d1190c24df802

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20210115-105702'
+# Version = '20210410-141359'
 
 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
@@ -431,7 +432,8 @@ class SushiApp
                               @logger.error("# Error in checking modules ")
                               @logger.error("# Please check if all modules are correctly installed, searched #{@modules.join(",")} but only detected #{modules_with_version.join(",")}")
                               @logger.error("#"*100)
-                              "exit # Please check if all modules are correctly installed, searched #{@modules.join(",")} but only detected #{modules_with_version.join(",")}"
+                              # "exit # Please check if all modules are correctly installed, searched #{@modules.join(",")} but only detected #{modules_with_version.join(",")}"
+                              ""
                             end
                           else
                             ""
@@ -466,12 +468,27 @@ 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

data/lib/sushi_fabric/version.rb

@@ -1,3 +1,3 @@
 module SushiFabric
-  VERSION = "1.0.4"
+  VERSION = "1.0.9"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 1.0.4
+  version: 1.0.9
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-01-15 00:00:00.000000000 Z
+date: 2021-04-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler