sushi_fabric 1.0.7 → 1.1.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 437c1a17818ce1c691886fface6c5395eae69d72024f542eb6497885814d7b82
-  data.tar.gz: d08bf18f1fd4d58285df67b682e134951afa6325a6192097b3ecd7b0d8f3b823
+  metadata.gz: f27bf481942df3066dc10ead974eb849cbc0c2f7ad010599d2d75b7cdf9d6762
+  data.tar.gz: fd39ea3911fd3f9571ceb4c3b2071e51103109d85f7e9e042edabddc95733adc
 SHA512:
-  metadata.gz: ab3b854e32de48cfe000dc4d524a3fb6a3998ca60b23ee3754f10755faee45b9e5c50de6d37e2ab48e91f3dbea415eb8675c4b30256bed7df297fac6ab98860f
-  data.tar.gz: 5b4ddc75fe749426e0765e5bca55fc41003387e46d9ac53317c1462552c71d5f82efebb3b93166128efd9e7a2784460ec4a1146eb77cd1314b25319cabfbfb96
+  metadata.gz: 36560e6365fe052621295480761c71b1082601f645261a728910e8c03372a601fdfd8ea9883233a68212eaf0cbd60598a32c62fcbc068445b6c150bdf170aeb8
+  data.tar.gz: 930e64f997d8383991e88c5c6f21fab27d5c1f40e59e16987b002a62615d96aa65571eca1c055708c75b0f96496bd3bf3a9ee72d025e5a75e1e1e79b8143c973

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20210211-145021'
+# Version = '20210813-192118'
 
 require 'csv'
 require 'fileutils'
@@ -432,7 +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
                             ""
@@ -467,12 +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
@@ -507,8 +523,8 @@ rm -rf #{@scratch_dir} || exit 1
     script_content = File.read(job_script)
     job_id = 0
     begin
-      job_id = @workflow_manager.start_monitoring(job_script, @user, 0, script_content, project_number, gsub_options.join(' '), @gstore_script_dir)
-      #job_id = @workflow_manager.start_monitoring2(job_script, script_content, @user, project_number, gsub_options.join(' '), @gstore_script_dir)
+      #job_id = @workflow_manager.start_monitoring(job_script, @user, 0, script_content, project_number, gsub_options.join(' '), @gstore_script_dir)
+      job_id = @workflow_manager.start_monitoring3(job_script, script_content, @user, project_number, gsub_options.join(' '), @gstore_script_dir, @next_dataset_id)
     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 = "1.0.7"
+  VERSION = "1.1.1"
 end

data/sushi_fabric.gemspec

@@ -19,6 +19,6 @@ Gem::Specification.new do |spec|
   spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
   spec.require_paths = ["lib"]
 
-  spec.add_development_dependency "bundler", "~> 1.3"
+  spec.add_development_dependency "bundler", "~> 2.2.10"
   spec.add_development_dependency "rake"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 1.0.7
+  version: 1.1.1
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-02-11 00:00:00.000000000 Z
+date: 2021-08-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -16,14 +16,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.3'
+        version: 2.2.10
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.3'
+        version: 2.2.10
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
@@ -84,7 +84,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3
+rubygems_version: 3.0.3.1
 signing_key: 
 specification_version: 4
 summary: workflow manager client.