sushi_fabric 1.0.6 → 1.1.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: cfe59c9648980949d93b531a0bd3346d46b7dc21c9feea0a81deb7a30c13fc9e
-  data.tar.gz: f29b974e1bbc6d6d47895ec6ff8a4789623542ff176ab53455b23308a838db2d
+  metadata.gz: 4e8c7afdc3db914867cb23a1274fe257e8d16f60904c867e84ada16b3faeec5b
+  data.tar.gz: 9e0db5e3421c31767b1c089652831dee04fd536e557969ad17519dbd1f681d0a
 SHA512:
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-  data.tar.gz: ce5e49baed8af919d9803b3dfbfbcb7e6c47c789c4b06224db46e53fbf4c7277cf7cf412dafe212ec6688399651a160af07d9e62a196f092b005fda7b39d482a
+  metadata.gz: ff6aa500c3ce2f3bdf1a33d3829b1aed9031c949fc894f69d23b9cbb7e47b4fbdb5c4477d3cb916e139c944521eeae0b619e7f1cc1df1991054d1b94cf7dd528
+  data.tar.gz: a491d23bef554e292253aa28f08677b940bf8f2fd6a6d798a7423a1a62fba439bb378321ceb99464fd68a044f6031a3e25c578387406951a1c2f5b18e797196f

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20210205-155336'
+# Version = '20210730-151826'
 
 require 'csv'
 require 'fileutils'
@@ -412,12 +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(":")
-                                "#SBATCH --dependency=afterany:#{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
@@ -433,7 +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
                             ""
@@ -468,12 +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
@@ -508,8 +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)
     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 = "1.0.6"
+  VERSION = "1.1.0"
 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: 1.0.6
+  version: 1.1.0
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-02-05 00:00:00.000000000 Z
+date: 2021-07-30 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.