sushi_fabric 1.1.7 → 1.1.9

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: a109369c8f10c36f910587e9185ba71e66f56ad1985671cf1a13084b84e9162b
+  metadata.gz: a1018e406de9a52abc0c904f94990e5370ae7791cb7460081b6d5f9d38b1292c
+  data.tar.gz: e70a1fa7f02f6947ec6752bcd65c55aae2151badc6797d16fa1024a5f13b248d
 SHA512:
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+  data.tar.gz: c165c1dd223dbbb9eb508576935d92e6254611cfabb19654085224a418d2980b9012fa2d8241ac0d6828e6c189718764f9db92e81b76c9c7c95aef5bf086e10d

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20220207-142315'
+# Version = '20230404-132741'
 
 require 'csv'
 require 'fileutils'
@@ -118,8 +118,6 @@ class ::Hash
     else
       if @defaults
         @defaults[k]
-      else
-        ""
       end
     end
   end
@@ -369,7 +367,9 @@ class SushiApp
                           end
       end
       (@params.keys - headers).each do |key|
-        @params[key] = @params.default_value(key)
+        unless @params[key]
+          @params[key] = @params.default_value(key)
+        end
       end
     end
     @params
@@ -813,6 +813,7 @@ rm -rf #{@scratch_dir} || exit 1
   end
   def save_parameters_in_sushi_db
     if @next_dataset_id and next_dataset = DataSet.find_by_id(@next_dataset_id)
+      @output_params['sushi_app'] = self.class
       next_dataset.job_parameters = @output_params
       next_dataset.save
     end
@@ -851,7 +852,12 @@ rm -rf #{@scratch_dir} || exit 1
                           else
                             "#{@name.gsub(/\s/,'').gsub(/_/,'')}_#{dataset.id}"
                           end
-      data_set_arr = {'DataSetName'=>next_dataset_name, 'ProjectNumber'=>@project.gsub(/p/,''), 'ParentID'=>@dataset_sushi_id, 'Comment'=>@next_dataset_comment.to_s}
+      data_set_arr = if @params['next_dataset_root']
+                       {'DataSetName'=>next_dataset_name, 'ProjectNumber'=>@project.gsub(/p/,''), 'Comment'=>@next_dataset_comment.to_s}
+                     else
+                       {'DataSetName'=>next_dataset_name, 'ProjectNumber'=>@project.gsub(/p/,''), 'ParentID'=>@dataset_sushi_id, 'Comment'=>@next_dataset_comment.to_s}
+                     end
+
       csv = CSV.readlines(@next_dataset_tsv_path, :col_sep=>"\t")
       csv.each do |row|
         if headers.empty?

data/lib/sushi_fabric/version.rb

@@ -1,3 +1,3 @@
 module SushiFabric
-  VERSION = "1.1.7"
+  VERSION = "1.1.9"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 1.1.7
+  version: 1.1.9
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-02-07 00:00:00.000000000 Z
+date: 2023-04-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -84,7 +84,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.2.32
+rubygems_version: 3.3.26
 signing_key:
 specification_version: 4
 summary: workflow manager client.