sushi_fabric 1.1.9 → 1.2.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: a1018e406de9a52abc0c904f94990e5370ae7791cb7460081b6d5f9d38b1292c
-  data.tar.gz: e70a1fa7f02f6947ec6752bcd65c55aae2151badc6797d16fa1024a5f13b248d
+  metadata.gz: 4b09cd3b4d6a3357e0dcb22f20446c1bba615316d6aba33f13eb84608d4ffa25
+  data.tar.gz: 2f0ebf4ad1ac5df177df7371565da896eaebc9adea188ecbca6648c2339412c1
 SHA512:
-  metadata.gz: 2425522c912c4d289053d97027d8c53553f1fa0503c610db77b67db7ad4786865c642ea6d5f3d380c41f38df0b0371dd6bb6603927af98f54369e7b9062ac5cb
-  data.tar.gz: c165c1dd223dbbb9eb508576935d92e6254611cfabb19654085224a418d2980b9012fa2d8241ac0d6828e6c189718764f9db92e81b76c9c7c95aef5bf086e10d
+  metadata.gz: '0548d2078159ddd9c926663ec250bc1869ec02ea92b8e2689ffb048c731c982556f745e77f021b33b214ea568444f6096537b5b3aef0dcfc956276a13e20060f'
+  data.tar.gz: de17c3cad3cc3bf8f81e7d37f3bb65ca2135624d3efa5c235a48ba70c32a33d2bcc3ef1e9e6a52301da224c33adb05d82f6e5fb9a3379886602badf2f7aa60e1

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20230404-132741'
+# Version = '20230622-143640'
 
 require 'csv'
 require 'fileutils'
@@ -349,7 +349,7 @@ class SushiApp
   end
   def check_application_parameters
     if @required_params and (@required_params - @params.keys).empty?
-      @output_params = @params.clone
+      @output_params = {"sushi_app" => self.class}.merge(@params.clone)
     end
   end
   def set_user_parameters
@@ -588,9 +588,8 @@ rm -rf #{@scratch_dir} || exit 1
   def save_parameters_as_tsv
     file_path = File.join(@scratch_result_dir, @parameter_file)
     CSV.open(file_path, 'w', :col_sep=>"\t") do |out|
-      out << ["sushi_app", self.class.name]
       @output_params.each do |key, value|
-        if @output_params[key, 'file_upload']
+        if @output_params[key, 'file_upload'] and !value.to_s.empty?
           uploaded_file_path = File.join(@result_dir, "uploaded", File.basename(value))
           out << [key, uploaded_file_path]
           @params[key] = uploaded_file_path
@@ -651,7 +650,7 @@ rm -rf #{@scratch_dir} || exit 1
   end
   def copy_uploaded_files
     if not @uploaded_files.empty?
-      @uploaded_files.each do |file|
+      @uploaded_files.compact.select{|file| !file.empty?}.each do |file|
         FileUtils.cp(file, @uploaded_files_dir)
         command = "cp #{file} #{@uploaded_files_dir}"
         puts command
@@ -813,7 +812,6 @@ 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

data/lib/sushi_fabric/version.rb

@@ -1,3 +1,3 @@
 module SushiFabric
-  VERSION = "1.1.9"
+  VERSION = "1.2.1"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 1.1.9
+  version: 1.2.1
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2023-04-04 00:00:00.000000000 Z
+date: 2023-06-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler