sushi_fabric 1.1.4 → 1.1.8

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 5d7f45f91531ecb9c7014b6b3694622694b6257845b607cec8819256cbff9a2f
+  metadata.gz: 9fcb6060694f934b06aaa331d68ce7494a4db25f310cfdf771249d19af201176
+  data.tar.gz: 0f97798abd3e030a36878d009cae200c285da65544d108446cd56ffb45fb1997
 SHA512:
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+  data.tar.gz: 4e5569562947413786252375c7819628a31b16be8f14ca032cd1969f1d2db7e0dabeea8fa2c8ec0b4ea71fd23fe4136296d5f1162cc175413ef5ef29fb2d5c96

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20211207-151042'
+# Version = '20220217-160253'
 
 require 'csv'
 require 'fileutils'
@@ -116,7 +116,9 @@ class ::Hash
     if v
       @defaults[k] = v
     else
-      @defaults[k]
+      if @defaults
+        @defaults[k]
+      end
     end
   end
   def data_type(k)
@@ -252,7 +254,7 @@ class SushiApp
   end
   def set_input_dataset
     if @dataset_tsv_file
-      dataset_tsv = CSV.readlines(@dataset_tsv_file, {:headers=>true, :col_sep=>"\t"})
+      dataset_tsv = CSV.readlines(@dataset_tsv_file, :headers=>true, :col_sep=>"\t")
       @dataset_hash = []
       @dataset = []
       dataset_tsv.each do |row|
@@ -365,7 +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
@@ -587,8 +591,10 @@ rm -rf #{@scratch_dir} || exit 1
       out << ["sushi_app", self.class.name]
       @output_params.each do |key, value|
         if @output_params[key, 'file_upload']
-          uploaded_file_path = File.join(@gstore_uploaded_dir, File.basename(value))
+          uploaded_file_path = File.join(@result_dir, "uploaded", File.basename(value))
           out << [key, uploaded_file_path]
+          @params[key] = uploaded_file_path
+          @output_params[key] = uploaded_file_path
         else
           out << [key, value]
         end
@@ -805,6 +811,12 @@ rm -rf #{@scratch_dir} || exit 1
       data_set.id
     end
   end
+  def save_parameters_in_sushi_db
+    if @next_dataset_id and next_dataset = DataSet.find_by_id(@next_dataset_id)
+      next_dataset.job_parameters = @output_params
+      next_dataset.save
+    end
+  end
   def main(mock=false)
     ## sushi writes creates the job scripts and builds the result data set that is to be generated
     @result_dataset = []
@@ -851,6 +863,7 @@ rm -rf #{@scratch_dir} || exit 1
       unless NO_ROR
         @current_user ||= nil
         @next_dataset_id = save_data_set(data_set_arr.to_a.flatten, headers, rows, @current_user, @child)
+        save_parameters_in_sushi_db
 
         unless @off_bfabric_registration
           if next_dataset = DataSet.find_by_id(@next_dataset_id)

data/lib/sushi_fabric/version.rb

@@ -1,3 +1,3 @@
 module SushiFabric
-  VERSION = "1.1.4"
+  VERSION = "1.1.8"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 1.1.4
+  version: 1.1.8
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-12-07 00:00:00.000000000 Z
+date: 2022-02-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -69,7 +69,7 @@ homepage: ''
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -84,8 +84,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3.1
-signing_key: 
+rubygems_version: 3.2.32
+signing_key:
 specification_version: 4
 summary: workflow manager client.
 test_files: