sushi_fabric 0.4.3 → 0.4.6

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20150716-161756'
+# Version = '20150904-134632'
 
 require 'csv'
 require 'fileutils'
@@ -125,7 +125,7 @@ class ::String
     scan(/\[(.*)\]/).flatten.join =~ /#{tag}/
   end
 end
-def save_data_set(data_set_arr, headers, rows)
+def save_data_set(data_set_arr, headers, rows, user=nil)
   data_set_hash = Hash[*data_set_arr]
   unless project = Project.find_by_number(data_set_hash['ProjectNumber'].to_i)
     project = Project.new
@@ -134,7 +134,9 @@ def save_data_set(data_set_arr, headers, rows)
   end
   if project = Project.find_by_number(data_set_hash['ProjectNumber'].to_i)
     data_set = DataSet.new
-    #data_set.user = user
+    if user
+      data_set.user = user
+    end
     data_set.name = data_set_hash['DataSetName']
     data_set.project = project
     if parent_id = data_set_hash['ParentID'] and parent_data_set = DataSet.find_by_id(parent_id.to_i)
@@ -160,6 +162,10 @@ def save_data_set(data_set_arr, headers, rows)
       project.data_sets << data_set
       parent_data_set.data_sets << data_set if parent_data_set
       data_set.save
+      if user
+        user.data_sets << data_set
+        user.save
+      end
     end
     data_set.id
   end
@@ -186,6 +192,7 @@ class SushiApp
   attr_accessor :dataset_name
   attr_accessor :next_dataset_comment
   attr_accessor :workflow_manager
+  attr_accessor :current_user
   def initialize
     @gstore_dir = GSTORE_DIR
     @project = nil
@@ -229,7 +236,8 @@ class SushiApp
         end
       end
       unless NO_ROR
-        @dataset_sushi_id = save_data_set(data_set_arr.to_a.flatten, headers, rows)
+        @current_user ||= nil
+        @dataset_sushi_id = save_data_set(data_set_arr.to_a.flatten, headers, rows, @current_user)
       end
     elsif @dataset_sushi_id
       @dataset_hash = []
@@ -512,9 +520,7 @@ rm -rf #{@scratch_dir} || exit 1
     @job_scripts << @job_script
     @result_dataset << next_dataset
   end
-  def save_data_set(data_set_arr, headers, rows)
-    #SushiFabric.save_data_set(data_set_arr, headers, rows, user)
-#=begin
+  def save_data_set(data_set_arr, headers, rows, user=nil)
     data_set_hash = Hash[*data_set_arr]
     unless project = Project.find_by_number(data_set_hash['ProjectNumber'].to_i)
       project = Project.new
@@ -523,7 +529,9 @@ rm -rf #{@scratch_dir} || exit 1
     end
     if project = Project.find_by_number(data_set_hash['ProjectNumber'].to_i)
       data_set = DataSet.new
-      #data_set.user = user
+      if user
+        data_set.user = user
+      end
       data_set.name = data_set_hash['DataSetName']
       data_set.project = project
       if parent_id = data_set_hash['ParentID'] and parent_data_set = DataSet.find_by_id(parent_id.to_i)
@@ -549,10 +557,13 @@ rm -rf #{@scratch_dir} || exit 1
         project.data_sets << data_set
         parent_data_set.data_sets << data_set if parent_data_set
         data_set.save
+        if user
+          user.data_sets << data_set
+          user.save
+        end
       end
       data_set.id
     end
-#=end
   end
   def main
     ## sushi writes creates the job scripts and builds the result data set that is to be generated
@@ -604,8 +615,8 @@ rm -rf #{@scratch_dir} || exit 1
         end
       end
       unless NO_ROR
-        #@next_dataset_id = save_data_set(data_set_arr.to_a.flatten, headers, rows, current_user)
-        @next_dataset_id = save_data_set(data_set_arr.to_a.flatten, headers, rows)
+        @current_user ||= nil
+        @next_dataset_id = save_data_set(data_set_arr.to_a.flatten, headers, rows, @current_user)
 
         # save job and dataset relation in Sushi DB
         job_ids.each do |job_id|

data/lib/sushi_fabric/version.rb

@@ -1,3 +1,3 @@
 module SushiFabric
-  VERSION = "0.4.3"
+  VERSION = "0.4.6"
 end

metadata

@@ -1,57 +1,49 @@
---- !ruby/object:Gem::Specification
+--- !ruby/object:Gem::Specification 
 name: sushi_fabric
-version: !ruby/object:Gem::Version
-  version: 0.4.3
+version: !ruby/object:Gem::Version 
   prerelease: 
+  version: 0.4.6
 platform: ruby
-authors:
+authors: 
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-07-16 00:00:00.000000000 Z
-dependencies:
-- !ruby/object:Gem::Dependency
+
+date: 2015-09-04 00:00:00 Z
+dependencies: 
+- !ruby/object:Gem::Dependency 
   name: bundler
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '1.3'
-  type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
+  requirement: &id001 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
+    requirements: 
     - - ~>
-      - !ruby/object:Gem::Version
-        version: '1.3'
-- !ruby/object:Gem::Dependency
-  name: rake
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
+      - !ruby/object:Gem::Version 
+        version: "1.3"
   type: :development
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: rake
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
+  requirement: &id002 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-description: This library provides us with the methods to submit a job cooperating
-  with workflow manager.
-email:
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :development
+  version_requirements: *id002
+description: This library provides us with the methods to submit a job cooperating with workflow manager.
+email: 
 - masaomi.hatakeyama@fgcz.uzh.ch
-executables:
+executables: 
 - sushi_fabric
 extensions: []
+
 extra_rdoc_files: []
-files:
+
+files: 
 - .bzrignore
 - Gemfile
 - LICENSE.txt
@@ -67,29 +59,32 @@ files:
 - sample/sample_dataset.tsv
 - sample/sample_parameterset.tsv
 - sushi_fabric.gemspec
-homepage: ''
-licenses:
+homepage: ""
+licenses: 
 - MIT
 post_install_message: 
 rdoc_options: []
-require_paths:
+
+require_paths: 
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement
+required_ruby_version: !ruby/object:Gem::Requirement 
   none: false
-  requirements:
-  - - ! '>='
-    - !ruby/object:Gem::Version
-      version: '0'
-required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
   none: false
-  requirements:
-  - - ! '>='
-    - !ruby/object:Gem::Version
-      version: '0'
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
 requirements: []
+
 rubyforge_project: 
-rubygems_version: 1.8.23.2
+rubygems_version: 1.8.23
 signing_key: 
 specification_version: 3
 summary: workflow manager client.
 test_files: []
+