Merge branch 'development' of https://github.com/rautenberg/opentox-ruby into development

1 files changed, 16 insertions, 20 deletions

diff --git a/lib/dataset.rb b/lib/dataset.rb
index bbd8b8b..aba7754 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -6,7 +6,6 @@ module OpenTox
     include OpenTox
 
     attr_reader :features, :compounds, :data_entries, :metadata
-    attr_accessor :token_id
 
     # Create dataset with optional URI. Does not load data into the dataset - you will need to execute one of the load_* methods to pull data from a service or to insert it from other representations.
     # @example Create an empty dataset
@@ -15,9 +14,8 @@ module OpenTox
     #   dataset = OpenTox::Dataset.new("http:://webservices.in-silico/ch/dataset/1")
     # @param [optional, String] uri Dataset URI
     # @return [OpenTox::Dataset] Dataset object
-    def initialize(uri=nil,token_id=nil)
+    def initialize(uri=nil)
       super uri
-      @token_id = token_id
       @features = {}
       @compounds = []
       @data_entries = {}
@@ -28,10 +26,9 @@ module OpenTox
     #   dataset = OpenTox::Dataset.create
     # @param [optional, String] uri Dataset URI
     # @return [OpenTox::Dataset] Dataset object
-    def self.create(uri=CONFIG[:services]["opentox-dataset"], token_id=nil)
+    def self.create(uri=CONFIG[:services]["opentox-dataset"], subjectid=nil)
       dataset = Dataset.new
-      dataset.token_id = token_id if token_id
-      dataset.save
+      dataset.save(subjectid)
       dataset
     end
 
@@ -41,12 +38,12 @@ module OpenTox
     # - you will have to set remaining metadata manually
     # @param [String] file CSV file path
     # @return [OpenTox::Dataset] Dataset object with CSV data
-    def self.create_from_csv_file(file) 
-      dataset = Dataset.create
+    def self.create_from_csv_file(file, subjectid=nil) 
+      dataset = Dataset.create(CONFIG[:services]["opentox-dataset"], subjectid)
       parser = Parser::Spreadsheets.new
       parser.dataset = dataset
       parser.load_csv(File.open(file).read)
-      dataset.save
+      dataset.save(subjectid)
       dataset
     end
 
@@ -92,8 +89,8 @@ module OpenTox
     # - you will have to set remaining metadata manually
     # @param [String] csv CSV representation of the dataset
     # @return [OpenTox::Dataset] Dataset object with CSV data
-    def load_csv(csv) 
-      save unless @uri # get a uri for creating features
+    def load_csv(csv, subjectid=nil) 
+      save(subjectid) unless @uri # get a uri for creating features
       parser = Parser::Spreadsheets.new
       parser.dataset = self
       parser.load_csv(csv)
@@ -105,8 +102,8 @@ module OpenTox
     # - you will have to set remaining metadata manually
     # @param [Excel] book Excel workbook object (created with roo gem)
     # @return [OpenTox::Dataset] Dataset object with Excel data
-    def load_spreadsheet(book)
-      save unless @uri # get a uri for creating features
+    def load_spreadsheet(book, subjectid=nil)
+      save(subjectid) unless @uri # get a uri for creating features
       parser = Parser::Spreadsheets.new
       parser.dataset = self
       parser.load_spreadsheet(book)
@@ -250,29 +247,29 @@ module OpenTox
     # - creates a new dataset if uri is not set
     # - overwrites dataset if uri exists
     # @return [String] Dataset URI
-    def save
+    def save(subjectid=nil)
       # TODO: rewrite feature URI's ??
       @compounds.uniq!
       if @uri
         if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
-          RestClientWrapper.post(@uri,{:content_type =>  "application/x-yaml", :token_id => @token_id},self.to_yaml)
+          RestClientWrapper.post(@uri,{:content_type =>  "application/x-yaml", :subjectid => subjectid},self.to_yaml)
         else
           File.open("ot-post-file.rdf","w+") { |f| f.write(self.to_rdfxml); @path = f.path }
-          task_uri = RestClient.post(@uri, {:file => File.new(@path)},{:accept => "text/uri-list"}).to_s.chomp
+          task_uri = RestClient.post(@uri, {:file => File.new(@path)},{:accept => "text/uri-list" , :subjectid => subjectid}).to_s.chomp
           #task_uri = `curl -X POST -H "Accept:text/uri-list" -F "file=@#{@path};type=application/rdf+xml" http://apps.ideaconsult.net:8080/ambit2/dataset`
           Task.find(task_uri).wait_for_completion
           self.uri = RestClientWrapper.get(task_uri,:accept => 'text/uri-list')
         end
       else
         # create dataset if uri is empty
-        self.uri = RestClientWrapper.post(CONFIG[:services]["opentox-dataset"],{:token_id => @token_id}).to_s.chomp
+        self.uri = RestClientWrapper.post(CONFIG[:services]["opentox-dataset"],{:subjectid => subjectid}).to_s.chomp
       end
       @uri
     end
 
     # Delete dataset at the dataset service
-    def delete
-      RestClientWrapper.delete @uri
+    def delete(subjectid=nil)
+      RestClientWrapper.delete(@uri, :subjectid => subjectid)
     end
 
     private
@@ -282,7 +279,6 @@ module OpenTox
       @data_entries = dataset.data_entries
       @compounds = dataset.compounds
       @features = dataset.features
-      @token_id = dataset.token_id
       if @uri
         self.uri = @uri 
       else