owl-dl (temporarily) removed, switched to YAML representation

1 files changed, 41 insertions, 38 deletions

diff --git a/lib/dataset.rb b/lib/dataset.rb
index b5b2e06..5caaa2c 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -3,12 +3,47 @@ LOGGER.progname = File.expand_path(__FILE__)
 module OpenTox
 
 	class Dataset 
-		include Owl
+		#include Owl
+
+		attr_accessor :uri, :title, :source, :identifier, :data, :features, :compounds
 
 		def initialize 
-			super
+			@data = {}
+			@features = []
+			@compounds = []
+			#super
+		end
+
+		def self.find(uri)
+			#dataset = Dataset.new
+			LOGGER.debug "Getting data from #{uri}"
+			YAML.load RestClient.get(uri, :accept => 'application/x-yaml').to_s # unclear why this does not work for complex uris, Dataset.find works from irb
+			#data = `curl "#{uri}"`
+			#LOGGER.debug data
+			#dataset.rdf = data
+			#dataset
+		end
+
+
+		def save
+			LOGGER.debug "Saving dataset"
+			@features.uniq!
+			@compounds.uniq!
+			#task_uri = RestClient.post(@@config[:services]["opentox-dataset"], self.rdf, :content_type =>  "application/rdf+xml").to_s
+      task_uri = RestClient::Resource.new(@@config[:services]["opentox-dataset"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0]).post(self.to_yaml, :content_type =>  "application/x-yaml").chomp.to_s		
+			task = OpenTox::Task.find(task_uri)
+			LOGGER.debug "Waiting for task #{task_uri}"
+			task.wait_for_completion
+			LOGGER.debug "Dataset task #{task_uri} completed"
+			if task.failed?
+				LOGGER.error "Saving dataset failed"
+				task.failed
+				exit
+			end
+			task.resource
 		end
 
+=begin
 		# create/add to entry from uris or Redland::Resources
 		def add(compound,feature,value)
 			compound = self.find_or_create_compound compound unless compound.class == Redland::Resource
@@ -87,17 +122,7 @@ module OpenTox
       resource = RestClient::Resource.new(@@config[:services]["opentox-dataset"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])		  
 		  uri = resource.post data, :content_type => content_type
 			dataset = Dataset.new
-			dataset.read uri.to_s
-			dataset
-		end
-
-		def self.find(uri)
-			dataset = Dataset.new
-			LOGGER.debug "Getting data from #{uri}"
-			data = `curl "#{uri}"`
-			#LOGGER.debug data
-			#data = RestClient.get(uri, :accept => 'application/rdf+xml') # unclear why this does not work for complex uris, Dataset.find works from irb
-			dataset.rdf = data
+			dataset.read uri.chomp.to_s
 			dataset
 		end
 
@@ -165,35 +190,13 @@ module OpenTox
       resource.delete
     end
 
-		def save
-			LOGGER.debug "Saving dataset"
-			#task_uri = RestClient.post(@@config[:services]["opentox-dataset"], self.rdf, :content_type =>  "application/rdf+xml").to_s
-      task_uri = RestClient::Resource.new(@@config[:services]["opentox-dataset"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0]).post(self.rdf, :content_type =>  "application/rdf+xml").to_s		
-			task = OpenTox::Task.find(task_uri)
-			LOGGER.debug "Waiting for task #{task_uri}"
-			task.wait_for_completion
-			LOGGER.debug "Dataset task #{task_uri} completed"
-			if task.failed?
-				LOGGER.error "Saving dataset failed"
-				task.failed
-				exit
-			end
-			task.resource
+		def to_owl
 		end
 
-		def to_yaml
-			{
-				:uri => self.uri,
-				:opentox_class => self.owl_class,
-				:title => self.title,
-				:source => self.source,
-				:identifier => self.identifier,
-				:compounds => self.compounds.collect{|c| c.to_s.to_s.sub(/^\[(.*)\]$/,'\1')},
-				:features => self.features.collect{|f| f.to_s },
-				:data => self.data
-			}.to_yaml
+		def from_owl
 		end
 
+=end
 	end
 
 end