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

5 files changed, 70 insertions, 46 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index 817340f..c17159e 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -51,7 +51,7 @@ module OpenTox
 				LOGGER.debug File.basename(__FILE__) + ": creating model"
 				#@uri = RestClient.post File.join(@@config[:services]["opentox-algorithm"], "lazar"), :dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer")
         resource = RestClient::Resource.new(File.join(@@config[:services]["opentox-algorithm"], "lazar"), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
-        @uri = resource.post :dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer")
+        @uri = resource.post :dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer").chomp
 			end
 
 			def self.uri
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
diff --git a/lib/model.rb b/lib/model.rb
index b5129d7..5dcc462 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -2,6 +2,27 @@ module OpenTox
 	module Model
    
 		class Lazar
+
+			attr_accessor :dependent_variable, :activity_dataset_uri, :feature_dataset_uri, :effects, :activities, :p_values, :fingerprints, :features
+			
+			def initialize
+				@source = "http://github.com/helma/opentox-model"
+				@algorithm = File.join(@@config[:services]["opentox-algorithm"],"lazar")
+				#@independent_variables = File.join(@@config[:services]["opentox-algorithm"],"fminer#BBRC_representative")
+				@features = []
+				@effects = {}
+				@activities = {}
+				@p_values = {}
+				@fingerprints = {}
+			end
+
+			def save
+				@features.uniq!
+			  resource = RestClient::Resource.new(@@config[:services]["opentox-model"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+			  resource.post(self.to_yaml, :content_type => "application/x-yaml").chomp.to_s
+			end
+
+=begin
 			include Owl
 
 			# Create a new prediction model from a dataset
@@ -50,7 +71,7 @@ module OpenTox
 
 			def self.create(data)
 			  resource = RestClient::Resource.new(@@config[:services]["opentox-model"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
-			  resource.post(data, :content_type => "application/x-yaml").to_s
+			  resource.post(data, :content_type => "application/x-yaml").chomp.to_s
 			end
 
 			def delete
@@ -101,6 +122,7 @@ module OpenTox
 				@model.add me, OT['predictedVariables'], Redland::Uri.new(predictedVariables) # untyped individual comes from this line, why??
 				@model.add Redland::Uri.new(predictedVariables), RDF['type'], OT['Feature']
 			end
+=end
 		end
 	end
 end
diff --git a/lib/owl.rb b/lib/owl.rb
index 82d6e0e..f8958cd 100644
--- a/lib/owl.rb
+++ b/lib/owl.rb
@@ -20,7 +20,7 @@ module OpenTox
 		end
 
 		def uri=(uri)
-			@uri = uri
+			@uri = uri.chomp
 			uri = Redland::Uri.new(uri)
 			# rewrite uri
 			@model.subjects(RDF['type'],OT[self.owl_class]).each do |me|
diff --git a/lib/task.rb b/lib/task.rb
index a6a54d5..6a80d1a 100644
--- a/lib/task.rb
+++ b/lib/task.rb
@@ -7,16 +7,15 @@ module OpenTox
 		attr_accessor :uri
 
 		def initialize(uri)
-			#super()
-			@uri = uri
+			@uri = uri.chomp
 		end
 
 		def self.create
 			#uri = RestClient.post @@config[:services]["opentox-task"], {}
       resource = RestClient::Resource.new(@@config[:services]["opentox-task"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
 			#uri = resource.post(nil)
-			uri = resource.post({})
-			Task.new(uri)
+			uri = resource.post({}).chomp
+			Task.new(uri.chomp)
 		end
 
 		def self.find(uri)
@@ -28,7 +27,7 @@ module OpenTox
 		end
 
 		def self.all
-			task_uris = RestClient.get(@@config[:services]["opentox-task"]).split(/\n/)
+			task_uris = RestClient.get(@@config[:services]["opentox-task"]).chomp.split(/\n/)
 			task_uris.collect{|uri| Task.new(uri)}
 		end