resolved confilct

2 files changed, 58 insertions, 40 deletions

diff --git a/.gitignore b/.gitignore
index 1441bd2..b42cb55 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,3 +3,4 @@ api_key.rb
 tmp/*
 log/*
 datasets/*
+public/*
diff --git a/application.rb b/application.rb
index 4222f3d..c83ba7f 100644
--- a/application.rb
+++ b/application.rb
@@ -1,23 +1,38 @@
 require 'rubygems'
-gem 'opentox-ruby-api-wrapper', '= 1.2.7'
+gem 'opentox-ruby-api-wrapper', '= 1.4.0'
 require 'opentox-ruby-api-wrapper'
+#require 'sinatra/respond_to'
+#Sinatra::Application.register Sinatra::RespondTo
+
+
+LOGGER.progname = File.expand_path(__FILE__)
 
 class Dataset
 	include DataMapper::Resource
 	property :id, Serial
 	property :uri, String, :length => 255
 	property :file, String, :length => 255
-	#property :owl, Text, :length => 1000000
+	property :yaml, Text, :length => 2**32-1 
+	property :owl, Text, :length => 2**32-1 
 	property :created_at, DateTime
 
-	def owl
-		File.read self.file
+	def to_owl
+		data = YAML.load(yaml)
+		owl = OpenTox::Owl.create 'Dataset', uri
+		['title', 'source'].each do |method|
+			eval "owl.#{method} = data.#{method}"
+		end
+		if data.data
+			data.data.each do |compound,features|
+				owl.add_data_entries compound,features
+			end
+		end
+		owl.rdf
 	end
 
-	def owl=(owl)
-		self.file = File.join(File.dirname(File.expand_path(__FILE__)),'public',"#{id}.owl")
-		File.open(self.file,"w+") { |f| f.write owl }
-	end
+	#def from_owl
+	#end
+
 end
 
 DataMapper.auto_upgrade!
@@ -26,26 +41,38 @@ DataMapper.auto_upgrade!
 
 get '/?' do
 	response['Content-Type'] = 'text/uri-list'
-	Dataset.all.collect{|d| d.uri}.join("\n")
+	Dataset.all.collect{|d| d.uri}.join("\n") + "\n"
 end
 
-get '/:id/?' do
+get '/:id' do
+	accept = request.env['HTTP_ACCEPT']
+	accept = 'application/rdf+xml' if accept == '*/*' or accept == '' or accept.nil?
+	# workaround for browser links
+	case params[:id]
+	when /.yaml$/
+		params[:id].sub!(/.yaml$/,'')
+		accept =  'application/x-yaml'
+	when /.rdf$/
+		params[:id].sub!(/.rdf$/,'')
+		accept =  'application/rdf+xml'
+	end
 	begin
 		dataset = Dataset.get(params[:id])
 	rescue => e
-		LOGGER.error e.message
-		LOGGER.warn e.backtrace
+		raise e.message + e.backtrace
 		halt 404, "Dataset #{params[:id]} not found."
 	end
-	accept = request.env['HTTP_ACCEPT']
-	accept = 'application/rdf+xml' if accept == '*/*' or accept == '' or accept.nil?
 	case accept
 	when /rdf/ # redland sends text/rdf instead of application/rdf+xml
 		response['Content-Type'] = 'application/rdf+xml'
+		unless dataset.owl # lazy owl creation
+			dataset.owl = dataset.to_owl
+			dataset.save
+		end
 		dataset.owl
 	when /yaml/
 		response['Content-Type'] = 'application/x-yaml'
-		OpenTox::Dataset.find(dataset.uri).to_yaml
+		dataset.yaml
 	else
 		halt 400, "Unsupported MIME type '#{accept}'"
 	end
@@ -56,57 +83,47 @@ get '/:id/features/:feature_id/?' do
 end
 
 get '/:id/features/?' do
-	OpenTox::Dataset.find(url_for("/#{params[:id]}", :full)).features
+	YAML.load(Dataset.get(params[:id]).yaml).features.join("\n") + "\n"
 end
 
-post '/?' do
-	task = OpenTox::Task.create
-	pid = Spork.spork(:logger => LOGGER) do
+get '/:id/compounds/?' do
+	YAML.load(Dataset.get(params[:id]).yaml).compounds.join("\n") + "\n"
+end
 
-		task.started
-		LOGGER.debug "Dataset task #{task.uri} started"
+post '/?' do
 
 		dataset = Dataset.new
 		dataset.save
-		uri = url_for("/#{dataset.id}", :full)
+		dataset.uri = url_for("/#{dataset.id}", :full)
 		content_type = request.content_type
 		content_type = "application/rdf+xml" if content_type.nil?
 		case request.content_type
+		when /yaml/
+			dataset.yaml =	request.env["rack.input"].read
+		when /csv/
+			dataset.yaml =	csv2yaml request.env["rack.input"].read
 		when "application/rdf+xml"
-			rdf =	request.env["rack.input"].read
-			d= OpenTox::Dataset.new
-			d.rdf = rdf
-			d.uri = uri
+			dataset.yaml =	owl2yaml request.env["rack.input"].read
 		else
 			halt 404, "MIME type \"#{request.content_type}\" not supported."
 		end
-		LOGGER.debug "Saving dataset #{uri}."
 		begin
-			dataset.owl = d.rdf
-      dataset.uri = uri 
+			#dataset.owl = d.rdf
+      #dataset.uri = uri 
 			dataset.save
-			task.completed(uri) 
 		rescue => e
 			LOGGER.error e.message
 			LOGGER.info e.backtrace
-			halt 500, "Could not save dataset #{uri}."
+			halt 500, "Could not save dataset #{dataset.uri}."
 		end
 		LOGGER.debug "#{dataset.uri} saved."
-	end
-	task.pid = pid
-	#status 303 # rest client tries to redirect
 	response['Content-Type'] = 'text/uri-list'
- 	task.uri
-  
-  
-  
-  
+	dataset.uri + "\n"
 end
 
 delete '/:id/?' do
 	begin
 		dataset = Dataset.get(params[:id])
-		File.delete dataset.file
 		dataset.destroy!
 		response['Content-Type'] = 'text/plain'
 		"Dataset #{params[:id]} deleted."