tests successful

1 files changed, 24 insertions, 168 deletions

diff --git a/application.rb b/application.rb
index b9f518d..2ebbbc8 100644
--- a/application.rb
+++ b/application.rb
@@ -1,5 +1,5 @@
 # SETUP
-[ 'rubygems', 'redis', 'opentox-ruby-api-wrapper', 'openbabel' ].each do |lib|
+[ 'rubygems', 'redis', 'opentox-ruby-api-wrapper' ].each do |lib|
   require lib
 end
 
@@ -15,8 +15,6 @@ end
 
 set :default_content, :yaml
 load File.join(File.dirname(__FILE__), 'dataset.rb')
-load File.join(File.dirname(__FILE__), 'compound.rb')
-load File.join(File.dirname(__FILE__), 'feature.rb')
 
 helpers do
 
@@ -26,206 +24,64 @@ helpers do
 	end
 
 	def uri(name)
-		uri = url_for("/", :full) + URI.encode(name) #.gsub(/\s|\n/,'_')
+		uri = url_for("/dataset/", :full) + URI.encode(name)
 	end
 
 end
 
-=begin
-# current sinatra version does not halt in before filter, should be resolved in future versions
-before do
-	if params[:name] and !request.post?
-		halt 404, "Dataset \"#{params[:name]}\" not found." unless @dataset = Dataset.find(url_for("/", :full) + name.gsub(/\s|\n/,'_'))
-	end
-end
-=end
-
 ## REST API
 
-get '/?' do
+load 'compound.rb'
+load 'feature.rb'
+
+get '/datasets/?' do
 	Dataset.find_all.join("\n")
 end
 
-get '/*/tanimoto/*/?' do
+get '/dataset/*/tanimoto/*/?' do
 	find
 	@set.tanimoto(uri(params[:splat][1]))
 end
 
-get '/*/weighted_tanimoto/*/?' do
+get '/dataset/*/weighted_tanimoto/*/?' do
 	find
 	@set.weighted_tanimoto(uri(params[:splat][1]))
 end
 
 # catch the rest
-get '/*/?' do
+get '/dataset/*/?' do
 	find
-	@set.to_yaml
+	@set.members.join("\n")
 end
 
-post '/?' do
-
+# create a dataset
+post '/datasets/?' do
 	dataset_uri = uri(params[:name])
 	halt 403, "Dataset \"#{dataset_uri}\" exists." if Dataset.find(dataset_uri)
-
 	@set = Dataset.create(dataset_uri)
-	@compounds_set = Dataset.create File.join(dataset_uri, "compounds")
-	#@activities_set = Dataset.create File.join(dataset_uri, "activities")
-	#@features_set = Dataset.create File.join(dataset_uri, "features")
-	@set.add(@compounds_set.uri)
-	#@set.add(@activities_set.uri)
-	#@set.add(@features_set.uri)
-	@set.uri
-
-end
-
-post '/*/activities/?' do
-
-	find
-	@compounds_set = Dataset.find File.join(@set.uri, "compounds")
-	#@activities_set = Dataset.find File.join(@set.uri, "activities")
-	File.open(params[:file][:tempfile].path).each_line do |line|
-		record = line.chomp.split(/,\s*/)
-		inchi = Compound.new(:smiles => record[0]).inchi
-		feature = Feature.new(:name => @set.name, :values => {:classification => record[1]})
-		@compound_activities = Dataset.find_or_create File.join(@set.uri, inchi)
-		#@activity_compounds = Dataset.find_or_create File.join(@set.uri, feature.path)
-		@compounds_set.add(inchi)
-		#@activities_set.add(feature.path)
-		@compound_activities.add(feature.path)
-		#@activity_compounds.add(inchi)
-	end
+	@set.add Dataset.create(File.join(dataset_uri, "compounds")).uri
 	@set.uri
-
 end
 
-post '/*/features/?' do
+load 'import.rb'
 
+# import yaml
+post '/dataset/*/?' do
 	find
 	@compounds_set = Dataset.find File.join(@set.uri, "compounds")
-	#@features_set = Dataset.find File.join(@set.uri, "features")
-	YAML.load(params[:features]).each do |inchi,features|
-		@compound_features = Dataset.find_or_create File.join(@set.uri, inchi)
-		features.each do |feature|
-			#@feature_compounds = Dataset.find_or_create File.join(@set.uri, feature)
-			@compounds_set.add(inchi)
-			#@features_set.add(feature)
-			@compound_features.add(feature)
-			#@feature_compounds.add(inchi)
+	YAML.load(params[:features]).each do |compound_uri,feature_uris|
+		# key: /dataset/:dataset/compound/:inchi/:feature_type
+		@compound_features = Dataset.find_or_create File.join(@set.uri,'compound',OpenTox::Compound.new(:uri => compound_uri).inchi,URI.escape(params[:feature_type]))
+		feature_uris.each do |feature_uri|
+			@compounds_set.add compound_uri
+			@compound_features.add feature_uri
 		end
   end
 	@set.uri
-
 end
 
-delete '/*/?' do
+delete '/dataset/*/?' do
 	find
-	@set.members.each{|m| Dataset.find(m).delete}
+	@set.members.each{|m| Dataset.find(m).delete} if @set.members
 	@set.delete
 end
-
-put '/*/?' do
-	find
-	@set.add(params[:uri])
-end
-
-=begin
-get '/:name' do
-  not_found?
-  respond_to do |format|
-    format.yaml { @dataset.to_yaml }
-    format.xml {  builder :dataset }
-  end
-end
-
-get '/:name/name' do
-  not_found?
-  URI.decode(params[:name])
-end
-
-get '/:name/compounds' do
-  not_found?
-  @dataset.compound_uris.join("\n")
-end
-
-get '/:name/features' do
-  not_found?
-  @dataset.feature_uris.join("\n")
-end
-
-get '/:name/compound/*/features' do 
-	not_found?
-	compound_uri = params[:splat].first.gsub(/ /,'+')
-	@dataset.feature_uris_for_compound(compound_uri).join("\n")
-end
-
-get '/:name/feature/*/compounds' do 
-	not_found?
-	@dataset.compound_uris_for_feature(params[:splat].first).join("\n")
-end
-
-get '/tanimoto/:name0/compound/*/:name1/compound/*/?' do 
-	compound_uris = params[:splat].collect{ |c| c.gsub(/ /,'+') }
-	features = [ {:dataset_uri => uri(params[:name0]), :compound_uri => compound_uris[0]}, {:dataset_uri => uri(params[:name1]), :compound_uri => compound_uris[1]} ]
-	"#{Dataset.tanimoto(features)}"
-end
-
-get '/weighted_tanimoto/:name0/compound/*/:name1/compound/*/?' do 
-	compound_uris = params[:splat].collect{ |c| c.gsub(/ /,'+') }
-	features = [ {:dataset_uri => uri(params[:name0]), :compound_uri => compound_uris[0]}, {:dataset_uri => uri(params[:name1]), :compound_uri => compound_uris[1]} ]
-	Dataset.weighted_tanimoto(features)
-end
-
-post '/?' do
-  #protected!
-  halt 403, "Dataset \"#{name}\" exists - please choose another name." if Dataset.exists?(uri params[:name])
-
-	dataset = Dataset.create(uri params[:name])
-
-  if params[:file]
-		File.open(params[:file][:tempfile].path).each_line do |line|
-			record = line.chomp.split(/,\s*/)
-			compound_uri = OpenTox::Compound.new(:smiles => record[0]).uri
-			feature_uri = OpenTox::Feature.new(:name => params[:name], :values => {:classification => record[1]}).uri
-			dataset.add(compound_uri, feature_uri)
-		end
-  end
-	dataset.uri
-end
-
-put '/:name/?' do
-  #protected!
-  not_found?
-	@dataset.add(params[:compound_uri],params[:feature_uri])
-  @dataset.uri + " sucessfully updated."
-end
-
-delete '/:name/?' do
-  #protected!
-  not_found?
-	@dataset.destroy
-  "Successfully deleted dataset \"#{params[:name]}\"."
-end
-
-# Dataset collections
-get '/collections/?' do
-	DatasetCollection.find_all.join("\n")
-end
-
-get '/collection/:name/?' do
-	@collection = DatasetCollection.find(uri params[:name])
-  respond_to do |format|
-    format.yaml { @collection.to_yaml }
-    format.xml {  builder :collection }
-  end
-end
-
-post '/collections/?' do
-  halt 403, "Dataset collection \"#{name}\" exists - please choose another name." if DatasetCollection.exists?(uri params[:name])
-	DatasetCollection.create(uri params[:name], :dataset_uris => params[:datasets]).uri
-end
-
-delete '/collection/:name/?' do
-	DatasetCollection.find(uri params[:name]).destroy
-  "Successfully deleted dataset collection \"#{params[:name]}\"."
-end
-=end