dataset class separated from application

3 files changed, 200 insertions, 115 deletions

diff --git a/application.rb b/application.rb
index f26d664..a23b52a 100644
--- a/application.rb
+++ b/application.rb
@@ -14,106 +14,12 @@ when 'test'
 end
 
 set :default_content, :yaml
-
-class Dataset
-
-	include OpenTox::Utils
-	attr_reader :uri, :name
-
-	def initialize(uri)
-		@name = File.basename(uri)
-		@uri = uri
-	end
-
-	def self.create(uri)
-		dataset = Dataset.new(uri)
-		dataset.save
-		dataset
-	end
-
-	def self.find(uri)
-		if @@redis.set_member? "datasets", uri
-			Dataset.new(uri)
-		else
-			nil
-		end
-	end
-
-	def self.exists?(uri)
-		@@redis.set_member? "datasets", uri
-	end
-
-	def self.find_all_uris
-		@@redis.set_members("datasets")
-	end
-
-	def save
-		@@redis.set_add "datasets", uri
-	end
-
-	def destroy
-		@@redis.set_members(@uri + '::compounds').each do |compound_uri|
-			@@redis.delete @uri + '::' + compound_uri
-		end
-		@@redis.delete @uri + '::compounds'
-		@@redis.set_members(@uri + '::features').each do |feature_uri|
-			@@redis.delete @uri + '::' + feature_uri
-		end
-		@@redis.delete @uri + '::features'
-		@@redis.set_delete "datasets", @uri
-	end
-
-	def add(compound_uri,feature_uri)
-		@@redis.set_add @uri + '::compounds', compound_uri
-		@@redis.set_add @uri + '::features', feature_uri
-		@@redis.set_add @uri + '::' + compound_uri + '::features', feature_uri
-		@@redis.set_add @uri + '::' + feature_uri + '::compounds', compound_uri
-	end
-
-	def compound_uris
-		@@redis.set_members(@uri + "::compounds")
-	end
-
-	def feature_uris
-		@@redis.set_members(@uri + "::features")
-	end
-
-	def feature_uris_for_compound(compound_uri)
-		@@redis.set_members(@uri + '::' + compound_uri + '::features')
-	end
-	 
-	def compound_uris_for_feature(feature_uri)
-		@@redis.set_members(@uri + '::' + feature_uri + '::compounds')
-	end
-
-	def tanimoto(compound_uris)
-		raise "Exactly 2 compounds are needed for similarity calculations" unless compound_uris.size == 2
-		compound_keys = compound_uris.collect{ |c| @uri + '::' + c + "::features" }
-		union_size = @@redis.set_union(compound_keys[0], compound_keys[1]).size
-		intersect_size = @@redis.set_intersect(compound_keys[0], compound_keys[1]).size
-		intersect_size.to_f/union_size.to_f
-	end
-
-	def weighted_tanimoto(compound_uris)
-		raise "Exactly 2 compounds are needed for similarity calculations" unless compound_uris.size == 2
-		compound_keys = compound_uris.collect{ |c| @uri + '::' + c + "::features" }
-		union = @@redis.set_union(compound_keys[0], compound_keys[1])
-		intersect = @@redis.set_intersect(compound_keys[0], compound_keys[1])
-
-		p_sum_union = 0.0
-		p_sum_intersect = 0.0
-
-		union.each{ |f| p_sum_union += gauss(OpenTox::Feature.new(:uri => f).value('p_value').to_f) }
-		intersect.each{ |f| p_sum_intersect += gauss(OpenTox::Feature.new(:uri => f).value('p_value').to_f) }
-		"#{p_sum_intersect/p_sum_union}"
-	end
-
-end
+load File.join(File.dirname(__FILE__), 'dataset.rb')
 
 helpers do
 
 	def not_found?
-		halt 404, "Dataset \"#{params[:name]}\" not found." unless Dataset.exists? uri(params[:name])
+		halt 404, "Dataset \"#{params[:name]}\" not found." unless @dataset = Dataset.find(uri(params[:name]))
 	end
 
 	def uri(name)
@@ -122,15 +28,23 @@ helpers do
 
 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
-	Dataset.find_all_uris.join("\n")
+	Dataset.find_all.join("\n")
 end
 
 get '/:name' do
   not_found?
-	@dataset = Dataset.find(uri params[:name])
   respond_to do |format|
     format.yaml { @dataset.to_yaml }
     format.xml {  builder :dataset }
@@ -144,35 +58,35 @@ end
 
 get '/:name/compounds' do
   not_found?
-  Dataset.find(uri params[:name]).compound_uris.join("\n")
+  @dataset.compound_uris.join("\n")
 end
 
 get '/:name/features' do
   not_found?
-  Dataset.find(uri params[:name]).feature_uris.join("\n")
+  @dataset.feature_uris.join("\n")
 end
 
 get '/:name/compound/*/features' do 
 	not_found?
 	compound_uri = params[:splat].first.gsub(/ /,'+')
-	Dataset.find(uri params[:name]).feature_uris_for_compound(compound_uri).join("\n")
+	@dataset.feature_uris_for_compound(compound_uri).join("\n")
 end
 
 get '/:name/feature/*/compounds' do 
 	not_found?
-	Dataset.find(uri params[:name]).compound_uris_for_feature(params[:splat].first).join("\n")
+	@dataset.compound_uris_for_feature(params[:splat].first).join("\n")
 end
 
-get '/:name/tanimoto/compound/*/compound/*/?' do 
-	not_found?
+get '/tanimoto/:name0/compound/*/:name1/compound/*/?' do 
 	compound_uris = params[:splat].collect{ |c| c.gsub(/ /,'+') }
-	"#{Dataset.find(uri params[:name]).tanimoto(compound_uris)}"
+	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 '/:name/weighted_tanimoto/compound/*/compound/*/?' do 
-	not_found?
+get '/weighted_tanimoto/:name0/compound/*/:name1/compound/*/?' do 
 	compound_uris = params[:splat].collect{ |c| c.gsub(/ /,'+') }
-	Dataset.find(uri params[:name]).weighted_tanimoto(compound_uris)
+	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
@@ -195,15 +109,36 @@ end
 put '/:name/?' do
   #protected!
   not_found?
-	dataset = Dataset.find(uri params[:name])
-	dataset.add(params[:compound_uri],params[:feature_uri])
-  dataset.uri + " sucessfully updated."
+	@dataset.add(params[:compound_uri],params[:feature_uri])
+  @dataset.uri + " sucessfully updated."
 end
 
 delete '/:name/?' do
-  # dangerous, because other datasets might refer to it
   #protected!
   not_found?
-	Dataset.find(uri params[:name]).destroy
+	@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
diff --git a/dataset.rb b/dataset.rb
new file mode 100644
index 0000000..00872b9
--- /dev/null
+++ b/dataset.rb
@@ -0,0 +1,148 @@
+class Dataset
+
+	#include OpenTox::Utils
+	attr_reader :uri, :name
+
+	def initialize(uri)
+		@name = File.basename(uri)
+		@uri = uri
+	end
+
+	def self.create(uri)
+		dataset = Dataset.new(uri)
+		dataset.save
+		dataset
+	end
+
+	def self.find(uri)
+		if @@redis.set_member? "datasets", uri
+			Dataset.new(uri)
+		else
+			nil
+		end
+	end
+
+	def self.exists?(uri)
+		@@redis.set_member? "datasets", uri
+	end
+
+	def self.find_all
+		@@redis.set_members("datasets")
+	end
+
+	def save
+		@@redis.set_add "datasets", @uri
+	end
+
+	def destroy
+		@@redis.set_members(@uri + '::compounds').each do |compound_uri|
+			@@redis.delete @uri + '::' + compound_uri
+		end
+		@@redis.delete @uri + '::compounds'
+		@@redis.set_members(@uri + '::features').each do |feature_uri|
+			@@redis.delete @uri + '::' + feature_uri
+		end
+		@@redis.delete @uri + '::features'
+		@@redis.set_delete "datasets", @uri
+	end
+
+	def add(compound_uri,feature_uri)
+		@@redis.set_add @uri + '::compounds', compound_uri
+		@@redis.set_add @uri + '::features', feature_uri
+		@@redis.set_add @uri + '::' + compound_uri + '::features', feature_uri
+		@@redis.set_add @uri + '::' + feature_uri + '::compounds', compound_uri
+	end
+
+	def compound_uris
+		@@redis.set_members(@uri + "::compounds")
+	end
+
+	def feature_uris
+		@@redis.set_members(@uri + "::features")
+	end
+
+	def feature_uris_for_compound(compound_uri)
+		@@redis.set_members(@uri + '::' + compound_uri + '::features')
+	end
+	 
+	def compound_uris_for_feature(feature_uri)
+		@@redis.set_members(@uri + '::' + feature_uri + '::compounds')
+	end
+
+	def self.tanimoto(features)
+		raise "Exactly 2 compounds are needed for similarity calculations" unless features.size == 2
+		compound_keys = features.collect{ |f| f[:dataset_uri] + '::' + f[:compound_uri] + "::features" }
+		union_size = @@redis.set_union(compound_keys[0], compound_keys[1]).size
+		intersect_size = @@redis.set_intersect(compound_keys[0], compound_keys[1]).size
+		intersect_size.to_f/union_size.to_f
+	end
+
+	def self.weighted_tanimoto(features)
+		raise "Exactly 2 compounds are needed for similarity calculations" unless features.size == 2
+		compound_keys = features.collect{ |f| f[:dataset_uri] + '::' + f[:compound_uri] + "::features" }
+		union = @@redis.set_union(compound_keys[0], compound_keys[1])
+		intersect = @@redis.set_intersect(compound_keys[0], compound_keys[1])
+
+		p_sum_union = 0.0
+		p_sum_intersect = 0.0
+
+		union.each{ |f| p_sum_union += OpenTox::Utils::gauss(OpenTox::Feature.new(:uri => f).value('p_value').to_f) }
+		intersect.each{ |f| p_sum_intersect += OpenTox::Utils::gauss(OpenTox::Feature.new(:uri => f).value('p_value').to_f) }
+		"#{p_sum_intersect/p_sum_union}"
+	end
+
+end
+
+class Set
+
+	attr_accessor :uri, :set_uris
+
+	def initialize(uri, set_uris)
+		@uri = uri
+		@set_uris = set_uris
+	end
+
+	def self.create(uri, set_uris)
+		collection = DatasetCollection.new(uri, set_uris)
+		collection.save
+		collection
+	end
+
+	def self.find(uri)
+		if @@redis.set_member? "collections", uri
+			set_uris = @@redis.set_members uri
+			DatasetCollection.new(uri, set_uris)
+		else
+			nil
+		end
+	end
+
+	def self.exists?(uri)
+		@@redis.set_member? "collections", uri
+	end
+
+	def self.find_all
+		@@redis.set_members("collections").collect{ |uri| self.find(uri) }
+	end
+
+	def save
+		@@redis.set_add "collections", @uri
+		@set_uris.each do |uri|
+			@@redis.set_add @uri + '::sets', uri
+		end
+	end
+
+	def destroy
+		@set_uris.each do |uri|
+			Dataset.new(uri).destroy
+		end
+		@@redis.delete @uri + '::sets'
+		@@redis.set_delete "collections", @uri
+	end
+
+	def add(set_uri)
+		@set_uris << set_uri
+		@@redis.set_add @uri, set_uri
+	end
+
+end
diff --git a/test/test.rb b/test/test.rb
index b1bae83..65959bf 100644
--- a/test/test.rb
+++ b/test/test.rb
@@ -135,6 +135,8 @@ class DatasetsTest < Test::Unit::TestCase
 		uri = last_response.body
 		get uri
 		assert last_response.ok?
+		get uri + '/name'
+		name = last_response.body
 
 		data.each do |smiles,features|
 			compound_uri = OpenTox::Compound.new(:smiles => smiles).uri
@@ -150,7 +152,7 @@ class DatasetsTest < Test::Unit::TestCase
 			data.each do |s,f|
 				unless s == smiles
 					neighbor_uri = OpenTox::Compound.new(:smiles => s).uri
-					get uri + "/tanimoto/compound/#{compound_uri}/compound/#{neighbor_uri}"
+					get "/tanimoto/#{name}/compound/#{compound_uri}/#{name}/compound/#{neighbor_uri}"
 					assert last_response.ok?
 					sim = last_response.body
 					features_a = data[smiles].keys
@@ -160,7 +162,7 @@ class DatasetsTest < Test::Unit::TestCase
 					mysim = intersect.size.to_f/union.size.to_f
 					assert_equal sim, mysim.to_s
 					puts "tanimoto::#{smiles}::#{s}::#{last_response.body}"
-					get uri + "/weighted_tanimoto/compound/#{compound_uri}/compound/#{neighbor_uri}"
+					get "/weighted_tanimoto/#{name}/compound/#{compound_uri}/#{name}/compound/#{neighbor_uri}"
 					assert last_response.ok?
 					puts "weighted_tanimoto::#{smiles}::#{s}::#{last_response.body}"
 				end