similarity calculations added

1 files changed, 115 insertions, 48 deletions

diff --git a/application.rb b/application.rb
index 26bb3c3..f26d664 100644
--- a/application.rb
+++ b/application.rb
@@ -15,33 +15,105 @@ end
 
 set :default_content, :yaml
 
-helpers do
+class Dataset
 
-	def create_dataset(uri)
-		@@redis.set_add "datasets", uri
+	include OpenTox::Utils
+	attr_reader :uri, :name
+
+	def initialize(uri)
+		@name = File.basename(uri)
+		@uri = uri
 	end
 
-	def	add_feature(dataset_uri, compound_uri, feature_uri)
-		@@redis.set_add dataset_uri + '::compounds', compound_uri
-		@@redis.set_add dataset_uri + '::features', feature_uri
-		@@redis.set_add dataset_uri + '::' + compound_uri + '::features', feature_uri
-		@@redis.set_add dataset_uri + '::' + feature_uri + '::compounds', compound_uri
+	def self.create(uri)
+		dataset = Dataset.new(uri)
+		dataset.save
+		dataset
 	end
 
-	def delete_dataset(uri)
-		@@redis.set_members(uri + '::compounds').each do |compound_uri|
-			@@redis.delete uri + '::' + compound_uri
+	def self.find(uri)
+		if @@redis.set_member? "datasets", uri
+			Dataset.new(uri)
+		else
+			nil
 		end
-		@@redis.delete uri + '::compounds'
-		@@redis.set_members(uri + '::features').each do |feature_uri|
-			@@redis.delete uri + '::' + feature_uri
+	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
+		@@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
+
+helpers do
+
 	def not_found?
-		halt 404, "Dataset \"#{params[:name]}\" not found." unless @@redis.set_member? "datasets", uri(params[:name])
+		halt 404, "Dataset \"#{params[:name]}\" not found." unless Dataset.exists? uri(params[:name])
 	end
 
 	def uri(name)
@@ -53,12 +125,12 @@ end
 ## REST API
 
 get '/?' do
-	@@redis.set_members("datasets").collect{|d| uri(d)}.join("\n")
+	Dataset.find_all_uris.join("\n")
 end
 
 get '/:name' do
   not_found?
-  @dataset = {:uri => uri(params[:name]), :name => params[:name]}
+	@dataset = Dataset.find(uri params[:name])
   respond_to do |format|
     format.yaml { @dataset.to_yaml }
     format.xml {  builder :dataset }
@@ -72,71 +144,66 @@ end
 
 get '/:name/compounds' do
   not_found?
-  @@redis.set_members(uri(params[:name]) + "::compounds").join("\n")
+  Dataset.find(uri params[:name]).compound_uris.join("\n")
 end
 
 get '/:name/features' do
   not_found?
-  @@redis.set_members(uri(params[:name]) + "::features").join("\n")
+  Dataset.find(uri params[:name]).feature_uris.join("\n")
 end
 
-=begin
-get '/:name/:type/*/*/intersection' do
-  # CHECK/TEST
-  @@redis.set_intersect(params[:splat][0], params[:splat][1], URI.encode(params[:name]) + '/' + params[:type]).join("\n")
+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")
 end
 
-get '/:name/:type/*/*/union' do
-  # CHECK/TEST
-  @@redis.set_union(params[:splat][0], params[:splat][1], URI.encode(params[:name]) + '/' + params[:type]).join("\n")
+get '/:name/feature/*/compounds' do 
+	not_found?
+	Dataset.find(uri params[:name]).compound_uris_for_feature(params[:splat].first).join("\n")
 end
-=end
 
-get '/:name/*/features' do 
+get '/:name/tanimoto/compound/*/compound/*/?' do 
 	not_found?
-	# re-escape smiles (Sinatra unescapes params and splats)
-	compound_uri = params[:splat].first.sub(%r{(http://[\w\.:]+/)(.*)$}) {|s| $1 + URI.escape($2, /[^#{URI::PATTERN::UNRESERVED}]/)}
-	
-	#puts compound_uri
-  @@redis.set_members(uri(params[:name]) + '::' + compound_uri + '::features').join("\n")
+	compound_uris = params[:splat].collect{ |c| c.gsub(/ /,'+') }
+	"#{Dataset.find(uri params[:name]).tanimoto(compound_uris)}"
 end
 
-get '/:name/*/compounds' do 
+get '/:name/weighted_tanimoto/compound/*/compound/*/?' do 
 	not_found?
-  @@redis.set_members(uri(params[:name]) + '::' + params[:splat].first + '::compounds').join("\n")
+	compound_uris = params[:splat].collect{ |c| c.gsub(/ /,'+') }
+	Dataset.find(uri params[:name]).weighted_tanimoto(compound_uris)
 end
 
 post '/?' do
   #protected!
-	uri = uri(params[:name])
-  halt 403, "Dataset \"#{name}\" exists - please choose another name." if @@redis.set_member?("datasets", uri)
+  halt 403, "Dataset \"#{name}\" exists - please choose another name." if Dataset.exists?(uri params[:name])
 
-  @@redis.set_add "datasets", uri
+	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
-			add_feature(uri, compound_uri, feature_uri)
+			dataset.add(compound_uri, feature_uri)
 		end
   end
-	uri
+	dataset.uri
 end
 
 put '/:name/?' do
   #protected!
   not_found?
-	uri = uri(params[:name])
-	add_feature(uri, params[:compound_uri],params[:feature_uri])
-  uri + " sucessfully updated."
+	dataset = Dataset.find(uri params[:name])
+	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?
-	uri = uri(params[:name])
-	delete_dataset(uri)
-  "Successfully deleted dataset \"#{uri}\"."
+	Dataset.find(uri params[:name]).destroy
+  "Successfully deleted dataset \"#{params[:name]}\"."
 end