tests for dependent webservices successful

4 files changed, 45 insertions, 16 deletions

diff --git a/application.rb b/application.rb
index 2ebbbc8..5c4722c 100644
--- a/application.rb
+++ b/application.rb
@@ -13,9 +13,10 @@ when 'test'
   @@redis.flush_db
 end
 
-set :default_content, :yaml
 load File.join(File.dirname(__FILE__), 'dataset.rb')
 
+set :default_content, :yaml
+
 helpers do
 
 	def find
@@ -38,16 +39,27 @@ get '/datasets/?' do
 	Dataset.find_all.join("\n")
 end
 
-get '/dataset/*/tanimoto/*/?' do
+get '/algorithm/tanimoto/dataset/*/dataset/*/?' do
 	find
 	@set.tanimoto(uri(params[:splat][1]))
 end
 
-get '/dataset/*/weighted_tanimoto/*/?' do
+
+get '/algorithm/weighted_tanimoto/dataset/*/dataset/*/?' do
 	find
 	@set.weighted_tanimoto(uri(params[:splat][1]))
 end
 
+get '/dataset/*/name/?' do
+	find
+	URI.decode @set.name
+end
+
+get '/dataset/*/features/?' do
+	find
+	@set.features.join("\n")
+end
+
 # catch the rest
 get '/dataset/*/?' do
 	find
@@ -60,6 +72,7 @@ post '/datasets/?' do
 	halt 403, "Dataset \"#{dataset_uri}\" exists." if Dataset.find(dataset_uri)
 	@set = Dataset.create(dataset_uri)
 	@set.add Dataset.create(File.join(dataset_uri, "compounds")).uri
+	@set.add Dataset.create(File.join(dataset_uri, "features")).uri
 	@set.uri
 end
 
@@ -69,11 +82,13 @@ load 'import.rb'
 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 |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]))
+		# key: /dataset/:dataset/compound/:inchi
+		@compound_features = Dataset.find_or_create File.join(@set.uri,'compound',OpenTox::Compound.new(:uri => compound_uri).inchi)
 		feature_uris.each do |feature_uri|
 			@compounds_set.add compound_uri
+			@features_set.add feature_uri
 			@compound_features.add feature_uri
 		end
   end
diff --git a/dataset.rb b/dataset.rb
index 82d228f..435e9dc 100644
--- a/dataset.rb
+++ b/dataset.rb
@@ -6,7 +6,7 @@ class Dataset
 	def initialize(uri)
 		@uri = uri
 		begin
-			@name = URI.split(uri)[5]
+			@name = URI.split(uri)[5].sub(/\/dataset\//,'')
 		rescue
 			puts "Bad URI #{uri}"
 		end
@@ -56,6 +56,10 @@ class Dataset
 		@@redis.set_intersect(@uri,set_uri)
 	end
 
+	def features
+		@@redis.set_members(File.join(@uri,'features'))
+	end
+
 	def tanimoto(set_uri)
 		union_size = @@redis.set_union(@uri,set_uri).size
 		intersect_size = @@redis.set_intersect(@uri,set_uri).size
@@ -63,6 +67,8 @@ class Dataset
 	end
 
 	def weighted_tanimoto(set_uri)
+		puts set_uri
+		puts	@@redis.set_members(set_uri).to_yaml
 		union = @@redis.set_union(@uri,set_uri)
 		intersect = @@redis.set_intersect(@uri,set_uri)
 
diff --git a/import.rb b/import.rb
index de6f60b..86b5480 100644
--- a/import.rb
+++ b/import.rb
@@ -2,15 +2,17 @@ post '/dataset/*/import/?' do
 	find
 	halt 404, "Compound format #{params[:compound_format]} not (yet) supported" unless params[:compound_format] =~ /smiles|inchi|name/
 	@compounds_set = Dataset.find File.join(@set.uri, "compounds")
+	@features_set = Dataset.find File.join(@set.uri, "features")
 	case	params[:file][:type]
 	when "text/csv"
 		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 => @set.name.sub(/dataset\//,''), :values => {:classification => record[1]}).uri
-			@compounds_set.add compound_uri unless @compounds_set.member? compound_uri
-			# 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]))
+			@compounds_set.add compound_uri #unless @compounds_set.member? compound_uri
+			@features_set.add feature_uri #unless @features_set.member? feature_uri
+			# key: /dataset/:dataset/compound/:inchi
+			@compound_features = Dataset.find_or_create File.join(@set.uri,'compound',OpenTox::Compound.new(:uri => compound_uri).inchi)
 			@compound_features.add feature_uri
 		end
 	else
diff --git a/test/test.rb b/test/test.rb
index 603e27d..8da6c88 100644
--- a/test/test.rb
+++ b/test/test.rb
@@ -26,6 +26,10 @@ class DatasetsTest < Test::Unit::TestCase
 		assert_equal "http://example.org/dataset/Test%20dataset", uri
 		get uri
 		assert last_response.ok?
+		get uri + '/name'
+		puts last_response.body
+		assert last_response.ok?
+		assert_equal "Test dataset", last_response.body
 		delete uri
 		assert last_response.ok?
 		get uri
@@ -38,15 +42,17 @@ class DatasetsTest < Test::Unit::TestCase
 		post '/datasets', :name => "Hamster Carcinogenicity"
 		uri = last_response.body
 		assert last_response.ok?
-		post uri + '/import', :file => Rack::Test::UploadedFile.new(File.join(File.dirname(__FILE__), "hamster_carcinogenicity.csv"), "text/csv"), :compound_format => "smiles", :feature_type => "in vivo carcinogenicity"
+		post uri + '/import', :file => Rack::Test::UploadedFile.new(File.join(File.dirname(__FILE__), "hamster_carcinogenicity.csv"), "text/csv"), :compound_format => "smiles"
 		get uri
 		assert last_response.ok?
 		get uri + '/compounds'
 		assert last_response.ok?
 		assert last_response.body.include?(compound.inchi)
-		get File.join(uri , 'compound', compound.inchi, URI.encode("in vivo carcinogenicity"))
+		get File.join(uri , 'compound', compound.inchi)
 		assert last_response.ok?
     assert last_response.body.include?("Hamster%20Carcinogenicity/classification/true")
+		get File.join(uri , 'features')
+    puts last_response.body.to_yaml
 		delete uri
 		assert last_response.ok?
 		get uri
@@ -57,7 +63,7 @@ class DatasetsTest < Test::Unit::TestCase
 	def test_create_large_dataset_from_csv
 		post '/datasets', :name => "Salmonella Mutagenicity"
 		uri = last_response.body
-		post uri + '/import', :file => Rack::Test::UploadedFile.new(File.join(File.dirname(__FILE__), "kazius.csv"), "text/csv"), :compound_format => "smiles", :feature_type => "activity"
+		post uri + '/import', :file => Rack::Test::UploadedFile.new(File.join(File.dirname(__FILE__), "kazius.csv"), "text/csv"), :compound_format => "smiles"
 		uri = last_response.body
 		get uri
 		assert last_response.ok?
@@ -111,7 +117,7 @@ class DatasetsTest < Test::Unit::TestCase
 			end
 		end
 
-		post uri , :features => feature_data.to_yaml, :feature_type => 'test'
+		post uri , :features => feature_data.to_yaml
 		assert last_response.ok?
 
 		data.each do |smiles,features|
@@ -121,9 +127,9 @@ class DatasetsTest < Test::Unit::TestCase
 					neighbor= OpenTox::Compound.new(:smiles => s).inchi
 					get "/dataset/#{name}/compounds"
 					assert last_response.ok?
-					get "/dataset/#{name}/compound/#{compound}/test"
+					get "/dataset/#{name}/compound/#{compound}"
 					assert last_response.ok?
-					get "/dataset/#{name}/compound/#{compound}/test/tanimoto/#{name}/compound/#{neighbor}/test"
+					get "/algorithm/tanimoto/dataset/#{name}/compound/#{compound}/dataset/#{name}/compound/#{neighbor}"
 					puts last_response.body
 					assert last_response.ok?
 					sim = last_response.body
@@ -134,7 +140,7 @@ 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 "/dataset/#{name}/compound/#{compound}/test/weighted_tanimoto/#{name}/compound/#{neighbor}/test"
+					get "/algorithm/weighted_tanimoto/dataset/#{name}/compound/#{compound}/dataset/#{name}/compound/#{neighbor}"
 					assert last_response.ok?
 					puts "weighted_tanimoto::#{smiles}::#{s}::#{last_response.body}"
 				end