improved redis data store

2 files changed, 65 insertions, 50 deletions

diff --git a/application.rb b/application.rb
index 2742218..26bb3c3 100644
--- a/application.rb
+++ b/application.rb
@@ -17,36 +17,35 @@ set :default_content, :yaml
 
 helpers do
 
-	def not_found?
-		halt 404, "Dataset \"#{params[:name]}\" not found." unless @@redis.set_member? "datasets", sanitize_key(params[:name])
-	end
-
-	def sanitize_key(k)
-		k.gsub(/\s|\n/,'_')
+	def create_dataset(uri)
+		@@redis.set_add "datasets", uri
 	end
 
-	def name(uri)
-		URI.decode File.basename(uri)
+	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
 	end
 
-	def uri(name)
-		uri = url_for("/", :full) + URI.escape(URI.unescape(name)) # avoid escaping escaped names
+	def delete_dataset(uri)
+		@@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_feature(name, record)
-		compound = record[0]
-		feature = record[1] 
-		@@redis.set_add name + '::compounds', compound
-		@@redis.set_add name + '::features', name + '::' + feature
-		@@redis.set_add compound, name + '::' + feature
-		@@redis.set_add feature, compound
+	def not_found?
+		halt 404, "Dataset \"#{params[:name]}\" not found." unless @@redis.set_member? "datasets", uri(params[:name])
 	end
 
-	def delete_dataset(name)
-		# stale features/compounds under compound and name::feature ??
-		@@redis.delete name + '::compounds'
-		@@redis.delete name + '::features'
-		@@redis.set_delete "datasets", name
+	def uri(name)
+		uri = url_for("/", :full) + name.gsub(/\s|\n/,'_')
 	end
 
 end
@@ -73,14 +72,15 @@ end
 
 get '/:name/compounds' do
   not_found?
-  @@redis.set_members(URI.encode(params[:name]) + "::compounds").join("\n")
+  @@redis.set_members(uri(params[:name]) + "::compounds").join("\n")
 end
 
 get '/:name/features' do
   not_found?
-  @@redis.set_members(URI.encode(params[:name]) + "::features").join("\n")
+  @@redis.set_members(uri(params[:name]) + "::features").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")
@@ -90,50 +90,53 @@ get '/:name/:type/*/*/union' do
   # CHECK/TEST
   @@redis.set_union(params[:splat][0], params[:splat][1], URI.encode(params[:name]) + '/' + params[:type]).join("\n")
 end
+=end
 
 get '/:name/*/features' do 
-  compound = URI.encode(params[:splat].first, /[^#{URI::PATTERN::UNRESERVED}]/)
-  @@redis.set_intersect(params[:name] + '::features', compound ).join("\n")
-  @@redis.set_intersect(params[:name] + '::features', compound ).join("\n")
+	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")
 end
 
 get '/:name/*/compounds' do 
-  feature = params[:splat].first
-  @@redis.set_intersect(feature, params[:name] + '::compounds').join("\n")
+	not_found?
+  @@redis.set_members(uri(params[:name]) + '::' + params[:splat].first + '::compounds').join("\n")
 end
 
 post '/?' do
   #protected!
-	name = sanitize_key params[:name]
-  halt 403, "Dataset \"#{name}\" exists - please choose another name." if @@redis.set_member?("datasets", name)
+	uri = uri(params[:name])
+  halt 403, "Dataset \"#{name}\" exists - please choose another name." if @@redis.set_member?("datasets", uri)
 
-  @@redis.set_add "datasets", name
+  @@redis.set_add "datasets", uri
 
   if params[:file]
 		File.open(params[:file][:tempfile].path).each_line do |line|
 			record = line.chomp.split(/,\s*/)
-			add_feature(name, record)
+			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)
 		end
   end
-	uri name 
+	uri
 end
 
 put '/:name/?' do
   #protected!
-  pass if params[:finished]
   not_found?
-	name = sanitize_key params[:name]
-  compound =  params[:compound]
-  feature = sanitize_key params[:feature] 
-	add_feature(name, [compound,feature])
-  name + " sucessfully updated."
+	uri = uri(params[:name])
+	add_feature(uri, params[:compound_uri],params[:feature_uri])
+  uri + " sucessfully updated."
 end
 
 delete '/:name/?' do
   # dangerous, because other datasets might refer to it
   #protected!
   not_found?
-  name = sanitize_key params[:name]
-	delete_dataset(name)
-  "Successfully deleted dataset \"#{name}\"."
+	uri = uri(params[:name])
+	delete_dataset(uri)
+  "Successfully deleted dataset \"#{uri}\"."
 end
diff --git a/test/test.rb b/test/test.rb
index dacc9d5..5c4b2e7 100644
--- a/test/test.rb
+++ b/test/test.rb
@@ -31,27 +31,29 @@ class DatasetsTest < Test::Unit::TestCase
 	end
 
 	def test_create_dataset_and_insert_data
-		usmiles = OpenTox::Compound.new(:smiles => '[O-][N+](=O)C/C=C\C(=O)Cc1cc(C#N)ccc1').uid
-		puts usmiles
 		name = "Test dataset"
+		smiles = '[O-][N+](=O)C/C=C\C(=O)Cc1cc(C#N)ccc1'
+		compound_uri = OpenTox::Compound.new(:smiles => smiles).uri
+		feature_uri = OpenTox::Feature.new(:name => name, :values => {:classification => "true"}).uri
 		post '/', :name => name
 		assert last_response.ok?
 		uri = last_response.body.chomp
 		get uri
 		assert last_response.ok?
     assert last_response.body.include?("Test_dataset")
-		put uri, :compound => usmiles, :feature => "true"
+		put uri, :compound_uri => compound_uri, :feature_uri => feature_uri
 		assert last_response.ok?
 		get uri + '/compounds'
 		assert last_response.ok?
-    assert last_response.body.include?(usmiles)
+		assert_equal compound_uri, last_response.body
 		get uri + '/features'
 		assert last_response.ok?
     assert last_response.body.include?("true")
-		get uri + '/' + usmiles + '/features'
-		puts last_response.body
+		assert_equal feature_uri, last_response.body
+		get uri + '/' + compound_uri + '/features'
 		assert last_response.ok?
     assert last_response.body.include?("true")
+		assert_equal feature_uri, last_response.body
 		delete uri
 		assert last_response.ok?
 		get "/Test_dataset"
@@ -59,14 +61,25 @@ class DatasetsTest < Test::Unit::TestCase
 	end
 
 	def test_create_dataset_from_csv
+		smiles = 'CC(=O)Nc1scc(n1)c1ccc(o1)[N+](=O)[O-]'
+		compound_uri = OpenTox::Compound.new(:smiles => smiles).uri
 		post '/', :name => "Hamster Carcinogenicity", :file => Rack::Test::UploadedFile.new(File.join(File.dirname(__FILE__), "hamster_carcinogenicity.csv"))
 		uri = last_response.body
 		get uri
 		assert last_response.ok?
 		get uri + '/compounds'
 		assert last_response.ok?
+		assert last_response.body.include?(compound_uri)
+		get uri + '/' + compound_uri + '/features'
+		assert last_response.ok?
+    assert last_response.body.include?("Hamster%20Carcinogenicity/classification/true")
+		delete uri
+		assert last_response.ok?
+		get uri
+		assert !last_response.ok?
 	end
 
+=begin
 	def test_create_large_dataset_from_csv
 		post '/', :name => "Salmonella Mutagenicity", :file => Rack::Test::UploadedFile.new(File.join(File.dirname(__FILE__), "kazius.csv"))
 		uri = last_response.body
@@ -74,7 +87,6 @@ class DatasetsTest < Test::Unit::TestCase
 		assert last_response.ok?
 	end
 
-=begin
 	def test_unauthorized_create
 		post '/', :name => "Test dataset"
 		assert !last_response.ok?