InChI escaping fixed

3 files changed, 45 insertions, 27 deletions

diff --git a/application.rb b/application.rb
index 5c4722c..ad60764 100644
--- a/application.rb
+++ b/application.rb
@@ -20,12 +20,22 @@ set :default_content, :yaml
 helpers do
 
 	def find
-		uri = uri(params[:splat].first)
+		# + charges are dropped
+		uri = uri(params[:splat].first.gsub(/(InChI.*) (.*)/,'\1+\2')) # reinsert dropped '+' signs in InChIs
+		#puts uri
 		halt 404, "Dataset \"#{uri}\" not found." unless @set = Dataset.find(uri)
 	end
 
 	def uri(name)
-		uri = url_for("/dataset/", :full) + URI.encode(name)
+=begin
+		if name =~ /InChI/
+			name = URI.encode(name,/[^#{URI::PATTERN::UNRESERVED}]/)
+		else
+			name = URI.encode(name)
+		end
+=end
+		name = URI.encode(name)
+		uri = url_for("/dataset/", :full) + name
 	end
 
 end
diff --git a/dataset.rb b/dataset.rb
index 435e9dc..5b4f95c 100644
--- a/dataset.rb
+++ b/dataset.rb
@@ -19,6 +19,7 @@ class Dataset
 	end
 
 	def self.find(uri)
+		#puts uri
 		if @@redis.set_member? "datasets", uri
 			Dataset.new(uri)
 		else
@@ -67,8 +68,6 @@ 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/test/test.rb b/test/test.rb
index 8da6c88..b6d9a99 100644
--- a/test/test.rb
+++ b/test/test.rb
@@ -27,7 +27,6 @@ class DatasetsTest < Test::Unit::TestCase
 		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
@@ -37,26 +36,36 @@ class DatasetsTest < Test::Unit::TestCase
 	end
 
 	def test_create_dataset_from_csv
-		smiles = 'CC(=O)Nc1scc(n1)c1ccc(o1)[N+](=O)[O-]'
-		compound = OpenTox::Compound.new(:smiles => smiles)
-		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"
-		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)
-		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
-		assert !last_response.ok?
+		[
+			['F[B-](F)(F)F.[Na+]','false'],
+			['CC(=O)Nc1scc(n1)c1ccc(o1)[N+](=O)[O-]','true'],
+			['NN.OS(=O)(=O)O','true'],
+			['[Cd+2].[O-]S(=O)(=O)[O-]','false']
+		].each do |items|
+			smiles = items[0]
+			activity = items[1]
+
+			compound = OpenTox::Compound.new(:smiles => smiles)
+			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"
+			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)
+			puts last_response.body
+			assert last_response.ok?
+			assert last_response.body.include?("Hamster%20Carcinogenicity/classification/#{activity}")
+			get File.join(uri , 'features')
+			puts last_response.body.to_yaml
+			delete uri
+			assert last_response.ok?
+			get uri
+			assert !last_response.ok?
+		end
 	end
 
 =begin
@@ -74,8 +83,8 @@ class DatasetsTest < Test::Unit::TestCase
 		#@feature_set = OpenTox::Algorithms::Fminer.new :dataset_uri => @dataset
 		name = "Similarity test dataset"
 		data = {
-			'c1ccccc1' =>
-			#'[O-][N+](=O)C/C=C\C(=O)Cc1cc(C#N)ccc1' =>
+			#'c1ccccc1' =>
+			'[O-][N+](=O)C/C=C\C(=O)Cc1cc(C#N)ccc1' =>
 			{
 				'A' => 1.0,
 				'B' => 0.9,