intermediary commit

3 files changed, 146 insertions, 4 deletions

diff --git a/test/hamster_carcinogenicity.csv b/test/hamster_carcinogenicity.csv
new file mode 100644
index 0000000..009808f
--- /dev/null
+++ b/test/hamster_carcinogenicity.csv
@@ -0,0 +1,85 @@
+CC=O,true

+C12C3=C(C=CC=C3)CC1=CC(=CC=2)NC(C)=O,true

+O=C(N)\C(C2=CC=CO2)=C/C1=CC=C([N+]([O-])=O)O1,true

+C1(N=CNN=1)N,false

+Br(=O)(=O)[O-].[K+],true

+[Cl-].[Cd+2].[Cl-],false

+O=S(=O)([O-])[O-].[Cd+2],false

+ClC1=CC(=NC(=N1)SCC(=O)O)NC2=CC=CC(=C2C)C,false

+ClCOC,true

+C=C(Cl)C=C,false

+Clc1ccc(cc1)c2ccc(COC(C)(C)C(O)=O)cc2,false

+O=C1OC2=C(C=CC=C2)C=C1,false

+ClC(=C(C1=CC=C(C=C1)Cl)C2=CC=C(C=C2)Cl)Cl,true

+ClC(C(C1=CC=C(C=C1)Cl)C2=CC=C(C=C2)Cl)(Cl)Cl,false

+C=CCN(CC=C)N=O,true

+Cl\C2=C(/Cl)C3(Cl)C1C4CC(C1C2(Cl)C3(Cl)Cl)C5OC45,false

+O=C(N(C)C)Cl,true

+CN(C)N,true

+N(NC)C.[H]Cl.[H]Cl,true

+CCO,false

+O=C(N(CC)N=O)NCCO,true

+O=C(N(CC)N=O)NCC(=O)C,true

+C=O,false

+[O-][N+](=O)C1=CC=C(O1)C2=CSC(=N2)NNC=O,true

+O=CC1=CC=CO1,false

+OCC1CO1,true

+O=C2C1=C(OC)C=C(OC)C(Cl)=C1O[C@]32C(OC)=CC(C[C@@](C)3[H])=O,false

+ClC1=C(C(=C(C(=C1Cl)Cl)Cl)Cl)Cl,true

+NN,true

+OS(=O)(=O)O.NN,true

+CC(=O)N(O)C1=CC2=C(C=C1)C3=CC=CC=C3C2,true

+OCCNN,false

+O=C(C1=CC=NC=C1)NN,false

+OC(=O)C1=CC=NC=C1,false

+O=C(NC1=CC=CC(=C1)Cl)OC(C)C,false

+O=C(NC1=CC=CC=C1)OC(C)C,false

+[O-]C(C)=O.[O-]C(C)=O.[Pb+2].[OH-].[OH-].[Pb+2].[OH-].[OH-].[Pb+2],false

+CN(C)CCN(CC2=CC=CS2)C1=NC=CC=C1.Cl,false

+NC1=C2C(=NC(=N1)N)N=CC(=N2)CN(C3=CC=C(C=C3)C(=O)N[C@@H](CCC(=O)O)C(=O)O)C,false

+CN(N)C=O,true

+O=C(C(=C)C)OC,false

+CNN,true

+O=C(C1=CC=CN=C1)CCCN(N=O)C,false

+CC1=CC(=O)NC(=S)N1,true

+CC(C(O)=O)(OC1=CC=C(C=C1)C2CCCC3=C2C=CC=C3)C,false

+O=N[O-].[Na+],false

+[O-][N+](C1=CC=C(C2=CSC(NC(C)=O)=N2)O1)=O,true

+[O-][N+](=O)C1=CC=C(O1)C2=CSC(=N2)NC=O,true

+O=[N+](C1=CC=C2C3=C1C=CC=C3CC2)[O-],false

+N(CC(CO)O)(CC(O)C)N=O,true

+N(CC(CO)O)(CC(C)=O)N=O,true

+N(CC(CO)O)(CCO)N=O,false

+O=C(C)CN(N=O)CCO,true

+C1C(N(C(CN1N=O)C)C)C,true

+N(CC(C)=O)(CC=C)N=O,true

+N(CC(CO)O)(C)N=O,true

+O=NN1CCOCC1,true

+N1C=CC=C(C=1)C2N(N=O)CCC2,true

+C1=CC=C(C=[N+]1[O-])C2CCCN2N=O,false

+O=NN1CCCCC1,true

+O=NN1CCCC1,true

+O=C(N(CC(C)=O)N=O)NCCCl,true

+N(C(=O)N)(N=O)CC(C)=O,true

+C1(CCN=C=S)=CC=CC=C1,false

+O=C1C(C2=CC=CC=C2)(C(=O)NC(=O)N1)CC,false

+C1=C2C(=CC=C1NC3=CC=CC=C3)C=CC=C2,false

+O=C1N2C(C3=C(C=CC=C3)CC2)CN(C1)C(=O)C4CCCCC4,false

+C1(=CC(=C(O)C=C1)O)C(O)=O,false

+O=C1C2=C(C=C(C=C2O)O)O/C(=C\1O)C3=CC(=C(C=C3)O)O.O.O,false

+C1=C(C=CC(=C1)C(C2=CC=C(N)C(=C2)C)=C3C=CC(=N)C=C3)N.[H]Cl,false

+C(C1=CC=C(C=C1)N)(C2=CC=C(C=C2)N)=C3C=CC(C=C3)=N.[H]Cl,false

+OC2=CC1=C(C(O)=C2)C(C(O[C@@H]4O[C@@H]([C@H]([C@H](O)[C@H]4O)O)CO[C@H]3[C@H](O)[C@H](O)[C@H]([C@H](C)O3)O)=C(C5=CC(O)=C(C=C5)O)O1)=O,false

+ClC(=CCl)Cl,false

+NC(=O)OCC,true

+C=CCl,true

+N#[N+]C1=CC=CC=C1.F[B-](F)(F)F,false

+C1(CN(CC(N1N=O)C)N=O)C,true

+N(CCN(C)C)(C)N=O,true

+C1(CN(N=O)CC(O1)C)C,true

+O1C(N(CC1C)N=O)=O,true

+CCOC(=O)N(C)N=O,true

+C1N(COC1)N=O,true

+O=C(N(CCC1=CC=CC=C1)N=O)N,true

+O=NN1CCC1,true

+F[B-](F)(F)F.[Na+],false

diff --git a/test/opentox-ruby-api-wrapper_test.rb b/test/opentox-ruby-api-wrapper_test.rb
index 6f7f82e..256a06a 100644
--- a/test/opentox-ruby-api-wrapper_test.rb
+++ b/test/opentox-ruby-api-wrapper_test.rb
@@ -1,7 +1,64 @@
 require 'test_helper'
 
 class OpentoxRubyApiWrapperTest < Test::Unit::TestCase
-  should "probably rename this file and start testing for real" do
-    flunk "hey buddy, you should probably rename this file and start testing for real"
-  end
+
+	def setup
+		@pids = []
+		port = 5000
+		[ "opentox-compound", "opentox-feature" , "opentox-dataset" , "opentox-fminer" , "opentox-lazar" ].each do |component|
+			ENV[component.upcase.gsub(/-/,'_')] = "http://localhost:#{port}/"
+=begin
+			Dir.chdir ENV['HOME'] + '/webservices/' + component
+			Dir["test.sqlite3"].each { |f| FileUtils.rm_rf(f) }
+			file = 'application.rb'
+			@pids << fork {`urxvt -title #{component} -e thin --debug --rackup config.ru start -p #{port} -e test`}
+			Process.detach(@pids.last)
+=end
+			port += 1
+		end
+	end
+
+=begin
+	def teardown
+		@pids.each do |pid|
+			begin
+				Process.kill(9,pid)
+				puts "killed " + pid.to_s
+			rescue
+				puts "failed to kill process" + pid.to_s
+			end
+		end
+	end
+=end
+
+	def test_create_dataset_and_model_and_make_a_prediction
+		#sleep 15
+		dataset = OpenTox::Dataset.new :name => "Hamster Carcinogenicity", :filename => "test/hamster_carcinogenicity.csv"
+		puts dataset.uri
+		wait_for_completion dataset
+		assert_match(/#{ENV['OPENTOX_DATASET']}\d+$/,dataset.uri)
+		assert_equal("Hamster Carcinogenicity",dataset.name)
+		lazar = OpenTox::Lazar.new :dataset_uri => dataset.uri
+		puts lazar.uri
+		wait_for_completion lazar
+		assert_match(/#{ENV['OPENTOX_LAZAR']}model\/\d+$/,lazar.uri)
+		query_structure = OpenTox::Compound.new :smiles => 'c1ccccc1NN'
+		prediction = lazar.predict query_structure
+		puts prediction.uri
+		wait_for_completion prediction
+		puts prediction.to_yaml
+		assert_equal(true, prediction.classification)
+		assert_match(/\d+/, prediction.classification)
+	end
+
+end
+
+def wait_for_completion(object)
+	timeout = 60
+	time = 0 
+	while (!object.finished? and time < timeout)
+		sleep 1
+		time += 1
+	end
+	puts "timeout" if timeout >= 60
 end
diff --git a/test/test_helper.rb b/test/test_helper.rb
index 837ad16..4911cf4 100644
--- a/test/test_helper.rb
+++ b/test/test_helper.rb
@@ -1,9 +1,9 @@
 require 'rubygems'
 require 'test/unit'
-require 'shoulda'
 
 $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
 $LOAD_PATH.unshift(File.dirname(__FILE__))
+
 require 'opentox-ruby-api-wrapper'
 
 class Test::Unit::TestCase