From 5d5688fbe43806af8523e5481715b5969feeab60 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Tue, 6 Oct 2009 10:39:43 +0200 Subject: Passes tests in opentox-test --- test/hamster_carcinogenicity.csv | 85 ----------------------------------- test/opentox-ruby-api-wrapper_test.rb | 47 ------------------- test/start-local-webservices.rb | 13 ------ test/test_helper.rb | 10 ----- 4 files changed, 155 deletions(-) delete mode 100644 test/hamster_carcinogenicity.csv delete mode 100644 test/opentox-ruby-api-wrapper_test.rb delete mode 100755 test/start-local-webservices.rb delete mode 100644 test/test_helper.rb (limited to 'test') diff --git a/test/hamster_carcinogenicity.csv b/test/hamster_carcinogenicity.csv deleted file mode 100644 index 009808f..0000000 --- a/test/hamster_carcinogenicity.csv +++ /dev/null @@ -1,85 +0,0 @@ -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 deleted file mode 100644 index 0a394e2..0000000 --- a/test/opentox-ruby-api-wrapper_test.rb +++ /dev/null @@ -1,47 +0,0 @@ -require File.join(File.dirname(__FILE__), 'test_helper.rb') - -class OpentoxRubyApiWrapperTest < Test::Unit::TestCase - - def setup - if ENV['LOCAL'] - port = 5000 - [ "opentox-compound", "opentox-feature" , "opentox-dataset" , "opentox-fminer" , "opentox-lazar" ].each do |component| - ENV[component.upcase.gsub(/-/,'_')] = "http://localhost:#{port}/" - port += 1 - end - end - ENV['OPENTOX'] = "test" - end - - def test_create_dataset_and_model_and_make_a_prediction - 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+$/,dataset.uri) - assert_equal("Hamster Carcinogenicity",dataset.name) - assert_equal(true,dataset.finished?) - lazar = OpenTox::Lazar.new :dataset_uri => dataset.uri - puts lazar.uri - wait_for_completion lazar - assert_equal(true,lazar.finished?) - assert_match(/#{ENV['OPENTOX_LAZAR']}model\/\d+$/,lazar.uri) - query_structure = OpenTox::Compound.new :smiles => 'c1ccccc1NN' - puts query_structure.uri - prediction = lazar.predict query_structure - puts prediction.uri - wait_for_completion prediction - puts prediction.classification - puts prediction.confidence - puts prediction.neighbors - puts prediction.features - assert_equal(true, prediction.classification) - assert_match(/0\.\d+/, prediction.confidence.to_s) - end - -end - -def wait_for_completion(object) - while (!object.finished?) - sleep 1 - end -end diff --git a/test/start-local-webservices.rb b/test/start-local-webservices.rb deleted file mode 100755 index 66dea29..0000000 --- a/test/start-local-webservices.rb +++ /dev/null @@ -1,13 +0,0 @@ -#!/usr/bin/env ruby -require 'fileutils' - -port = 5000 -[ "opentox-compound", "opentox-feature" , "opentox-dataset" , "opentox-fminer" , "opentox-lazar" ].each do |component| - ENV[component.upcase.gsub(/-/,'_')] = "http://localhost:#{port}/" - Dir.chdir ENV['HOME'] + '/webservices/' + component - Dir["test.sqlite3"].each { |f| FileUtils.rm_rf(f) } - file = 'application.rb' - pid = fork {`urxvt -title #{component} -e thin --debug --rackup config.ru start -p #{port} -e test`} - Process.detach(pid) - port += 1 -end diff --git a/test/test_helper.rb b/test/test_helper.rb deleted file mode 100644 index 4911cf4..0000000 --- a/test/test_helper.rb +++ /dev/null @@ -1,10 +0,0 @@ -require 'rubygems' -require 'test/unit' - -$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib')) -$LOAD_PATH.unshift(File.dirname(__FILE__)) - -require 'opentox-ruby-api-wrapper' - -class Test::Unit::TestCase -end -- cgit v1.2.3