From a5adc95d43368b976d33be3f00068bdd8e4d255c Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Sun, 16 Aug 2009 19:02:00 +0200 Subject: intermediary commit --- Rakefile | 1 - lib/opentox-ruby-api-wrapper.rb | 31 ++++++++++--- opentox-ruby-api-wrapper.gemspec | 6 +-- test/hamster_carcinogenicity.csv | 85 +++++++++++++++++++++++++++++++++++ test/opentox-ruby-api-wrapper_test.rb | 63 ++++++++++++++++++++++++-- test/test_helper.rb | 2 +- 6 files changed, 174 insertions(+), 14 deletions(-) create mode 100644 test/hamster_carcinogenicity.csv diff --git a/Rakefile b/Rakefile index 72eebcf..5d13273 100644 --- a/Rakefile +++ b/Rakefile @@ -11,7 +11,6 @@ begin gem.homepage = "http://github.com/helma/opentox-ruby-api-wrapper" gem.authors = ["Christoph Helma"] gem.add_dependency "rest-client" - gem.add_development_dependency "thoughtbot-shoulda" # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings end rescue LoadError diff --git a/lib/opentox-ruby-api-wrapper.rb b/lib/opentox-ruby-api-wrapper.rb index 81a7292..001c9ac 100644 --- a/lib/opentox-ruby-api-wrapper.rb +++ b/lib/opentox-ruby-api-wrapper.rb @@ -1,4 +1,3 @@ - #['rubygems', 'rest_client', 'spork', 'helper' ].each do |lib| ['rubygems', 'rest_client', 'spork' ].each do |lib| require lib @@ -8,7 +7,7 @@ ENV['OPENTOX_COMPOUND'] = 'http://webservices.in-silico.ch/compound/v0/' unless ENV['OPENTOX_FEATURE'] = 'http://webservices.in-silico.ch/feature/v0/' unless ENV['OPENTOX_FEATURE'] ENV['OPENTOX_DATASET'] = 'http://webservices.in-silico.ch/dataset/v0/' unless ENV['OPENTOX_DATASET'] ENV['OPENTOX_FMINER'] = 'http://webservices.in-silico.ch/fminer/v0/' unless ENV['OPENTOX_FMINER'] -ENV['OPENTOX_LAZAR'] = 'http://webservices.in-silico.ch/lazar/v0/' unless ENV['OPENTOX_LAZAR'] +ENV['OPENTOX_LAZAR'] = 'http://webservices.in-silico.ch/lazar/v0/' unless ENV['OPENTOX_LAZAR'] module OpenTox @@ -19,6 +18,20 @@ module OpenTox def uri_escape(string) URI.escape(string, /[^\w]/) end + + def finished? + YAML.load(RestClient.get(@uri))[:finished] + end + + def finished + print "closing " + puts @uri + '/finished' + RestClient.post @uri + '/finished' + end + + def destroy + RestClient.delete @uri + end end class Compound < OpenTox @@ -87,11 +100,19 @@ module OpenTox def initialize(params) if params[:uri] @uri = params[:uri].to_s - elsif params[:name] + elsif params[:name] and params[:filename] + @uri = `curl -X POST -F file=@#{params[:filename]} -F name="#{params[:name]}" #{ENV['OPENTOX_DATASET']}` + elsif params[:name] @uri = RestClient.post ENV['OPENTOX_DATASET'], :name => params[:name] end end + def finished + print "closing " + puts @uri + '/finished' + RestClient.post(@uri + '/finished',nil) + end + # Get the dataset name def name RestClient.get @uri + '/name' @@ -143,8 +164,8 @@ module OpenTox def initialize(params) if params[:uri] @uri = params[:uri] - elsif params[:dataset_ur] - @uri = RestClient.post ENV['OPENTOX_LAZAR'] + 'models/' , :dataset_uri => training_dataset.uri + elsif params[:dataset_uri] + @uri = RestClient.post ENV['OPENTOX_LAZAR'] + 'models' , :dataset_uri => params[:dataset_uri] end end diff --git a/opentox-ruby-api-wrapper.gemspec b/opentox-ruby-api-wrapper.gemspec index a583120..0e5ab5e 100644 --- a/opentox-ruby-api-wrapper.gemspec +++ b/opentox-ruby-api-wrapper.gemspec @@ -9,7 +9,7 @@ Gem::Specification.new do |s| s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version= s.authors = ["Christoph Helma"] - s.date = %q{2009-08-15} + s.date = %q{2009-08-16} s.description = %q{Ruby wrapper for the OpenTox REST API (http://www.opentox.org)} s.email = %q{helma@in-silico.ch} s.extra_rdoc_files = [ @@ -27,6 +27,7 @@ Gem::Specification.new do |s| "lib/opentox-ruby-api-wrapper.rb", "lib/spork.rb", "opentox-ruby-api-wrapper.gemspec", + "test/hamster_carcinogenicity.csv", "test/opentox-ruby-api-wrapper_test.rb", "test/test_helper.rb" ] @@ -46,13 +47,10 @@ Gem::Specification.new do |s| if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then s.add_runtime_dependency(%q, [">= 0"]) - s.add_development_dependency(%q, [">= 0"]) else s.add_dependency(%q, [">= 0"]) - s.add_dependency(%q, [">= 0"]) end else s.add_dependency(%q, [">= 0"]) - s.add_dependency(%q, [">= 0"]) end end 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 -- cgit v1.2.3