opentox-client 0.0.1pre

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+ SMILES, Hamster Carcinogenicity, numeric feature, classification, mixed, string
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+ c1ccccc1NN , 1, 1, true , true , "test"
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+ C12C3=C(C=CC=C3)CC1=CC(=CC=2)NC(C)=O , 1, 2, false, 7.5 , "test"
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+ O=C(N)\C(C2=CC=CO2)=C/C1=CC=C([N+]([O-])=O)O1, 1, 3, true , 5 , "test"
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+ C1(N=CNN=1)N , 0, 4, false, false, "test"
data/test/dataset.rb ADDED
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+ require 'test/unit'
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+ $LOAD_PATH << File.join(File.dirname(__FILE__),'..','lib')
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+ require File.join File.dirname(__FILE__),'..','lib','opentox-client.rb'
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+
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+ class DatasetTest < Test::Unit::TestCase
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+
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+ def test_all
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+ datasets = OpenTox::Dataset.all "http://ot-dev.in-silico.ch/dataset"
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+ assert_equal OpenTox::Dataset, datasets.first.class
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+ end
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+
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+ def test_create_empty
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+ service_uri = "http://ot-dev.in-silico.ch/dataset"
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+ d = OpenTox::Dataset.create service_uri
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+ assert_equal OpenTox::Dataset, d.class
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+ assert_match /#{service_uri}/, d.uri.to_s
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+ d.delete
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+ end
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+
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+ def test_create_from_file
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+ d = OpenTox::Dataset.from_file "http://ot-dev.in-silico.ch/dataset", File.join(File.dirname(__FILE__),"data","EPAFHM.mini.csv")
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+ assert_equal OpenTox::Dataset, d.class
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+ d.delete
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+ assert_raise OpenTox::NotFoundError do
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+ d.get
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+ end
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+ end
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+
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+
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+ =begin
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+ def test_metadata
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+ d = OpenTox::Dataset.from_file "http://ot-dev.in-silico.ch/dataset", "data/EPAFHM.mini.csv"
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+ assert_equal OpenTox::Dataset, d.class
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+ # TODO fix metadata retrieval
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+ metadata = d.metadata
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+ assert_equal RDF::OT.Dataset, metadata[RDF.type]
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+ assert_equal dataset.uri, metadata[RDF::XSD.anyURI]
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+ d.delete
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+ end
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+ def test_save
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+ d = OpenTox::Dataset.create "http://ot-dev.in-silico.ch/dataset"
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+ d.metadata
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+ d.metadata[RDF::DC.title] = "test"
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+ d.save
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+ # TODO: save does not work with datasets
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+ #puts d.response.code.inspect
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+ #assert_equal "test", d.metadata[RDF::DC.title] # should reload metadata
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+ d.delete
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+ end
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+ =end
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+
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+
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+ end
data/test/error.rb ADDED
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+ require 'test/unit'
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+ $LOAD_PATH << File.join(File.dirname(__FILE__),'..','lib')
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+ require File.join File.dirname(__FILE__),'..','lib','opentox-client.rb'
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+
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+ class ErrorTest < Test::Unit::TestCase
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+
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+ def test_bad_request
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+ object = OpenTox::Feature.new "http://this-is-a/fantasy/url"
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+ assert_raise OpenTox::NotFoundError do
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+ response = object.get
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+ end
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+ end
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+
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+ def test_error_methods
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+ assert_raise OpenTox::NotFoundError do
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+ not_found_error "This is a test"
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+ end
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+ end
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+
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+ def test_exception
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+ assert_raise Exception do
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+ raise Exception.new "Basic Exception"
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+ end
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+ end
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+
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+ def test_backtick
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+ assert_raise OpenTox::InternalServerError do
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+ `this call will not work`
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+ end
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+ assert_raise OpenTox::InternalServerError do
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+ `ls inexisting_directory`
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+ end
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+ end
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+
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+ end
data/test/feature.rb ADDED
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+ require 'test/unit'
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+ $LOAD_PATH << File.join(File.dirname(__FILE__),'..','lib')
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+ require File.join File.dirname(__FILE__),'..','lib','opentox-client.rb'
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+
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+ class FeatureTest < Test::Unit::TestCase
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+
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+ def setup
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+ @features = [
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+ #@@classification_training_dataset.features.keys.first,
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+ "http://apps.ideaconsult.net:8080/ambit2/feature/35796",
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+ #File.join(OpenTox::Model::Lazar.all.last,"predicted","value")
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+
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+ ]
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+ end
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+
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+ def test_feature
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+ @features.each do |uri|
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+ f = OpenTox::Feature.new(uri)
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+ assert_equal [RDF::OT1.TUM_CDK_nAtom], f[RDF::OWL.sameAs]
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+ assert_equal RDF::OT1.TUM_CDK_nAtom, f.metadata[RDF::OWL.sameAs].first
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+ assert_equal [RDF::OT1.Feature,RDF::OT1.NumericFeature].sort, f[RDF.type].sort
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+ end
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+ end
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+
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+ =begin
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+ def test_owl
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+ #@features.each do |uri|
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+ validate_owl @features.first, @@subjectid unless CONFIG[:services]["opentox-dataset"].match(/localhost/)
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+ validate_owl @features.last, @@subjectid unless CONFIG[:services]["opentox-dataset"].match(/localhost/)
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+ # Ambit does not validate
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+ #end
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+ end
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+ =end
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+
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+
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+ end
data/test/task.rb ADDED
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+ require 'test/unit'
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+ $LOAD_PATH << File.join(File.dirname(__FILE__),'..','lib')
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+ require File.join File.dirname(__FILE__),'..','lib','opentox-client.rb'
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+ #require "./validate-owl.rb"
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+
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+ TASK_SERVICE_URI = "http://ot-dev.in-silico.ch/task"
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+ #TASK_SERVICE_URI = "http://ot-test.in-silico.ch/task"
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+ #TASK_SERVICE_URI = "https://ambit.uni-plovdiv.bg:8443/ambit2/task" #not compatible
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+
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+ class TaskTest < Test::Unit::TestCase
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+
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+
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+ =begin
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+ =end
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+ def test_all
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+ all = OpenTox::Task.all(TASK_SERVICE_URI)
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+ assert_equal Array, all.class
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+ t = all.last
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+ assert_equal OpenTox::Task, t.class
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+ assert_equal RDF::OT1.Task, t[RDF.type].first
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+ end
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+
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+ def test_create_and_complete
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+ task = OpenTox::Task.create TASK_SERVICE_URI, :description => "test" do
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+ sleep 1
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+ TASK_SERVICE_URI
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+ end
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+ assert task.running?
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+ assert_equal "Running", task.hasStatus
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+ task.wait
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+ assert task.completed?
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+ assert_equal "Completed", task.hasStatus
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+ assert_equal TASK_SERVICE_URI, task.resultURI
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+ end
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+
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+
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+ def test_create_and_cancel
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+ task = OpenTox::Task.create TASK_SERVICE_URI do
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+ sleep 2
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+ TASK_SERVICE_URI
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+ end
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+ assert task.running?
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+ task.cancel
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+ assert task.cancelled?
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+ end
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+
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+ def test_create_and_fail
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+ task = OpenTox::Task.create TASK_SERVICE_URI, :description => "test failure", :creator => "http://test.org/fake_creator" do
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+ sleep 0.5
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+ raise "A runtime error occured"
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+ end
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+ assert task.running?
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+ assert_equal "Running", task.hasStatus
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+ task.wait
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+ assert task.error?
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+ assert_equal "Error", task.hasStatus
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+ end
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+
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+ def test_create_and_fail_with_opentox_error
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+ task = OpenTox::Task.create TASK_SERVICE_URI, :description => "test failure", :creator => "http://test.org/fake_creator" do
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+ sleep 0.5
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+ raise OpenTox::Error.new 500, "An OpenTox::Error occured"
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+ end
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+ assert task.running?
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+ assert_equal "Running", task.hasStatus
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+ task.wait
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+ assert task.error?
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+ assert_equal "Error", task.hasStatus
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+ end
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+
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+ def test_wrong_result_uri
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+ task = OpenTox::Task.create TASK_SERVICE_URI, :description => "test wrong result uri", :creator => "http://test.org/fake_creator" do
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+ sleep 0.5
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+ "Asasadasd"
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+ end
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+ assert task.running?
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+ assert_equal "Running", task.hasStatus
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+ task.wait
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+ assert task.error?
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+ assert_equal "Error", task.hasStatus
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+ end
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+ =begin
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+ =end
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+
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+ end
metadata ADDED
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+ --- !ruby/object:Gem::Specification
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+ name: opentox-client
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+ version: !ruby/object:Gem::Version
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+ version: 0.0.1pre
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+ prerelease: 5
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+ platform: ruby
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+ authors:
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+ - Christoph Helma, Martin Guetlein, Andreas Maunz, Micha Rautenberg, David Vorgrimmler
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+ autorequire:
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+ bindir: bin
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+ cert_chain: []
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+ date: 2012-03-09 00:00:00.000000000 Z
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: bundler
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+ requirement: &82129140 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: *82129140
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+ - !ruby/object:Gem::Dependency
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+ name: rest-client
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+ requirement: &82128400 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: *82128400
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+ - !ruby/object:Gem::Dependency
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+ name: rdf
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+ requirement: &82127910 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: *82127910
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+ - !ruby/object:Gem::Dependency
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+ name: rdf-raptor
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+ requirement: &82127560 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: *82127560
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+ - !ruby/object:Gem::Dependency
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+ name: open4
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+ requirement: &82127200 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: *82127200
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+ description: Ruby wrapper for the OpenTox REST API (http://www.opentox.org)
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+ email:
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+ - helma@in-silico.ch
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+ executables: []
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+ extensions: []
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+ extra_rdoc_files: []
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+ files:
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+ - .gitignore
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+ - Gemfile
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+ - LICENSE
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+ - README.markdown
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+ - Rakefile
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+ - lib/algorithm.rb
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+ - lib/authorization.rb
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+ - lib/compound.rb
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+ - lib/dataset.rb
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+ - lib/error.rb
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+ - lib/model.rb
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+ - lib/opentox-client.rb
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+ - lib/opentox.rb
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+ - lib/otlogger.rb
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+ - lib/overwrite.rb
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+ - lib/policy.rb
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+ - lib/rest-client-wrapper.rb
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+ - lib/task.rb
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+ - lib/templates/default_guest_policy.xml
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+ - lib/templates/default_policy.xml
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+ - opentox-client.gemspec
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+ - test/compound.rb
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+ - test/data/CPDBAS_v5c_1547_29Apr2008part.sdf
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+ - test/data/EPAFHM.csv
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+ - test/data/EPAFHM.mini.csv
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+ - test/data/ISSCAN-multi.csv
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+ - test/data/cpdb_100.csv
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+ - test/data/hamster_carcinogenicity.csv
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+ - test/data/hamster_carcinogenicity.mini.csv
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+ - test/data/hamster_carcinogenicity.sdf
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+ - test/data/hamster_carcinogenicity.xls
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+ - test/data/hamster_carcinogenicity.yaml
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+ - test/data/hamster_carcinogenicity_with_errors.csv
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+ - test/data/kazius.csv
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+ - test/data/multi_cell_call.csv
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+ - test/data/multicolumn.csv
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+ - test/dataset.rb
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+ - test/error.rb
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+ - test/feature.rb
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+ - test/task.rb
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+ homepage: http://github.com/opentox/opentox-client
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+ licenses:
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+ - GPL-3
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+ post_install_message:
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+ rdoc_options: []
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+ require_paths:
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+ - lib
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+ required_ruby_version: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ segments:
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+ - 0
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+ hash: -394211199
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+ required_rubygems_version: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>'
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+ - !ruby/object:Gem::Version
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+ version: 1.3.1
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+ requirements: []
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+ rubyforge_project: opentox-client
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+ rubygems_version: 1.8.11
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+ signing_key:
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+ specification_version: 3
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+ summary: Ruby wrapper for the OpenTox REST API
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+ test_files: []