opentox-client 0.0.1pre

data/test/data/multicolumn.csv

@@ -0,0 +1,5 @@
+SMILES, Hamster Carcinogenicity, numeric feature, classification, mixed, string
+c1ccccc1NN                                   , 1, 1, true , true , "test"
+C12C3=C(C=CC=C3)CC1=CC(=CC=2)NC(C)=O         , 1, 2, false, 7.5  , "test"
+O=C(N)\C(C2=CC=CO2)=C/C1=CC=C([N+]([O-])=O)O1, 1, 3, true , 5    , "test"
+C1(N=CNN=1)N                                 , 0, 4, false, false, "test"

data/test/dataset.rb

@@ -0,0 +1,53 @@
+require 'test/unit'
+$LOAD_PATH << File.join(File.dirname(__FILE__),'..','lib')
+require File.join File.dirname(__FILE__),'..','lib','opentox-client.rb'
+
+class DatasetTest < Test::Unit::TestCase
+
+  def test_all
+    datasets = OpenTox::Dataset.all "http://ot-dev.in-silico.ch/dataset"
+    assert_equal OpenTox::Dataset, datasets.first.class
+  end
+
+  def test_create_empty
+    service_uri = "http://ot-dev.in-silico.ch/dataset" 
+    d = OpenTox::Dataset.create service_uri
+    assert_equal OpenTox::Dataset, d.class
+    assert_match /#{service_uri}/, d.uri.to_s
+    d.delete
+  end
+
+  def test_create_from_file
+    d = OpenTox::Dataset.from_file "http://ot-dev.in-silico.ch/dataset", File.join(File.dirname(__FILE__),"data","EPAFHM.mini.csv")
+    assert_equal OpenTox::Dataset, d.class
+    d.delete
+    assert_raise OpenTox::NotFoundError do
+      d.get
+    end
+  end
+
+
+=begin
+  def test_metadata
+    d = OpenTox::Dataset.from_file "http://ot-dev.in-silico.ch/dataset", "data/EPAFHM.mini.csv"
+    assert_equal OpenTox::Dataset, d.class
+    # TODO fix metadata retrieval
+    metadata =  d.metadata
+    assert_equal RDF::OT.Dataset, metadata[RDF.type]
+    assert_equal dataset.uri, metadata[RDF::XSD.anyURI]
+    d.delete
+  end
+  def test_save
+    d = OpenTox::Dataset.create "http://ot-dev.in-silico.ch/dataset"
+    d.metadata
+    d.metadata[RDF::DC.title] = "test"
+    d.save
+    # TODO: save does not work with datasets
+    #puts d.response.code.inspect
+    #assert_equal "test", d.metadata[RDF::DC.title] # should reload metadata
+    d.delete
+  end
+=end
+
+
+end

data/test/error.rb

@@ -0,0 +1,35 @@
+require 'test/unit'
+$LOAD_PATH << File.join(File.dirname(__FILE__),'..','lib')
+require File.join File.dirname(__FILE__),'..','lib','opentox-client.rb'
+
+class ErrorTest < Test::Unit::TestCase
+
+  def test_bad_request
+    object = OpenTox::Feature.new "http://this-is-a/fantasy/url"
+    assert_raise OpenTox::NotFoundError do
+      response = object.get
+    end
+  end
+
+  def test_error_methods
+    assert_raise OpenTox::NotFoundError do
+      not_found_error "This is a test"
+    end
+  end
+
+  def test_exception
+    assert_raise Exception do
+      raise Exception.new "Basic Exception"
+    end
+  end
+
+  def test_backtick
+    assert_raise OpenTox::InternalServerError do
+      `this call will not work`
+    end
+    assert_raise OpenTox::InternalServerError do
+      `ls inexisting_directory`
+    end
+  end
+
+end

data/test/feature.rb

@@ -0,0 +1,36 @@
+require 'test/unit'
+$LOAD_PATH << File.join(File.dirname(__FILE__),'..','lib')
+require File.join File.dirname(__FILE__),'..','lib','opentox-client.rb'
+
+class FeatureTest < Test::Unit::TestCase
+
+  def setup
+    @features = [
+      #@@classification_training_dataset.features.keys.first,
+      "http://apps.ideaconsult.net:8080/ambit2/feature/35796",
+      #File.join(OpenTox::Model::Lazar.all.last,"predicted","value")
+
+    ]
+  end
+
+  def test_feature
+    @features.each do |uri|
+      f = OpenTox::Feature.new(uri)
+      assert_equal [RDF::OT1.TUM_CDK_nAtom], f[RDF::OWL.sameAs]
+      assert_equal RDF::OT1.TUM_CDK_nAtom, f.metadata[RDF::OWL.sameAs].first
+      assert_equal [RDF::OT1.Feature,RDF::OT1.NumericFeature].sort, f[RDF.type].sort
+    end
+  end
+
+=begin
+  def test_owl
+    #@features.each do |uri|
+      validate_owl @features.first, @@subjectid unless CONFIG[:services]["opentox-dataset"].match(/localhost/)
+      validate_owl @features.last, @@subjectid unless CONFIG[:services]["opentox-dataset"].match(/localhost/)
+      # Ambit does not validate
+    #end
+  end
+=end
+
+
+end

data/test/task.rb

@@ -0,0 +1,85 @@
+require 'test/unit'
+$LOAD_PATH << File.join(File.dirname(__FILE__),'..','lib')
+require File.join File.dirname(__FILE__),'..','lib','opentox-client.rb'
+#require "./validate-owl.rb"
+
+TASK_SERVICE_URI = "http://ot-dev.in-silico.ch/task" 
+#TASK_SERVICE_URI = "http://ot-test.in-silico.ch/task" 
+#TASK_SERVICE_URI = "https://ambit.uni-plovdiv.bg:8443/ambit2/task" #not compatible
+
+class TaskTest < Test::Unit::TestCase
+
+
+=begin
+=end
+  def test_all
+    all = OpenTox::Task.all(TASK_SERVICE_URI)
+    assert_equal Array, all.class
+    t = all.last
+    assert_equal OpenTox::Task, t.class
+    assert_equal RDF::OT1.Task, t[RDF.type].first
+  end
+
+  def test_create_and_complete
+    task = OpenTox::Task.create TASK_SERVICE_URI, :description => "test" do
+      sleep 1
+      TASK_SERVICE_URI
+    end
+    assert task.running?
+    assert_equal "Running", task.hasStatus
+    task.wait
+    assert task.completed?
+    assert_equal "Completed", task.hasStatus
+    assert_equal TASK_SERVICE_URI, task.resultURI
+  end
+
+
+  def test_create_and_cancel
+    task = OpenTox::Task.create TASK_SERVICE_URI do
+      sleep 2
+      TASK_SERVICE_URI
+    end
+    assert task.running?
+    task.cancel
+    assert task.cancelled?
+  end
+
+  def test_create_and_fail
+    task = OpenTox::Task.create TASK_SERVICE_URI, :description => "test failure", :creator => "http://test.org/fake_creator" do
+      sleep 0.5
+      raise "A runtime error occured"
+    end
+    assert task.running?
+    assert_equal "Running", task.hasStatus
+    task.wait
+    assert task.error?
+    assert_equal "Error", task.hasStatus
+  end
+
+  def test_create_and_fail_with_opentox_error
+    task = OpenTox::Task.create TASK_SERVICE_URI, :description => "test failure", :creator => "http://test.org/fake_creator" do
+      sleep 0.5
+      raise OpenTox::Error.new 500, "An OpenTox::Error occured"
+    end
+    assert task.running?
+    assert_equal "Running", task.hasStatus
+    task.wait
+    assert task.error?
+    assert_equal "Error", task.hasStatus
+  end
+
+  def test_wrong_result_uri
+    task = OpenTox::Task.create TASK_SERVICE_URI, :description => "test wrong result uri", :creator => "http://test.org/fake_creator" do
+      sleep 0.5
+      "Asasadasd"
+    end
+    assert task.running?
+    assert_equal "Running", task.hasStatus
+    task.wait
+    assert task.error?
+    assert_equal "Error", task.hasStatus
+  end
+=begin
+=end
+
+end

metadata

@@ -0,0 +1,144 @@
+--- !ruby/object:Gem::Specification
+name: opentox-client
+version: !ruby/object:Gem::Version
+  version: 0.0.1pre
+  prerelease: 5
+platform: ruby
+authors:
+- Christoph Helma, Martin Guetlein, Andreas Maunz, Micha Rautenberg, David Vorgrimmler
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-03-09 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &82129140 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: *82129140
+- !ruby/object:Gem::Dependency
+  name: rest-client
+  requirement: &82128400 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: *82128400
+- !ruby/object:Gem::Dependency
+  name: rdf
+  requirement: &82127910 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: *82127910
+- !ruby/object:Gem::Dependency
+  name: rdf-raptor
+  requirement: &82127560 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: *82127560
+- !ruby/object:Gem::Dependency
+  name: open4
+  requirement: &82127200 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: *82127200
+description: Ruby wrapper for the OpenTox REST API (http://www.opentox.org)
+email:
+- helma@in-silico.ch
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- .gitignore
+- Gemfile
+- LICENSE
+- README.markdown
+- Rakefile
+- lib/algorithm.rb
+- lib/authorization.rb
+- lib/compound.rb
+- lib/dataset.rb
+- lib/error.rb
+- lib/model.rb
+- lib/opentox-client.rb
+- lib/opentox.rb
+- lib/otlogger.rb
+- lib/overwrite.rb
+- lib/policy.rb
+- lib/rest-client-wrapper.rb
+- lib/task.rb
+- lib/templates/default_guest_policy.xml
+- lib/templates/default_policy.xml
+- opentox-client.gemspec
+- test/compound.rb
+- test/data/CPDBAS_v5c_1547_29Apr2008part.sdf
+- test/data/EPAFHM.csv
+- test/data/EPAFHM.mini.csv
+- test/data/ISSCAN-multi.csv
+- test/data/cpdb_100.csv
+- test/data/hamster_carcinogenicity.csv
+- test/data/hamster_carcinogenicity.mini.csv
+- test/data/hamster_carcinogenicity.sdf
+- test/data/hamster_carcinogenicity.xls
+- test/data/hamster_carcinogenicity.yaml
+- test/data/hamster_carcinogenicity_with_errors.csv
+- test/data/kazius.csv
+- test/data/multi_cell_call.csv
+- test/data/multicolumn.csv
+- test/dataset.rb
+- test/error.rb
+- test/feature.rb
+- test/task.rb
+homepage: http://github.com/opentox/opentox-client
+licenses:
+- GPL-3
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: -394211199
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>'
+    - !ruby/object:Gem::Version
+      version: 1.3.1
+requirements: []
+rubyforge_project: opentox-client
+rubygems_version: 1.8.11
+signing_key: 
+specification_version: 3
+summary: Ruby wrapper for the OpenTox REST API
+test_files: []