opentox-client 0.0.2pre → 1.0.0pre1

data/test/data/multicolumn.csv

@@ -1,5 +0,0 @@
-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

@@ -1,99 +0,0 @@
-require 'test/unit'
-$LOAD_PATH << File.join(File.dirname(__FILE__),'..','lib')
-require File.join File.dirname(__FILE__),'..','lib','opentox-client.rb'
-DATASET = "http://ot-dev.in-silico.ch/dataset"
-AA ||= "https://opensso.in-silico.ch"
-AA_USER = "guest"
-AA_PASS = "guest"
-@@subjectid = OpenTox::Authorization.authenticate(AA_USER,AA_PASS)
-
-DATA_DIR = File.join(File.dirname(__FILE__),"data")
-# TODO: add subjectids
-
-
-class DatasetTest < Test::Unit::TestCase
-
-  def test_all
-    puts @@subjectid
-    datasets = OpenTox::Dataset.all(DATASET, @@subjectid)
-    assert_equal OpenTox::Dataset, datasets.first.class
-  end
-
-  def test_create_empty
-    d = OpenTox::Dataset.create(DATASET, @@subjectid)
-    assert_equal OpenTox::Dataset, d.class
-    assert_match /#{DATASET}/, d.uri.to_s
-    d.delete
-  end
-
-  def test_create_from_file
-    d = OpenTox::Dataset.from_file DATASET, File.join(DATA_DIR,"EPAFHM.mini.csv"), @@subjectid
-    assert_equal OpenTox::Dataset, d.class
-    assert_equal d.uri, d[RDF::XSD.anyURI]
-    assert_equal "EPAFHM.mini",  d.metadata[RDF::URI("http://purl.org/dc/elements/1.1/title")].first.to_s # DC.title is http://purl.org/dc/terms/title
-    assert_equal "EPAFHM.mini",  d[RDF::URI("http://purl.org/dc/elements/1.1/title")]
-    d.delete
-    assert_raise OpenTox::NotFoundError do
-      d.get
-    end
-  end
-
-  def test_from_yaml
-    @dataset = OpenTox::Dataset.from_file DATASET, File.join(DATA_DIR,"hamster_carcinogenicity.yaml"), @@subjectid
-    assert_equal OpenTox::Dataset, @dataset.class
-    assert_equal "hamster_carcinogenicity", @dataset[RDF::URI("http://purl.org/dc/elements/1.1/title")]
-    hamster_carc?
-    @dataset.delete
-  end
-
-=begin
-# TODO: fix (mime type??0 and add Egons example
-  def test_sdf_with_multiple_features
-    @dataset = OpenTox::Dataset.from_file DATASET, "#{DATA_DIR}/CPDBAS_v5c_1547_29Apr2008part.sdf"
-    assert_equal OpenTox::Dataset, @dataset.class
-    puts @dataset.features.size
-    puts @dataset.compounds.size
-    @dataset.delete
-  end
-=end
-
-  def test_multicolumn_csv
-    @dataset = OpenTox::Dataset.from_file DATASET, "#{DATA_DIR}/multicolumn.csv", @@subjectid
-    assert_equal 5, @dataset.features.size
-    assert_equal 4, @dataset.compounds.size
-    @dataset.delete
-  end
-
-  def test_from_csv
-    @dataset = OpenTox::Dataset.from_file DATASET, "#{DATA_DIR}/hamster_carcinogenicity.csv", @@subjectid
-    assert_equal OpenTox::Dataset, @dataset.class
-    hamster_carc?
-    @dataset.delete
-  end
-
-=begin
-  def test_save
-    d = OpenTox::Dataset.create 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
-=begin
-=end
-
-
-  def hamster_carc?
-    assert_kind_of OpenTox::Dataset, @dataset
-    #require 'yaml'
-    #puts @dataset.data_entries.to_yaml
-    assert_equal 85, @dataset.data_entries.size
-    assert_equal 85, @dataset.compounds.size
-    assert_equal 1, @dataset.features.size
-    assert_equal @dataset.uri, @dataset[RDF::XSD.anyURI]
-  end
-end

data/test/error.rb

@@ -1,35 +0,0 @@
-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

@@ -1,36 +0,0 @@
-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.to_s
-      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/policy.rb

@@ -1,120 +0,0 @@
-require 'test/unit'
-$LOAD_PATH << File.join(File.dirname(__FILE__),'..','lib')
-require File.expand_path(File.join(File.dirname(__FILE__),'..','lib','opentox-client.rb'))
-
-TEST_URI    = "http://only_a_test/test/" + rand(1000000).to_s
-USER_TYPE   = "LDAPUsers"
-USER_VALUE  = "uid=guest,ou=people,dc=opentox,dc=org"
-USER_GROUP  = "member"
-GROUP_TYPE  = "LDAPGroups"
-GROUP_VALUE = "cn=member,ou=groups,dc=opentox,dc=org"
-POLICY_NAME = "test_policy_#{rand(100000)}"
-RULE_NAME = "test_rule_#{rand(100000)}"
-SUBJECT_NAME = "test_subject_#{rand(100000)}"
-
-AA ||= "https://opensso.in-silico.ch"
-AA_USER = "guest"
-AA_PASS = "guest"
-
-@@subjectid = OpenTox::Authorization.authenticate(AA_USER,AA_PASS)
-
-class PolicyTest < Test::Unit::TestCase
-
-  def test_01_class
-    policies = OpenTox::Policies.new()
-    assert_equal(policies.class, OpenTox::Policies)
-    assert_kind_of Array, policies.names
-    assert_kind_of Array, policies.uris
-    assert_kind_of Array, policies.names
-  end
-
-  def test_02_subclasses
-    policies = OpenTox::Policies.new()
-    policies.new_policy(POLICY_NAME)
-    assert_equal(policies.names[0], POLICY_NAME)
-    assert_equal(policies.policies[policies.names[0]].class, OpenTox::Policy)
-    policy = policies.policies[policies.names[0]]
-    policy.rule.name = RULE_NAME
-    policy.uri = TEST_URI
-    assert_equal(policy.rule.class, OpenTox::Policy::Rule)
-    assert_equal(policy.rule.name, RULE_NAME)
-    assert_equal(policy.rule.uri, TEST_URI)
-    assert_equal(policy.uri, TEST_URI)
-    policy.subject.name = SUBJECT_NAME
-    policy.type = USER_TYPE
-    policy.value = USER_VALUE
-    assert_equal(policy.subject.class, OpenTox::Policy::Subject)
-    assert_equal(policy.subject.name, SUBJECT_NAME)
-    assert_equal(policy.subject.type, USER_TYPE)
-    assert_equal(policy.type, USER_TYPE)
-    assert_equal(policy.subject.value, USER_VALUE)
-    assert_equal(policy.value, USER_VALUE)
-  end
-
-  def test_03_read_readwrite
-    policies = OpenTox::Policies.new()
-    policies.new_policy(POLICY_NAME)
-    policy = policies.policies[policies.names[0]]
-    policy.rule.name = RULE_NAME
-    policy.uri = TEST_URI
-    policy.rule.get = "allow"
-    assert policy.rule.read
-    assert !policy.rule.readwrite
-    policy.rule.post = "allow"
-    policy.rule.put = "allow"
-    assert !policy.rule.read
-    assert policy.rule.readwrite
-  end
-
-  def test_04_group_user
-    policies = OpenTox::Policies.new()
-    policies.load_default_policy(AA_USER, TEST_URI, "member")
-    assert_equal "member", policies.policies["policy_group"].group
-    assert_equal AA_USER, policies.policies["policy_user"].user
-  end
-
-  def test_05_DN
-    policies = OpenTox::Policies.new()
-    policies.new_policy(POLICY_NAME)
-    policy = policies.policies[policies.names[0]]
-    policy.set_ot_user(AA_USER)
-    assert_equal USER_VALUE, policy.value
-    assert_equal USER_TYPE, policy.type
-    policy.set_ot_group(USER_GROUP)
-    assert_equal GROUP_VALUE, policy.value
-    assert_equal GROUP_TYPE, policy.type
-  end
-
-  def test_06_load_xml_and_check_defaults
-    policies = OpenTox::Policies.new()
-    xml = File.read(File.join(File.dirname(__FILE__), "../lib/templates/default_policy.xml"))
-    policies.load_xml(xml)
-    # check user policy
-    policy = policies.policies["policy_user"]
-    assert policy.name == "policy_user"
-    assert policy.rule.name == "rule_user"
-    assert policy.rule.uri == "uri"
-    assert policy.rule.get == "allow"
-    assert policy.rule.post == "allow"
-    assert policy.rule.delete == "allow"
-    assert policy.rule.put == "allow"
-    assert policy.subject_group == "subjects_user"
-    assert policy.subject.name == "subject_user"
-    assert policy.subject.type == USER_TYPE
-    assert policy.subject.value == USER_VALUE
-    # check group policy
-    policy = policies.policies["policy_group"]
-    assert policy.name == "policy_group"
-    assert policy.rule.name == "rule_group"
-    assert policy.rule.uri == "uri"
-    assert policy.rule.get == "allow"
-    assert !policy.rule.post
-    assert !policy.rule.delete
-    assert !policy.rule.put
-    assert policy.subject_group == "subjects_group"
-    assert policy.subject.name == "subject_group"
-    assert policy.subject.type == GROUP_TYPE
-    assert policy.subject.value == GROUP_VALUE
-  end
-
-end

data/test/task.rb

@@ -1,85 +0,0 @@
-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]
-  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 1
-      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 1
-      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
-
-=begin
-  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 1
-      "Asasadasd"
-    end
-    assert task.running?
-    assert_equal "Running", task.hasStatus
-    task.wait
-    assert task.error?
-    assert_equal "Error", task.hasStatus
-  end
-=end
-
-end