opentox-client 0.0.1pre → 0.0.2pre

data/test/authorization.rb

@@ -0,0 +1,107 @@
+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
+AA ||= "https://opensso.in-silico.ch"
+AA_USER = "guest"
+AA_PASS = "guest"
+@@subjectid = OpenTox::Authorization.authenticate(AA_USER,AA_PASS)
+
+class TestOpenToxAuthorizationBasic < Test::Unit::TestCase
+ 
+  def test_01_server
+    assert_equal(AA, OpenTox::Authorization.server)
+  end
+ 
+  def test_02_get_token
+    assert_not_nil @@subjectid
+  end
+  
+  def test_03_is_valid_token
+    tok = login
+    assert_not_nil tok
+    assert OpenTox::Authorization.is_token_valid(tok)
+    logout(tok)
+  end
+  
+  def test_04_logout
+    tok = login
+    assert logout(tok)
+    assert_equal false, OpenTox::Authorization.is_token_valid(tok)
+  end
+  
+  def test_05_list_policies
+    assert_kind_of Array, OpenTox::Authorization.list_policies(@@subjectid)
+  end
+  
+end
+
+class TestOpenToxAuthorizationLDAP < Test::Unit::TestCase
+
+  def test_01_list_user_groups
+    assert_kind_of Array, OpenTox::Authorization.list_user_groups(AA_USER, @@subjectid)
+  end
+  
+  def test_02_get_user
+    assert_equal AA_USER, OpenTox::Authorization.get_user(@@subjectid)
+  end
+
+end
+
+class TestOpenToxAuthorizationLDAP < Test::Unit::TestCase
+
+  def test_01_create_check_delete_default_policies
+    res = OpenTox::Authorization.send_policy(TEST_URI, @@subjectid)
+    assert res
+    assert OpenTox::Authorization.uri_has_policy(TEST_URI, @@subjectid)
+    policies = OpenTox::Authorization.list_uri_policies(TEST_URI, @@subjectid)
+    assert_kind_of Array, policies
+    policies.each do |policy|
+      assert OpenTox::Authorization.delete_policy(policy, @@subjectid)
+    end
+    assert_equal false, OpenTox::Authorization.uri_has_policy(TEST_URI, @@subjectid)
+  end
+
+  def test_02_check_policy_rules
+    tok_anonymous = OpenTox::Authorization.authenticate("anonymous","anonymous")
+    assert_not_nil tok_anonymous
+    res = OpenTox::Authorization.send_policy(TEST_URI, @@subjectid)
+    assert res
+    assert OpenTox::Authorization.uri_has_policy(TEST_URI, @@subjectid)
+    owner_rights = {"GET" => true, "POST" => true, "PUT" => true, "DELETE" => true}
+    groupmember_rights = {"GET" => true, "POST" => nil, "PUT" => nil, "DELETE" => nil}
+    owner_rights.each do |request, right|
+      assert_equal right, OpenTox::Authorization.authorize(TEST_URI, request, @@subjectid), "#{AA_USER} requests #{request} to #{TEST_URI}"
+    end
+    groupmember_rights.each do |request, r|
+      assert_equal r, OpenTox::Authorization.authorize(TEST_URI, request, tok_anonymous), "anonymous requests #{request} to #{TEST_URI}"
+    end
+    
+    policies = OpenTox::Authorization.list_uri_policies(TEST_URI, @@subjectid)
+    assert_kind_of Array, policies
+    policies.each do |policy|
+      assert OpenTox::Authorization.delete_policy(policy, @@subjectid)
+    end
+    logout(tok_anonymous)
+  end
+
+  def test_03_check_different_uris
+    res = OpenTox::Authorization.send_policy(TEST_URI, @@subjectid)
+    assert OpenTox::Authorization.uri_has_policy(TEST_URI, @@subjectid)
+    assert OpenTox::Authorization.authorize(TEST_URI, "GET", @@subjectid), "GET request"
+    policies = OpenTox::Authorization.list_uri_policies(TEST_URI, @@subjectid)
+    policies.each do |policy|
+      assert OpenTox::Authorization.delete_policy(policy, @@subjectid)
+    end
+ 
+  end  
+end
+
+
+def logout (token)
+   OpenTox::Authorization.logout(token)
+end
+
+def login
+  OpenTox::Authorization.authenticate(AA_USER,AA_PASS)
+end 

data/test/dataset.rb

@@ -1,44 +1,79 @@
 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
-    datasets = OpenTox::Dataset.all "http://ot-dev.in-silico.ch/dataset"
+    puts @@subjectid
+    datasets = OpenTox::Dataset.all(DATASET, @@subjectid)
     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
+    d = OpenTox::Dataset.create(DATASET, @@subjectid)
     assert_equal OpenTox::Dataset, d.class
-    assert_match /#{service_uri}/, d.uri.to_s
+    assert_match /#{DATASET}/, 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")
+    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
-  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
+# 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 "http://ot-dev.in-silico.ch/dataset"
+    d = OpenTox::Dataset.create DATASET
     d.metadata
     d.metadata[RDF::DC.title] = "test"
     d.save
@@ -48,6 +83,17 @@ class DatasetTest < Test::Unit::TestCase
     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/feature.rb

@@ -16,8 +16,8 @@ class FeatureTest < Test::Unit::TestCase
   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.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

data/test/policy.rb

@@ -0,0 +1,120 @@
+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

@@ -17,7 +17,7 @@ class TaskTest < Test::Unit::TestCase
     assert_equal Array, all.class
     t = all.last
     assert_equal OpenTox::Task, t.class
-    assert_equal RDF::OT1.Task, t[RDF.type].first
+    assert_equal RDF::OT1.Task, t[RDF.type]
   end
 
   def test_create_and_complete
@@ -46,7 +46,7 @@ class TaskTest < Test::Unit::TestCase
 
   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
+      sleep 1
       raise "A runtime error occured"
     end
     assert task.running?
@@ -58,7 +58,7 @@ class TaskTest < Test::Unit::TestCase
 
   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
+      sleep 1
       raise OpenTox::Error.new 500, "An OpenTox::Error occured"
     end
     assert task.running?
@@ -68,9 +68,10 @@ class TaskTest < Test::Unit::TestCase
     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 0.5
+      sleep 1
       "Asasadasd"
     end
     assert task.running?
@@ -79,7 +80,6 @@ class TaskTest < Test::Unit::TestCase
     assert task.error?
     assert_equal "Error", task.hasStatus
   end
-=begin
 =end
 
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: opentox-client
 version: !ruby/object:Gem::Version
-  version: 0.0.1pre
+  version: 0.0.2pre
   prerelease: 5
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-03-09 00:00:00.000000000 Z
+date: 2012-04-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &82129140 !ruby/object:Gem::Requirement
+  requirement: &76175050 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *82129140
+  version_requirements: *76175050
 - !ruby/object:Gem::Dependency
   name: rest-client
-  requirement: &82128400 !ruby/object:Gem::Requirement
+  requirement: &76185830 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *82128400
+  version_requirements: *76185830
 - !ruby/object:Gem::Dependency
   name: rdf
-  requirement: &82127910 !ruby/object:Gem::Requirement
+  requirement: &76706430 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +43,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *82127910
+  version_requirements: *76706430
 - !ruby/object:Gem::Dependency
   name: rdf-raptor
-  requirement: &82127560 !ruby/object:Gem::Requirement
+  requirement: &76705970 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *82127560
+  version_requirements: *76705970
 - !ruby/object:Gem::Dependency
   name: open4
-  requirement: &82127200 !ruby/object:Gem::Requirement
+  requirement: &76705540 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,7 +65,7 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *82127200
+  version_requirements: *76705540
 description: Ruby wrapper for the OpenTox REST API (http://www.opentox.org)
 email:
 - helma@in-silico.ch
@@ -94,6 +94,7 @@ files:
 - lib/templates/default_guest_policy.xml
 - lib/templates/default_policy.xml
 - opentox-client.gemspec
+- test/authorization.rb
 - test/compound.rb
 - test/data/CPDBAS_v5c_1547_29Apr2008part.sdf
 - test/data/EPAFHM.csv
@@ -112,11 +113,13 @@ files:
 - test/dataset.rb
 - test/error.rb
 - test/feature.rb
+- test/policy.rb
 - test/task.rb
 homepage: http://github.com/opentox/opentox-client
 licenses:
 - GPL-3
-post_install_message: 
+post_install_message: Please check the version of your libraptor library, if installation
+  of rdf.rb fails
 rdoc_options: []
 require_paths:
 - lib
@@ -128,14 +131,15 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -394211199
+      hash: -571051053
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
   - - ! '>'
     - !ruby/object:Gem::Version
       version: 1.3.1
-requirements: []
+requirements:
+- libraptor-dev
 rubyforge_project: opentox-client
 rubygems_version: 1.8.11
 signing_key: