opentox-client 0.0.2pre → 1.0.0pre1

data/lib/rest-client-wrapper.rb

@@ -17,14 +17,14 @@ module OpenTox
 
         # check input 
         @subjectid = headers[:subjectid] ? headers[:subjectid] : nil
-        bad_request_error "Invalid URI: '#{uri}'" unless URI.valid? uri
-        not_found_error "URI '#{uri}' not found." unless URI.accessible?(uri, @subjectid) unless URI.ssl?(uri)
-        bad_request_error "Headers are not a hash: #{headers.inspect}" unless headers==nil or headers.is_a?(Hash)
+        bad_request_error "Invalid URI: '#{uri}'", uri unless URI.valid? uri
+        #resource_not_found_error "URI '#{uri}' not found.", uri unless URI.accessible?(uri, @subjectid) unless URI.ssl?(uri)
+        bad_request_error "Headers are not a hash: #{headers.inspect}", uri unless headers==nil or headers.is_a?(Hash)
         # make sure that no header parameters are set in the payload
         [:accept,:content_type,:subjectid].each do |header|
           if defined? $aa || URI(uri).host == URI($aa[:uri]).host
           else
-            bad_request_error "#{header} should be submitted in the headers" if payload and payload.is_a?(Hash) and payload[header]
+            bad_request_error "#{header} should be submitted in the headers", uri if payload and payload.is_a?(Hash) and payload[header]
           end
         end
       
@@ -42,13 +42,32 @@ module OpenTox
         @response = @request.execute do |response, request, result|
           if [301, 302, 307].include? response.code and request.method == :get
             response.follow_redirection(request, result)
+          elsif response.code >= 400 and !URI.task?(uri)
+            message = response.to_s
+            parameters = request.args
+            parameters[:headers][:subjectid] = "REMOVED" if parameters[:headers] and parameters[:headers][:subjectid] 
+            message += "\nREST paramenters:\n#{parameters.inspect}" 
+            error = known_errors.collect{|e| e if e[:code] == response.code}.compact.first
+            Object.method(error[:method]).call message, uri # call error method
           else
-            raise OpenTox::RestCallError.new response.to_s, request, uri unless response.code < 400 or URI.task? uri
             response
           end
         end
       end
     end
 
+    def self.known_errors
+      errors = []
+      RestClient::STATUSES.each do |code,k|
+        if code >= 400
+          method = k.underscore.gsub(/ |'/,'_')
+          method += "_error" unless method.match(/_error$/)
+          klass = method.split("_").collect{|s| s.capitalize}.join("")
+          errors << {:code => code, :method => method.to_sym, :class => klass}
+        end
+      end
+      errors
+    end
+
   end
 end

data/lib/task.rb

@@ -6,15 +6,23 @@ module OpenTox
 
     attr_accessor :pid, :observer_pid
 
-    def self.create service_uri, params={}
+    def self.create service_uri, subjectid=nil, params={}
 
-      task = Task.new RestClientWrapper.post(service_uri,params).chomp
+      uri = File.join(service_uri,SecureRandom.uuid)
+      task = Task.new uri, subjectid
+      task[RDF::OT.hasStatus] = "Running"
+      params.each { |k,v| task[k] = v }
+      task.put false
       pid = fork do
         begin
           result_uri = yield 
           task.completed result_uri
         rescue 
-          RestClientWrapper.put(File.join(task.uri,'Error'),{:errorReport => $!.report.to_yaml}) if $!.respond_to? :report
+          if $!.respond_to? :to_ntriples
+            RestClientWrapper.put(File.join(task.uri,'Error'),:errorReport => $!.to_ntriples,:content_type => 'text/plain') 
+          else
+            RestClientWrapper.put(File.join(task.uri,'Error')) 
+          end
           task.kill
         end
       end
@@ -39,27 +47,27 @@ module OpenTox
     def kill
       Process.kill(9,@pid)
       Process.kill(9,@observer_pid)
-    rescue # no need to raise an exeption if processes are not running
+    rescue # no need to raise an exception if processes are not running
     end
 
     def description
-      pull
-      self.[](RDF::DC.description).uniq.first
+      self.[](RDF::DC.description)
     end
 
     def creator
-      pull
-      self.[](RDF::DC.creator).uniq.first
+      self.[](RDF::DC.creator)
     end
     
     def cancel
       kill
-      RestClientWrapper.put(File.join(@uri,'Cancelled'),{})
+      self.[]=(RDF::OT.hasStatus, "Cancelled")
+      put false
     end
 
     def completed(uri)
-      #not_found_error "Result URI \"#{uri}\" does not exist." unless URI.accessible? uri
-      RestClientWrapper.put(File.join(@uri,'Completed'),{:resultURI => uri})
+      self.[]=(RDF::OT.resultURI, uri)
+      self.[]=(RDF::OT.hasStatus, "Completed")
+      put false
     end
 
     # waits for a task, unless time exceeds or state is no longer running
@@ -68,7 +76,7 @@ module OpenTox
     def wait
       start_time = Time.new
       due_to_time = start_time + DEFAULT_TASK_MAX_DURATION
-      dur = 0
+      dur = 0.3
       while running? 
         sleep dur
         dur = [[(Time.new - start_time)/20.0,0.3].max,300.0].min
@@ -96,19 +104,29 @@ module OpenTox
     code >= 400 and code != 503
   end
 
-  def errorReport
-    # TODO: fix rdf output at task service
-    not_implemented_error "RDF output of errorReports has to be fixed at task service"
-  end
-
-  [:hasStatus, :resultURI].each do |method|
+  [:hasStatus, :resultURI, :finished_at].each do |method|
     define_method method do
+      get
       response = self.[](RDF::OT[method])
       response = self.[](RDF::OT1[method]) unless response  # API 1.1 compatibility
       response
     end
   end
 
+  def error_report
+    report = {}
+    query = RDF::Query.new({
+      :report => {
+        RDF.type  => RDF::OT.ErrorReport,
+        :property => :value,
+      }
+    })
+    query.execute(@rdf).each do |solution|
+      report[solution.property] = solution.value.to_s
+    end
+    report
+  end
+
   #TODO: subtasks (only for progress)
 
 end

data/opentox-client.gemspec

@@ -3,7 +3,7 @@ $:.push File.expand_path("../lib", __FILE__)
 
 Gem::Specification.new do |s|
   s.name        = "opentox-client"
-  s.version     = "0.0.2pre"
+  s.version     = File.read("./VERSION").strip
   s.authors     = ["Christoph Helma, Martin Guetlein, Andreas Maunz, Micha Rautenberg, David Vorgrimmler"]
   s.email       = ["helma@in-silico.ch"]
   s.homepage    = "http://github.com/opentox/opentox-client"
@@ -23,6 +23,7 @@ Gem::Specification.new do |s|
   s.add_runtime_dependency "rest-client"
   s.add_runtime_dependency "rdf"
   s.add_runtime_dependency "rdf-raptor"
+  s.add_runtime_dependency 'rdf-n3'
   s.add_runtime_dependency "open4"
   
   # external requirements

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: opentox-client
 version: !ruby/object:Gem::Version
-  version: 0.0.2pre
+  version: 1.0.0pre1
   prerelease: 5
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-04-02 00:00:00.000000000 Z
+date: 2012-08-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &76175050 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,15 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *76175050
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rest-client
-  requirement: &76185830 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +37,15 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *76185830
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rdf
-  requirement: &76706430 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +53,31 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *76706430
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rdf-raptor
-  requirement: &76705970 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rdf-n3
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +85,15 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *76705970
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: open4
-  requirement: &76705540 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,19 +101,29 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *76705540
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 description: Ruby wrapper for the OpenTox REST API (http://www.opentox.org)
 email:
 - helma@in-silico.ch
-executables: []
+executables:
+- opentox-client-install
 extensions: []
 extra_rdoc_files: []
 files:
 - .gitignore
+- ChangeLog
 - Gemfile
+- Gemfile.lock
 - LICENSE
 - README.markdown
 - Rakefile
+- VERSION
+- bin/opentox-client-install
 - lib/algorithm.rb
 - lib/authorization.rb
 - lib/compound.rb
@@ -94,27 +140,6 @@ 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
-- 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/policy.rb
-- test/task.rb
 homepage: http://github.com/opentox/opentox-client
 licenses:
 - GPL-3
@@ -129,9 +154,6 @@ required_ruby_version: !ruby/object:Gem::Requirement
   - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
-      segments:
-      - 0
-      hash: -571051053
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -141,7 +163,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements:
 - libraptor-dev
 rubyforge_project: opentox-client
-rubygems_version: 1.8.11
+rubygems_version: 1.8.18
 signing_key: 
 specification_version: 3
 summary: Ruby wrapper for the OpenTox REST API

data/test/authorization.rb

@@ -1,107 +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
-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