basic rest post get delete test working

6 files changed, 88 insertions, 59 deletions

diff --git a/Rakefile b/Rakefile
index 7e0bcf9..b670f39 100644
--- a/Rakefile
+++ b/Rakefile
@@ -11,37 +11,7 @@ begin
     gem.homepage = "http://github.com/opentox/opentox-ruby-minimal"
     gem.authors = ["Christoph Helma, Martin Guetlein, Andreas Maunz, Micha Rautenberg, David Vorgrimmler"]
     # dependencies with versions
-#    gem.add_dependency "sinatra", "=1.2.6"
-#    gem.add_dependency "emk-sinatra-url-for", "=0.2.1"
-#    gem.add_dependency "sinatra-respond_to", "=0.7.0"
-#    gem.add_dependency "sinatra-static-assets", "=0.5.0"
-    gem.add_dependency "rest-client", "=1.6.1"
-#    gem.add_dependency "rack", "=1.3.0"
-#    gem.add_dependency "rack-contrib", "=1.1.0"
-#    gem.add_dependency "rack-flash", "=0.1.1"
-    gem.add_dependency "nokogiri", "=1.4.4"
-#    gem.add_dependency "rubyzip", "=0.9.4"
-    gem.add_dependency "roo", "=1.9.3"
-    gem.add_dependency "spreadsheet", "=0.6.5.4"
-    gem.add_dependency "google-spreadsheet-ruby", "=0.1.5"
-    gem.add_dependency "yajl-ruby", "=0.8.2"
-    #gem.add_dependency "mail", "=2.3.0"
-#    gem.add_dependency "rinruby", "=2.0.2"
-#    gem.add_dependency "ohm", "=0.1.3"
-#    gem.add_dependency "ohm-contrib", "=0.1.1"
-#    gem.add_dependency "SystemTimer", "=1.2.3"
-#    gem.add_dependency "rjb", "=1.3.4"
-#    gem.add_dependency "haml", "=3.1.1"
-    #valiation-gems
-#    gem.add_dependency "dm-core",  "=1.1.0"
-#    gem.add_dependency "dm-serializer",  "=1.1.0"
-#    gem.add_dependency "dm-timestamps", "=1.1.0"
-#    gem.add_dependency "dm-types",  "=1.1.0"
-#    gem.add_dependency "dm-migrations",  "=1.1.0"
-#    gem.add_dependency "dm-validations",  "=1.1.0"
-#    gem.add_dependency "dm-sqlite-adapter", "=1.1.0"
-#    gem.add_dependency "ruby-plot", "=0.5.0"
-
+    gem.add_dependency "rest-client"
     gem.add_development_dependency 'jeweler'
     gem.files =  FileList["[A-Z]*", "{bin,generators,lib,test}/**/*", 'lib/jeweler/templates/.gitignore']
   end
@@ -74,7 +44,7 @@ task :test => :check_dependencies
 
 task :default => :test
 
-require 'rake/rdoctask'
+require 'rdoc/task'
 Rake::RDocTask.new do |rdoc|
   if File.exist?('VERSION')
     version = File.read('VERSION')
diff --git a/lib/opentox.rb b/lib/opentox.rb
index dbe2360..b0ffcb1 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -1,13 +1,18 @@
-require "./parser.rb"
-require "./rest_client_wrapper.rb"
-require "./error.rb"
-
+require 'rdf'
+require 'rdf/raptor'
+#require "parser.rb"
+require "rest_client_wrapper.rb"
+require "overwrite.rb"
+require "error.rb"
+
+RDF::OT =  RDF::Vocabulary.new 'http://www.opentox.org/api/1.1#'
+RDF::OTA =  RDF::Vocabulary.new 'http://www.opentox.org/algorithmTypes.owl#'
 SERVICES = ["Compound", "Feature", "Dataset", "Algorithm", "Model", "Validation", "Task"]
 
 module OpenTox
 
-  attr_accessor :subjectid, :uri
-  attr_writer :metadata
+  attr_accessor :subjectid, :uri #, :service_uri
+  #attr_writer :metadata
 
   # Initialize OpenTox object with optional subjectid
   # @param [optional, String] subjectid
@@ -17,7 +22,13 @@ module OpenTox
   end
 
   def metadata
-    @metadata ||= Parser::Owl::Generic.from_rdf get(:accept => "application/rdf+xml")
+    metadata = {}
+    RDF::Reader.open(@uri) do |reader|
+      reader.each_statement do |statement|
+        metadata[statement.predicate] = statement.object if statement.subject == @uri
+      end
+    end
+    metadata
   end
 
   # REST API
@@ -31,7 +42,7 @@ module OpenTox
   # @return [OpenTox::WrapperResult] a String containing the result-body of the REST call
   def get headers={}, wait=true 
     headers[:subjectid] = @subjectid
-    RestClientWrapper.get(@uri, headers, nil, wait).chomp
+    RestClientWrapper.get(@uri.to_s, headers, nil, wait).chomp
   end
 
   # performs a POST REST call
@@ -41,9 +52,9 @@ module OpenTox
   # @param [optional,Hash] headers contains params like accept-header
   # @param [wait,Boolean] wait set to false to NOT wait for task if result is task
   # @return [OpenTox::WrapperResult] a String containing the result-body of the REST call
-  def post payload=nil, headers={}, wait=true 
+  def post payload={}, headers={}, wait=true 
     headers[:subjectid] = @subjectid
-    RestClientWrapper.post(@uri, payload, headers, nil, wait).chomp
+    RestClientWrapper.post(@uri.to_s, payload, headers, nil, wait).chomp
   end
 
   # performs a PUT REST call
@@ -51,40 +62,33 @@ module OpenTox
   # @param [optional,String] payload data put to the service
   # @param [optional,Hash] headers contains params like accept-header
   # @return [OpenTox::WrapperResult] a String containing the result-body of the REST call
-  def put payload=nil, headers={} 
+  def put payload={}, headers={} 
     headers[:subjectid] = @subjectid
-    RestClientWrapper.put(@uri, payload, headers).chomp
+    RestClientWrapper.put(@uri.to_s, payload, headers).chomp
   end
 
   # performs a DELETE REST call
   # raises OpenTox::Error if call fails (rescued in overwrite.rb -> halt 502)
   # @return [OpenTox::WrapperResult] a String containing the result-body of the REST call
   def delete 
-    RestClientWrapper.delete(@uri,:subjectid => @subjectid)
+    RestClientWrapper.delete(@uri.to_s,:subjectid => @subjectid)
   end
 
-  # Tools
+  # create default classes
+  SERVICES.each { |s| eval "class #{s}; include OpenTox; end" }
 
-  # Get OWL-DL representation in RDF/XML format
-  # @return [application/rdf+xml] RDF/XML representation
-  def to_rdfxml
-    s = Serializer::Owl.new
-    s.add_metadata(@uri,@metadata)
-    s.to_rdfxml
-  end
+=begin
+  # Tools
 
   def uri_available?
     url = URI.parse(@uri)
-    #TODO: move subjectid to header
-    subjectidstr = @subjectid ? "?subjectid=#{CGI.escape @subjectid}" : ""
-    Net::HTTP.start(url.host, url.port) do |http|
+    req = Net::HTTP.new(url.host,url.port)
+    req['subjectid'] = @subjectid if @subjectid
+    req.start(url.host, url.port) do |http|
       return http.head("#{url.request_uri}#{subjectidstr}").code == "200"
     end
   end
 
-  # create default classes
-  SERVICES.each { |s| eval "class #{s}; include OpenTox; end" }
-
   module Collection
 
     include OpenTox
@@ -115,6 +119,7 @@ module OpenTox
     SERVICES.each { |s| eval "class #{s}; include Collection; end" }
 
   end
+=end
 
 end
 
diff --git a/lib/overwrite.rb b/lib/overwrite.rb
index efc570d..d541b61 100644
--- a/lib/overwrite.rb
+++ b/lib/overwrite.rb
@@ -1,3 +1,4 @@
+require 'uri'
 =begin
 # class overwrites aka monkey patches
 # hack: store sinatra instance in global var $url_provider to make url_for and halt methods accessible
diff --git a/lib/parser.rb b/lib/parser.rb
index 580f6f7..7475d6d 100644
--- a/lib/parser.rb
+++ b/lib/parser.rb
@@ -1,6 +1,35 @@
 #require 'spreadsheet'
 #require 'roo'
 
+# OWL Namespaces
+class OwlNamespace
+
+  attr_accessor :uri
+  def initialize(uri)
+    @uri = uri
+  end
+
+  def [](property)
+    @uri+property.to_s
+  end
+
+  def type # for RDF.type
+    "#{@uri}type"
+  end
+
+  def method_missing(property)
+    @uri+property.to_s
+  end
+
+end
+
+RDF = OwlNamespace.new 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'
+OWL = OwlNamespace.new 'http://www.w3.org/2002/07/owl#'
+DC =  OwlNamespace.new 'http://purl.org/dc/elements/1.1/'
+OT =  OwlNamespace.new 'http://www.opentox.org/api/1.1#'
+OTA =  OwlNamespace.new 'http://www.opentox.org/algorithmTypes.owl#'
+XSD = OwlNamespace.new 'http://www.w3.org/2001/XMLSchema#'
+
 class String
 
   # Split RDF statement into triples
diff --git a/lib/rest_client_wrapper.rb b/lib/rest_client_wrapper.rb
index 3dd3eff..30f04cc 100644
--- a/lib/rest_client_wrapper.rb
+++ b/lib/rest_client_wrapper.rb
@@ -1,3 +1,4 @@
+require 'rest-client'
 module OpenTox
   
   class WrapperResult < String
diff --git a/test/rest.rb b/test/rest.rb
new file mode 100644
index 0000000..576e712
--- /dev/null
+++ b/test/rest.rb
@@ -0,0 +1,23 @@
+$LOAD_PATH << File.expand_path( File.dirname(__FILE__) + '/../lib' )
+require 'rubygems'
+require 'opentox.rb'
+require 'test/unit'
+
+class RestTest < Test::Unit::TestCase
+
+  def test_post_get_delete
+    uristring = "http://ot-dev.in-silico.ch/dataset" 
+    uri = uristring
+    dataset_service = OpenTox::Dataset.new uri
+    assert_match /#{uristring}/, dataset_service.get
+    dataset_uri = dataset_service.post 
+    assert_match /#{uristring}/, dataset_uri.to_s
+    dataset = OpenTox::Dataset.new dataset_uri
+    assert_equal dataset_uri, dataset.uri
+    metadata =  dataset.metadata
+    assert_equal RDF::OT.Dataset, metadata[RDF.type]
+    assert_equal dataset.uri, metadata[RDF::XSD.anyURI]
+    dataset.delete
+  end
+
+end