all opentox-client tests pass

1 files changed, 35 insertions, 45 deletions

diff --git a/lib/opentox.rb b/lib/opentox.rb
index b0c786a..9225bb0 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -14,7 +14,14 @@ module OpenTox
   # @return [OpenTox] OpenTox object
   def initialize uri=nil, subjectid=nil
     @rdf = RDF::Graph.new
-    uri ?  @uri = uri.to_s.chomp : @uri = RDF::Node.uuid.to_s
+    if uri
+      @uri = uri.to_s.chomp
+    else
+      service = self.class.to_s.split('::').last.downcase
+      service_uri = eval("$#{service}[:uri]")
+      bad_request_error "$#{service}[:uri] variable not set. Please set $#{service}[:uri] or use an explicit uri as first constructor argument " unless service_uri
+      @uri = File.join service_uri, SecureRandom.uuid
+    end
     append RDF.type, eval("RDF::OT."+self.class.to_s.split('::').last)
     append RDF::DC.date, DateTime.now
     @subjectid = subjectid
@@ -24,7 +31,6 @@ module OpenTox
   # @return [Hash] Object metadata
   def metadata 
     # return plain strings instead of RDF objects
-    #puts @rdf.to_hash
     @rdf.to_hash[RDF::URI.new(@uri)].inject({}) { |h, (predicate, values)| h[predicate.to_s] = values.collect{|v| v.to_s}; h }
   end
 
@@ -32,6 +38,7 @@ module OpenTox
   # @param [String] Predicate URI
   # @return [Array, String] Predicate value(s)
   def [](predicate)
+    return nil if metadata[predicate.to_s].nil?
     metadata[predicate.to_s].size == 1 ? metadata[predicate.to_s].first : metadata[predicate.to_s]
   end
 
@@ -55,30 +62,30 @@ module OpenTox
   # Get object from webservice
   def get 
     parse_ntriples RestClientWrapper.get(@uri,{},{:accept => "text/plain", :subjectid => @subjectid})
-  rescue # fall back to rdfxml
-    parse_rdfxml RestClientWrapper.get(@uri,{},{:accept => "application/rdf+xml", :subjectid => @subjectid})
+  #rescue # fall back to rdfxml
+    #parse_rdfxml RestClientWrapper.get(@uri,{},{:accept => "application/rdf+xml", :subjectid => @subjectid})
   end
 
   # Post object to webservice
   def post service_uri
     RestClientWrapper.post service_uri, to_ntriples, { :content_type => "text/plain", :subjectid => @subjectid}
-  rescue # fall back to rdfxml
-    RestClientWrapper.post service_uri, to_rdfxml, { :content_type => "application/rdf+xml", :subjectid => @subjectid}
+  #rescue # fall back to rdfxml
+    #RestClientWrapper.post service_uri, to_rdfxml, { :content_type => "application/rdf+xml", :subjectid => @subjectid}
   end
 
   # Save object at webservice
   def put 
     append RDF::DC.modified, DateTime.now
-    begin
+    #begin
       RestClientWrapper.put @uri.to_s, self.to_ntriples, { :content_type => "text/plain", :subjectid => @subjectid}
-    rescue # fall back to rdfxml
-      RestClientWrapper.put @uri.to_s, self.to_rdfxml, { :content_type => "application/rdf+xml", :subjectid => @subjectid}
-    end
+    #rescue # fall back to rdfxml
+      #RestClientWrapper.put @uri.to_s, self.to_rdfxml, { :content_type => "application/rdf+xml", :subjectid => @subjectid}
+    #end
   end
 
   # Delete object at webservice
   def delete 
-    @response = RestClientWrapper.delete(@uri.to_s,nil,{:subjectid => @subjectid})
+    RestClientWrapper.delete(@uri.to_s,nil,{:subjectid => @subjectid})
   end
 
   RDF_FORMATS.each do |format|
@@ -100,42 +107,20 @@ module OpenTox
     end
   end
 
-  # class methods
-  module ClassMethods
-
-    def all service_uri, subjectid=nil
-      uris = RestClientWrapper.get(service_uri, {}, :accept => 'text/uri-list').split("\n").compact
-      uris.collect{|uri| URI.task?(service_uri) ? from_uri(uri, subjectid, false) : from_uri(uri, subjectid)}
+  def to_turtle # redefine to use prefixes (not supported by RDF::Writer)
+    prefixes = {:rdf => "http://www.w3.org/1999/02/22-rdf-syntax-ns#"}
+    ['OT', 'DC', 'XSD', 'OLO'].each{|p| prefixes[p.downcase.to_sym] = eval("RDF::#{p}.to_s") }
+    turtle = RDF::N3::Writer.for(:turtle).buffer(:prefixes => prefixes)  do |writer|
+      @rdf.each{|statement| writer << statement}
     end
+  end
 
-    def from_file service_uri, filename, subjectid=nil
-      file = File.new filename
-      # sdf files are incorrectly detected
-      file.mime_type = "chemical/x-mdl-sdfile" if File.extname(filename) == ".sdf"
-      from_uri RestClientWrapper.post(service_uri, {:file => file}, {:subjectid => subjectid, :content_type => file.mime_type, :accept => "text/uri-list"}), subjectid
+  {:title => RDF::DC.title, :dexcription => RDF::DC.description}.each do |method,predicate|
+    send :define_method, method do 
+      self.[](predicate) 
     end
-
-    private
-    def from_uri uri, subjectid=nil, wait=true
-        
-      uri.chomp!
-      # TODO add waiting task
-      if URI.task?(uri) and wait
-        t = OpenTox::Task.new(uri)
-        t.wait
-        uri = t.resultURI
-      end
-
-      # guess class from uri, this is potentially unsafe, but polling metadata from large uri lists is way too slow (and not all service provide RDF.type in their metadata)
-      result = CLASSES.collect{|s| s if uri =~ /#{s.downcase}/}.compact
-      if result.size == 1
-        klass = result.first
-      else
-        klass = OpenTox::Generic.new(uri)[RDF.type]
-        internal_server_error "Cannot determine class from URI '#{uri} (Candidate classes are #{result.inspect}) or matadata." unless klass
-      end
-      # initialize with/without subjectid
-      subjectid ? eval("#{self}.new(\"#{uri}\", \"#{subjectid}\")") : eval("#{self}.new(\"#{uri}\")")
+    send :define_method, "#{method}=" do |value|
+      self.[]=(predicate,value) 
     end
   end
 
@@ -143,7 +128,12 @@ module OpenTox
   CLASSES.each do |klass|
     c = Class.new do
       include OpenTox
-      extend OpenTox::ClassMethods
+      #extend OpenTox::ClassMethods
+
+      def self.all service_uri, subjectid=nil
+        uris = RestClientWrapper.get(service_uri, {}, :accept => 'text/uri-list').split("\n").compact
+        uris.collect{|uri| self.new(uri, subjectid)}
+      end
     end
     OpenTox.const_set klass,c
   end