improved integration of error reports, call stack added as errorDetails

1 files changed, 78 insertions, 40 deletions

diff --git a/lib/opentox.rb b/lib/opentox.rb
index 9ba64bd..342b04e 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -1,52 +1,73 @@
-#TODO: switch services to 1.2
-RDF::OT =  RDF::Vocabulary.new 'http://www.opentox.org/api/1.2#'
-RDF::OT1 =  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", "Investigation"]
-
-# Regular expressions for parsing classification data
-TRUE_REGEXP = /^(true|active|1|1.0|tox|activating|carcinogen|mutagenic)$/i
-FALSE_REGEXP = /^(false|inactive|0|0.0|low tox|deactivating|non-carcinogen|non-mutagenic)$/i
-
 # defaults to stderr, may be changed to file output (e.g in opentox-service)
 $logger = OTLogger.new(STDERR) 
 $logger.level = Logger::DEBUG
 
 module OpenTox
 
-  attr_accessor :subjectid, :uri, :response
-  attr_writer :metadata
+  attr_accessor :uri, :subjectid, :rdf, :response
 
+  # Ruby interface
+
+  # Create a new OpenTox object (does not load data from service)
+  # @param [optional,String] URI
+  # @param [optional,String] subjectid
+  # @return [OpenTox] OpenTox object
   def initialize uri=nil, subjectid=nil
-    @uri = uri.chomp
+    @uri = uri.to_s.chomp
     @subjectid = subjectid
+    @rdf = RDF::Graph.new
   end
 
-  # Ruby interface
+  # Load metadata from service
+  def pull
+    kind_of?(OpenTox::Dataset) ? uri = File.join(@uri,"metadata") : uri = @uri
+    # TODO generic method for all formats
+    parse_rdfxml RestClientWrapper.get(uri,{},{:accept => $default_rdf, :subjectid => @subjectid})
+  end
 
-  def metadata reload=true
-    if reload or @metadata.empty?
-      @metadata = {}
-      kind_of?(OpenTox::Dataset) ? uri = File.join(@uri,"metadata") : uri = @uri
-      RDF::Reader.for(:rdfxml).new( RestClientWrapper.get(uri) ) do |reader|
-        reader.each_statement do |statement|
-          @metadata[statement.predicate] = statement.object if statement.subject == @uri
-        end
-      end
+  # Get object metadata 
+  # @return [Hash] Metadata
+  def metadata 
+    pull if @rdf.empty?
+    metadata = {}
+    @rdf.query([RDF::URI.new(@uri),nil,nil]).collect do |statement|
+      metadata[statement.predicate] ||= []
+      metadata[statement.predicate] << statement.object
     end
-    @metadata
+    metadata
+  end
+
+  # Get metadata values 
+  # @param [RDF] Key from RDF Vocabularies
+  # @return [Array] Values for supplied key
+  def [](key)
+    pull if @rdf.empty?
+    @rdf.query([RDF::URI.new(@uri),key,nil]).collect{|statement| statement.object}
   end
 
+  # Save object at service
   def save
-    post self.to_rdfxml, { :content_type => 'application/rdf+xml'}
+    #TODO: dynamic assignment
+    post self.to_rdfxml, { :content_type => $default_rdf}
   end
 
-  def to_rdfxml
-    rdf = RDF::Writer.for(:rdfxml).buffer do |writer|
-      @metadata.each { |p,o| writer << RDF::Statement.new(RDF::URI.new(@uri), p, o) }
+  RDF_FORMATS.each do |format|
+
+    # rdf parse methods for all formats e.g. parse_rdfxml
+    send :define_method, "parse_#{format}".to_sym do |rdf|
+      @rdf = RDF::Graph.new
+      RDF::Reader.for(format).new(rdf) do |reader|
+        reader.each_statement{ |statement| @rdf << statement }
+      end
+    end
+
+    # rdf serialization methods for all formats e.g. to_rdfxml
+    send :define_method, "to_#{format}".to_sym do
+      rdf = RDF::Writer.for(format).buffer do |writer|
+        @rdf.each{|statement| writer << statement}
+      end
+      rdf
     end
-    rdf
   end
 
   # REST API
@@ -70,32 +91,49 @@ module OpenTox
 
   def delete headers={}
     headers[:subjectid] ||= @subjectid
-    @response = RestClientWrapper.delete(@uri.to_s,nil,nil,headers)
+    @response = RestClientWrapper.delete(@uri.to_s,nil,headers)
   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)}
+    end
+
     def create service_uri, subjectid=nil
-      uri = RestClientWrapper.post(service_uri, {}, :subjectid => subjectid).chomp
-      subjectid ? eval("#{self}.new(\"#{uri}\", #{subjectid})") : eval("#{self}.new(\"#{uri}\")")
+      uri = RestClientWrapper.post(service_uri, {}, {:accept => 'text/uri-list', :subjectid => subjectid})
+      URI.task?(service_uri) ? from_uri(uri, subjectid, false) : from_uri(uri, subjectid)
     end
 
     def from_file service_uri, filename, subjectid=nil
       file = File.new filename
-      uri = RestClientWrapper.post(service_uri, {:file => file}, {:subjectid => subjectid, :content_type => file.mime_type, :accept => "text/uri-list"})
-      puts uri
+      from_uri RestClientWrapper.post(service_uri, {:file => file}, {:subjectid => subjectid, :content_type => file.mime_type, :accept => "text/uri-list"}), subjectid
     end
 
-    def all service_uri, subjectid=nil
-      uris = RestClientWrapper.get(service_uri, {}, :accept => 'text/uri-list').split("\n").compact
-      uris.collect{|uri| subjectid ? eval("#{self}.new(\"#{uri}\", #{subjectid})") : eval("#{self}.new(\"#{uri}\")")}
-    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
+      internal_server_error "Cannot determine class from URI: '#{uri}.\nCandidate classes are #{result.inspect}" unless result.size == 1
+      klass = result.first
+      # initialize with/without subjectid
+      subjectid ? eval("#{self}.new(\"#{uri}\", #{subjectid})") : eval("#{self}.new(\"#{uri}\")")
+    end
   end
 
   # create default OpenTox classes
-  SERVICES.each do |klass|
+  CLASSES.each do |klass|
     c = Class.new do
       include OpenTox
       extend OpenTox::ClassMethods