diff options
Diffstat (limited to 'lib/model.rb')
| -rw-r--r-- | lib/model.rb | 57 |
1 files changed, 45 insertions, 12 deletions
diff --git a/lib/model.rb b/lib/model.rb index 8a07858..0b116c2 100644 --- a/lib/model.rb +++ b/lib/model.rb @@ -10,8 +10,8 @@ module OpenTox # @return [text/uri-list] Task or resource URI def run( params, accept_header=nil, waiting_task=nil ) unless accept_header - if CONFIG[:yaml_hosts].include?(URI.parse(@uri).host) - accept_header = 'application/x-yaml' + if CONFIG[:json_hosts].include?(URI.parse(@uri).host) + accept_header = 'application/json' else accept_header = 'application/rdf+xml' end @@ -144,7 +144,7 @@ module OpenTox # @param [String] uri Model URI # @return [OpenTox::Model::Lazar] lazar model def self.find(uri, subjectid=nil) - YAML.load RestClientWrapper.get(uri,{:accept => 'application/x-yaml', :subjectid => subjectid}) + OpenTox::Model::Lazar.from_json RestClientWrapper.get(uri,{:accept => 'application/json', :subjectid => subjectid}) end # Create a new lazar model @@ -157,10 +157,42 @@ module OpenTox OpenTox::Model::Lazar.find(model_uri, subjectid) end + def self.from_json(json) + hash = Yajl::Parser.parse(json) + #LOGGER.debug hash.to_yaml + lazar = OpenTox::Model::Lazar.new + #hash.each { |k,v| eval("lazar.#{k} = #{v}") } + lazar.uri = hash["uri"] if hash["uri"] + lazar.metadata = hash["metadata"] if hash["metadata"] + lazar.compound = hash["compound"] if hash["compound"] + lazar.prediction_dataset = hash["prediction_dataset"] if hash["prediction_dataset"] + lazar.features = hash["features"] if hash["features"] + lazar.effects = hash["effects"] if hash["effects"] + lazar.activities = hash["activities"] if hash["activities"] + lazar.p_values = hash["p_values"] if hash["p_values"] + lazar.fingerprints = hash["fingerprints"] if hash["fingerprints"] + lazar.feature_calculation_algorithm = hash["feature_calculation_algorithm"] if hash["feature_calculation_algorithm"] + lazar.similarity_algorithm = hash["similarity_algorithm"] if hash["similarity_algorithm"] + lazar.prediction_algorithm = hash["prediction_algorithm"] if hash["prediction_algorithm"] + lazar.min_sim = hash["min_sim"] if hash["min_sim"] + lazar.subjectid = hash["subjectid"] if hash["subjectid"] + lazar.prop_kernel = hash["prop_kernel"] if hash["prop_kernel"] + lazar.value_map = hash["value_map"] if hash["value_map"] + lazar.nr_hits = hash["nr_hits"] if hash["nr_hits"] + lazar.transform = hash["transform"] if hash["transform"] + lazar.conf_stdev = hash["conf_stdev"] if hash["conf_stdev"] + lazar.prediction_min_max = hash["prediction_min_max"] if hash["prediction_min_max"] + lazar + end + + def to_json + Yajl::Encoder.encode({:uri => @uri,:metadata => @metadata, :compound => @compound, :prediction_dataset => @prediction_dataset, :features => @features, :effects => @effects, :activities => @activities, :p_values => @p_values, :fingerprints => @fingerprints, :feature_calculation_algorithm => @feature_calculation_algorithm, :similarity_algorithm => @similarity_algorithm, :prediction_algorithm => @prediction_algorithm, :min_sim => @min_sim, :subjectid => @subjectid, :prop_kernel => @prop_kernel, :value_map => @value_map, :nr_hits => @nr_hits, :transform => @transform, :conf_stdev => @conf_stdev, :prediction_min_max => @prediction_min_max}) + end + def run( params, accept_header=nil, waiting_task=nil ) unless accept_header - if CONFIG[:yaml_hosts].include?(URI.parse(@uri).host) - accept_header = 'application/x-yaml' + if CONFIG[:json_hosts].include?(URI.parse(@uri).host) + accept_header = 'application/json' else accept_header = 'application/rdf+xml' end @@ -199,7 +231,7 @@ module OpenTox count += 1 waiting_task.progress( count/d.compounds.size.to_f*100.0 ) if waiting_task rescue => ex - LOGGER.warn "prediction for compound "+compound_uri.to_s+" failed: "+ex.message + LOGGER.warn "prediction for compound "+compound_uri.to_s+" failed: "+ex.message+" subjectid: #{subjectid}" end end #@prediction_dataset.save(subjectid) @@ -215,6 +247,7 @@ module OpenTox @compound = Compound.new compound_uri features = {} + #LOGGER.debug self.to_yaml unless @prediction_dataset @prediction_dataset = Dataset.create(CONFIG[:services]["opentox-dataset"], subjectid) @prediction_dataset.add_metadata( { @@ -225,7 +258,7 @@ module OpenTox } ) end - if OpenTox::Feature.find(metadata[OT.dependentVariables]).feature_type == "regression" + if OpenTox::Feature.find(metadata[OT.dependentVariables], subjectid).feature_type == "regression" all_activities = [] all_activities = @activities.values.flatten.collect! { |i| i.to_f } @prediction_min_max[0] = (all_activities.to_scale.min/2) @@ -255,7 +288,7 @@ module OpenTox @prediction_dataset.metadata[OT.predictedVariables] = [value_feature_uri, confidence_feature_uri] unless @prediction_dataset.metadata[OT.predictedVariables] if OpenTox::Feature.find(metadata[OT.dependentVariables], subjectid).feature_type == "classification" - @prediction_dataset.add @compound.uri, value_feature_uri, @value_map[prediction[:prediction]] + @prediction_dataset.add @compound.uri, value_feature_uri, @value_map[prediction[:prediction].to_s] else @prediction_dataset.add @compound.uri, value_feature_uri, prediction[:prediction] end @@ -365,7 +398,7 @@ module OpenTox def database_activity(subjectid) if @activities[@compound.uri] if OpenTox::Feature.find(metadata[OT.dependentVariables], subjectid).feature_type == "classification" - @activities[@compound.uri].each { |act| @prediction_dataset.add @compound.uri, @metadata[OT.dependentVariables], @value_map[act] } + @activities[@compound.uri].each { |act| @prediction_dataset.add @compound.uri, @metadata[OT.dependentVariables], @value_map[act.to_s] } else @activities[@compound.uri].each { |act| @prediction_dataset.add @compound.uri, @metadata[OT.dependentVariables], act } end @@ -385,7 +418,7 @@ module OpenTox dependent_uri = @metadata[OT.dependentVariables].first feature = OpenTox::Feature.new File.join( @uri, "predicted", "value") feature.add_metadata( { - RDF.type => [OT.ModelPrediction], + RDF.type => OT.ModelPrediction, OT.hasSource => @uri, DC.creator => @uri, DC.title => URI.decode(File.basename( dependent_uri )), @@ -398,7 +431,7 @@ module OpenTox dependent_uri = @metadata[OT.dependentVariables].first feature = OpenTox::Feature.new File.join( @uri, "predicted", "confidence") feature.add_metadata( { - RDF.type => [OT.ModelPrediction], + RDF.type => OT.ModelPrediction, OT.hasSource => @uri, DC.creator => @uri, DC.title => "#{URI.decode(File.basename( dependent_uri ))} confidence" @@ -408,7 +441,7 @@ module OpenTox # Save model at model service def save(subjectid) - self.uri = RestClientWrapper.post(@uri,self.to_yaml,{:content_type => "application/x-yaml", :subjectid => subjectid}) + self.uri = RestClientWrapper.post(@uri,self.to_json,{:content_type => "application/json", :subjectid => subjectid}) end # Delete model at model service |