From 4c2470353a1e3b69b4260d0052c9c48137ef76d3 Mon Sep 17 00:00:00 2001 From: mr Date: Tue, 14 Dec 2010 12:30:20 +0100 Subject: remove token_id from tables in database --- lib/model.rb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) (limited to 'lib/model.rb') diff --git a/lib/model.rb b/lib/model.rb index 5dc4d4a..9c2fb97 100644 --- a/lib/model.rb +++ b/lib/model.rb @@ -111,7 +111,7 @@ module OpenTox # @param [String] compound_uri Compound URI # @param [optinal,Boolean] verbose Verbose prediction (output includes neighbors and features) # @return [OpenTox::Dataset] Dataset with prediction - def predict(compound_uri,verbose=false) + def predict(compound_uri,verbose=false,token_id=nil) @compound = Compound.new compound_uri features = {} @@ -119,7 +119,7 @@ module OpenTox unless @prediction_dataset #@prediction_dataset = cached_prediction #return @prediction_dataset if cached_prediction - @prediction_dataset = Dataset.create + @prediction_dataset = Dataset.create(CONFIG[:services]["opentox-dataset"], token_id) @prediction_dataset.add_metadata( { OT.hasSource => @uri, DC.creator => @uri, @@ -217,7 +217,7 @@ module OpenTox end end - @prediction_dataset.save + @prediction_dataset.save(token_id) @prediction_dataset end @@ -257,8 +257,8 @@ module OpenTox end # Save model at model service - def save - self.uri = RestClientWrapper.post(@uri,{:content_type => "application/x-yaml", :token_id => @token_id},self.to_yaml) + def save(token_id) + self.uri = RestClientWrapper.post(@uri,{:content_type => "application/x-yaml", :token_id => token_id},self.to_yaml) end # Delete model at model service -- cgit v1.2.3 From 2fb2f4cd34f499f8c9def5e4091cb5998794c595 Mon Sep 17 00:00:00 2001 From: mr Date: Tue, 14 Dec 2010 16:39:01 +0100 Subject: rename token_id to subjectid --- lib/model.rb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) (limited to 'lib/model.rb') diff --git a/lib/model.rb b/lib/model.rb index 9c2fb97..953bb6c 100644 --- a/lib/model.rb +++ b/lib/model.rb @@ -32,7 +32,7 @@ module OpenTox include Model include Algorithm - attr_accessor :compound, :prediction_dataset, :features, :effects, :activities, :p_values, :fingerprints, :feature_calculation_algorithm, :similarity_algorithm, :prediction_algorithm, :min_sim, :token_id + attr_accessor :compound, :prediction_dataset, :features, :effects, :activities, :p_values, :fingerprints, :feature_calculation_algorithm, :similarity_algorithm, :prediction_algorithm, :min_sim, :subjectid def initialize(uri=nil) @@ -111,7 +111,7 @@ module OpenTox # @param [String] compound_uri Compound URI # @param [optinal,Boolean] verbose Verbose prediction (output includes neighbors and features) # @return [OpenTox::Dataset] Dataset with prediction - def predict(compound_uri,verbose=false,token_id=nil) + def predict(compound_uri,verbose=false,subjectid=nil) @compound = Compound.new compound_uri features = {} @@ -119,7 +119,7 @@ module OpenTox unless @prediction_dataset #@prediction_dataset = cached_prediction #return @prediction_dataset if cached_prediction - @prediction_dataset = Dataset.create(CONFIG[:services]["opentox-dataset"], token_id) + @prediction_dataset = Dataset.create(CONFIG[:services]["opentox-dataset"], subjectid) @prediction_dataset.add_metadata( { OT.hasSource => @uri, DC.creator => @uri, @@ -217,7 +217,7 @@ module OpenTox end end - @prediction_dataset.save(token_id) + @prediction_dataset.save(subjectid) @prediction_dataset end @@ -257,8 +257,8 @@ module OpenTox end # Save model at model service - def save(token_id) - self.uri = RestClientWrapper.post(@uri,{:content_type => "application/x-yaml", :token_id => token_id},self.to_yaml) + def save(subjectid) + self.uri = RestClientWrapper.post(@uri,{:content_type => "application/x-yaml", :subjectid => subjectid},self.to_yaml) end # Delete model at model service -- cgit v1.2.3 From b22110ae0d8e902d700e0a3dc629ebfde1edfe10 Mon Sep 17 00:00:00 2001 From: mr Date: Thu, 16 Dec 2010 10:59:46 +0100 Subject: A&A --- lib/model.rb | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) (limited to 'lib/model.rb') diff --git a/lib/model.rb b/lib/model.rb index 953bb6c..c645bdc 100644 --- a/lib/model.rb +++ b/lib/model.rb @@ -90,8 +90,8 @@ module OpenTox # Predict a dataset # @param [String] dataset_uri Dataset URI # @return [OpenTox::Dataset] Dataset with predictions - def predict_dataset(dataset_uri) - @prediction_dataset = Dataset.create + def predict_dataset(dataset_uri, subjectid=nil) + @prediction_dataset = Dataset.create(CONFIG[:services]["opentox-dataset"], subjectid) @prediction_dataset.add_metadata({ OT.hasSource => @uri, DC.creator => @uri, @@ -101,9 +101,9 @@ module OpenTox d = Dataset.new(dataset_uri) d.load_compounds d.compounds.each do |compound_uri| - predict(compound_uri,false) + predict(compound_uri,false,subjectid) end - @prediction_dataset.save + @prediction_dataset.save(subjectid) @prediction_dataset end @@ -129,7 +129,7 @@ module OpenTox } ) end - return @prediction_dataset if database_activity + return @prediction_dataset if database_activity(subjectid) neighbors prediction = eval("#{@prediction_algorithm}(@neighbors,{:similarity_algorithm => @similarity_algorithm, :p_values => @p_values})") @@ -245,11 +245,11 @@ module OpenTox # Find database activities and store them in @prediction_dataset # @return [Boolean] true if compound has databasse activities, false if not - def database_activity + def database_activity(subjectid) if @activities[@compound.uri] @activities[@compound.uri].each { |act| @prediction_dataset.add @compound.uri, @metadata[OT.dependentVariables], act } @prediction_dataset.add_metadata(OT.hasSource => @metadata[OT.trainingDataset]) - @prediction_dataset.save + @prediction_dataset.save(subjectid) true else false @@ -262,8 +262,8 @@ module OpenTox end # Delete model at model service - def delete - RestClientWrapper.delete @uri unless @uri == CONFIG[:services]["opentox-model"] + def delete(subjectid) + RestClientWrapper.delete(@uri, :subjectid => subjectid) unless @uri == CONFIG[:services]["opentox-model"] end end -- cgit v1.2.3