version bump;units;general class update;sort by

1 files changed, 40 insertions, 39 deletions

diff --git a/application.rb b/application.rb
index 8a218f4..baba620 100644
--- a/application.rb
+++ b/application.rb
@@ -1,8 +1,9 @@
 require 'qsar-report'
 require 'rdiscount'
+require File.join './npo.rb'
 $ambit_search = "http://data.enanomapper.net/substance?type=name&search="
-$npo_search = "http://bioportal.bioontology.org/search?q=%s&ontologies=NPO&include_properties=false&include_views=false&includeObsolete=false&require_definition=false&exact_match=false&categories="
 
+include OpenTox
 
 configure :development do
   #$logger = Logger.new(STDOUT)
@@ -17,11 +18,11 @@ get '/?' do
 end
 #=begin
 get '/qmrf-report/:id' do
-  prediction_model = OpenTox::Model::NanoPrediction.find(params[:id])
+  prediction_model = Model::NanoPrediction.find(params[:id])
   if prediction_model
     model = prediction_model.model
 		model_type = "regression"
-    report = OpenTox::QMRFReport.new
+    report = QMRFReport.new
 		if File.directory?("#{File.dirname(__FILE__)}/../../lazar")
     	lazar_commit = `cd #{File.dirname(__FILE__)}/../../lazar; git rev-parse HEAD`.strip
     	lazar_commit = "https://github.com/opentox/lazar/tree/#{lazar_commit}"
@@ -34,38 +35,38 @@ get '/qmrf-report/:id' do
     report.value "qmrf_date", "#{Time.now.strftime('%d %B %Y')}"
     report.change_catalog :authors_catalog, :firstauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Rastatterstrasse 41, CH-4057 Basel, Switzerland", :email => "helma@in-silico.ch", :number => "1", :url => "http://in-silico.ch"}
     report.ref_catalog :qmrf_authors, :authors_catalog, :firstauthor
-    report.change_catalog :authors_catalog, :modelauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Contact Address", :email => "Contact Email", :number => "1", :url => "Web Page"}
+    report.change_catalog :authors_catalog, :modelauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Rastatterstrasse 41, CH-4057 Basel, Switzerland", :email => "helma@in-silico.ch", :number => "1", :url => "http://in-silico.ch"}
     report.ref_catalog :model_authors, :authors_catalog, :modelauthor
     report.value "model_date", "#{Time.parse(model.created_at.to_s).strftime('%Y')}"
-    report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "Rautenberg, Gebele and Helma (2013), Validation of read across predictions for nanoparticle toxicities ", :url => "in preparation"}
+    report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "Helma, Rautenberg and Gebele (2013), Validation of read across predictions for nanoparticle toxicities ", :url => "in preparation"}
     report.ref_catalog :references, :publications_catalog, :publications_catalog_1
     report.value "model_species", prediction_model.species
     report.change_catalog :endpoints_catalog, :endpoints_catalog_1, {:name => prediction_model.endpoint, :group => ""}
     report.ref_catalog :model_endpoint, :endpoints_catalog, :endpoints_catalog_1
     report.value "endpoint_units", "#{prediction_model.unit}"
-    report.value "algorithm_type", "#{model.class.to_s.gsub('OpenTox::Model::Lazar','')}"
-    #TODO add more
-		report.change_catalog :algorithms_catalog, :algorithms_catalog_1, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "Neighbor algorithm: #{model.neighbor_algorithm.gsub('_',' ').titleize}#{(model.neighbor_algorithm_parameters[:min_sim] ? ' with similarity > ' + model.neighbor_algorithm_parameters[:min_sim].to_s : '')}"}
-		report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_1
-		report.change_catalog :algorithms_catalog, :algorithms_catalog_3, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "modified k-nearest neighbor #{model_type}"}
-		report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_3
-		if model.prediction_algorithm_parameters
-			pred_algorithm_params = (model.prediction_algorithm_parameters[:method] == "rf" ? "random forest" : model.prediction_algorithm_parameters[:method])
-		end
-		report.change_catalog :algorithms_catalog, :algorithms_catalog_2, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "Prediction algorithm: #{model.prediction_algorithm.gsub('OpenTox::Algorithm::','').gsub('_',' ').gsub('.', ' with ')} #{(pred_algorithm_params ? pred_algorithm_params : '')}"}
-		report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_2
+    report.value "algorithm_type", "#{model.class.to_s.gsub('Model::Lazar','')}"
+    #TODO add updated algorithms
+		#report.change_catalog :algorithms_catalog, :algorithms_catalog_1, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "Neighbor algorithm: #{model.neighbor_algorithm.gsub('_',' ').titleize}#{(model.neighbor_algorithm_parameters[:min_sim] ? ' with similarity > ' + model.neighbor_algorithm_parameters[:min_sim].to_s : '')}"}
+		#report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_1
+		#report.change_catalog :algorithms_catalog, :algorithms_catalog_3, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "modified k-nearest neighbor #{model_type}"}
+		#report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_3
+		#if model.prediction_algorithm_parameters
+		#	pred_algorithm_params = (model.prediction_algorithm_parameters[:method] == "rf" ? "random forest" : model.prediction_algorithm_parameters[:method])
+		#end
+		#report.change_catalog :algorithms_catalog, :algorithms_catalog_2, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "Prediction algorithm: #{model.prediction_algorithm.gsub('Algorithm::','').gsub('_',' ').gsub('.', ' with ')} #{(pred_algorithm_params ? pred_algorithm_params : '')}"}
+		#report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_2
 
 		# Descriptors in the model 4.3
-		if model.neighbor_algorithm_parameters[:type]
-			report.change_catalog :descriptors_catalog, :descriptors_catalog_1, {:description => "", :name => "#{model.neighbor_algorithm_parameters[:type]}", :publication_ref => "", :units => ""}
-			report.ref_catalog :algorithms_descriptors, :descriptors_catalog, :descriptors_catalog_1
-		end
+		#if model.neighbor_algorithm_parameters[:type]
+		#	report.change_catalog :descriptors_catalog, :descriptors_catalog_1, {:description => "", :name => "#{model.neighbor_algorithm_parameters[:type]}", :publication_ref => "", :units => ""}
+		#	report.ref_catalog :algorithms_descriptors, :descriptors_catalog, :descriptors_catalog_1
+		#end
 
 		# Descriptor selection 4.4
-		report.value "descriptors_selection", "#{model.feature_selection_algorithm.gsub('_',' ')} #{model.feature_selection_algorithm_parameters.collect{|k,v| k.to_s + ': ' + v.to_s}.join(', ')}" if model.feature_selection_algorithm  
-    response['Content-Type'] = "application/xml"
+		#report.value "descriptors_selection", "#{model.feature_selection_algorithm.gsub('_',' ')} #{model.feature_selection_algorithm_parameters.collect{|k,v| k.to_s + ': ' + v.to_s}.join(', ')}" if model.feature_selection_algorithm  
     
-		return report.to_xml
+    response['Content-Type'] = "application/xml"
+    return report.to_xml
   else
     bad_request_error "model with id: #{params[:id]} does not exist."
   end
@@ -73,23 +74,23 @@ end
 #=end
 get '/predict/?' do
   @prediction_models = []
-  prediction_models = OpenTox::Model::NanoPrediction.all
-  prediction_models.each{|m| m.model[:feature_selection_algorithm_parameters]["category"] == "P-CHEM" ? @prediction_models[0] = m : @prediction_models[1] = m}
+  prediction_models = Model::NanoPrediction.all
+  prediction_models.each{|m| m.model[:algorithms]["descriptors"]["categories"] == ["P-CHEM"] ? @prediction_models[0] = m : @prediction_models[1] = m}
   # define type (pc or pcp)
   @prediction_models.each_with_index{|m,idx| idx == 0 ? m[:pc_model] = true : m[:pcp_model] = true}
   # collect nanoparticles by training dataset (Ag + Au)
-  dataset = OpenTox::Dataset.find_by(:name=> "Protein Corona Fingerprinting Predicts the Cellular Interaction of Gold and Silver Nanoparticles")
+  dataset = Dataset.find_by(:name=> "Protein Corona Fingerprinting Predicts the Cellular Interaction of Gold and Silver Nanoparticles")
   nanoparticles = dataset.nanoparticles
   
-  # select physchem_parameters by relevant_features for of each model
-  @pc_relevant_features = @prediction_models[0].model.relevant_features.collect{|id, v| OpenTox::Feature.find(id)}
-  @pcp_relevant_features = @prediction_models[1].model.relevant_features.collect{|id, v| OpenTox::Feature.find(id)}
+  # select physchem_parameters by relevant features for each model
+  @pc_relevant_features = @prediction_models[0].model.descriptor_ids.collect{|id, v| Feature.find(id)}
+  @pcp_relevant_features = @prediction_models[1].model.descriptor_ids.collect{|id, v| Feature.find(id)}
   pcp = nanoparticles.sample
-  pcp.physchem_descriptors.delete_if{|id,v| !@pcp_relevant_features.include?(OpenTox::Feature.find(id))}
+  pcp.properties.delete_if{|id,v| !@pcp_relevant_features.include?(Feature.find(id))}
   @example_pcp = pcp
   
   pc = nanoparticles.sample
-  pc.physchem_descriptors.delete_if{|id,v| !@pc_relevant_features.include?(OpenTox::Feature.find(id))}
+  pc.properties.delete_if{|id,v| !@pc_relevant_features.include?(Feature.find(id))}
   @example_pc = pc
 
   haml :predict
@@ -102,7 +103,7 @@ end
 
 post '/predict/?' do
   # choose the right prediction model
-  prediction_model = OpenTox::Model::NanoPrediction.find(params[:prediction_model])
+  prediction_model = Model::NanoPrediction.find(params[:prediction_model])
   size = params[:size].to_i
   @type = params[:type]
 
@@ -123,28 +124,28 @@ post '/predict/?' do
 
   
   # define relevant_features by input
-  @type = "pc" ? (@pc_relevant_features = input_pc.collect{|id,v| OpenTox::Feature.find(id)}) : (@pc_relevant_features = [])
-  @type = "pcp" ? (@pcp_relevant_features = input_pc.collect{|id,v| OpenTox::Feature.find(id)}) : (@pcp_relevant_features = [])
+  @type = "pc" ? (@pc_relevant_features = input_pc.collect{|id,v| Feature.find(id)}) : (@pc_relevant_features = [])
+  @type = "pcp" ? (@pcp_relevant_features = input_pc.collect{|id,v| Feature.find(id)}) : (@pcp_relevant_features = [])
 
   if input_pc == example_pc && input_core == example_core && input_coating == example_coating
     # unchanged input = database hit
-    nanoparticle = OpenTox::Nanoparticle.find_by(:id => params[:example_id])
-    nanoparticle.physchem_descriptors = input_pc
+    nanoparticle = Nanoparticle.find_by(:id => params[:example_id])
+    nanoparticle.properties = input_pc
     @match = true
     @nanoparticle = nanoparticle
     @name = nanoparticle.name
   else
     # changed input = create nanoparticle to predict
-    nanoparticle = OpenTox::Nanoparticle.new
+    nanoparticle = Nanoparticle.new
     nanoparticle.core = input_core
     nanoparticle.coating = input_coating
-    nanoparticle.physchem_descriptors = input_pc
+    nanoparticle.properties = input_pc
     @match = false
     @nanoparticle = nanoparticle
   end
   # prediction output
   @input = input_pc
-  @prediction = prediction_model.model.predict_substance nanoparticle
+  @prediction = prediction_model.model.predict nanoparticle
   
   haml :prediction
 end