From 8ebb06ddc85b38cd6ec71d81f55b800fd5825c15 Mon Sep 17 00:00:00 2001 From: gebele Date: Thu, 10 Nov 2016 19:53:34 +0000 Subject: version bump;units;general class update;sort by --- application.rb | 79 +++++++++++++++++++++++++++++----------------------------- 1 file changed, 40 insertions(+), 39 deletions(-) (limited to 'application.rb') 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 -- cgit v1.2.3