From 4b8e18a19f375b8d4c12621ec8f8f9ee305d11fa Mon Sep 17 00:00:00 2001 From: gebele Date: Wed, 12 Oct 2016 13:45:37 +0000 Subject: stage save for transmission --- application.rb | 121 ++++++++++++++++++++++++++++++++++++++++++++++++++------- 1 file changed, 106 insertions(+), 15 deletions(-) (limited to 'application.rb') diff --git a/application.rb b/application.rb index 29c1aca..a702d9a 100644 --- a/application.rb +++ b/application.rb @@ -1,9 +1,11 @@ +require 'qsar-report' require 'rdiscount' $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=" + configure :development do - $logger = Logger.new(STDOUT) + #$logger = Logger.new(STDOUT) end before do @@ -13,27 +15,111 @@ end get '/?' do redirect to('/predict') end -=begin -get '/qsar-report/:id' do +#=begin +get '/qmrf-report/:id' do + prediction_model = OpenTox::Model::NanoPrediction.find(params[:id]) + if prediction_model + model = prediction_model.model + model_type = "regression" + report = OpenTox::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}" + else + lazar_commit = "https://github.com/opentox/lazar/releases/tag/v#{Gem.loaded_specs["lazar"].version}" + end + report.value "QSAR_title", "Model for #{prediction_model.species} #{prediction_model.endpoint}" + report.change_catalog :software_catalog, :firstsoftware, {:name => "nano-lazar", :description => "nano-lazar toxicity predictions", :number => "1", :url => "https://nano-lazar.in-silico.ch", :contact => "helma@in-silico.ch"} + report.ref_catalog :QSAR_software, :software_catalog, :firstsoftware + 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.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.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 + + # 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 + + # 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" + + return report.to_xml + else + bad_request_error "model with id: #{params[:id]} does not exist." + end end -=end +#=end get '/predict/?' do + # temporarily outstanding + nos = %w(S40.CIT + S40.MES + S40.MUTA + S40.cPEG5K-SH + S40.DDT@DOTAP + S40.MAA + S40.PLL-SH + S40.mPEG5K-SH + S40.MBA + S40.PVA + S40.LA + S40.AUT + S40.HDA + S40.SA + S40.nPEG5K-SH + S40.MHDA + ) @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} + # 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") - nanoparticles = dataset.nanoparticles - # select physchem_parameters by relevant_features out 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)} + # temporarily delete silver + nanoparticles = dataset.nanoparticles#.delete_if{|n| !nos.include?(n.name)} + + # select physchem_parameters by relevant_features out of each model; use @@ for global usage (prediction.haml) + @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)} + # check for outstanding nanoparticles pcp = nanoparticles.sample - pcp.physchem_descriptors.delete_if{|id,v| !@@pcp_relevant_features.include?(OpenTox::Feature.find(id))} + #while nos.include?(pcp.name) + # pcp = nanoparticles.sample + #end + # use only relevant features + pcp.physchem_descriptors.delete_if{|id,v| !@pcp_relevant_features.include?(OpenTox::Feature.find(id))} @example_pcp = pcp + + # check for outstanding nanoparticles pc = nanoparticles.sample - pc.physchem_descriptors.delete_if{|id,v| !@@pc_relevant_features.include?(OpenTox::Feature.find(id))} + #while nos.include?(pc.name) + # pcp = nanoparticles.sample + #end + # use only relevant features + #pc.physchem_descriptors.delete_if{|id,v| OpenTox::Feature.find(id).category != "P-CHEM"} + pc.physchem_descriptors.delete_if{|id,v| !@pc_relevant_features.include?(OpenTox::Feature.find(id))} @example_pc = pc haml :predict @@ -45,7 +131,6 @@ get '/license' do end post '/predict/?' do - # choose the right prediction model prediction_model = OpenTox::Model::NanoPrediction.find(params[:prediction_model]) size = params[:size].to_i @@ -64,7 +149,13 @@ post '/predict/?' do input_coating = in_coating input_pc = {} - (1..size).each{|i| input_pc["#{params["input_key_#{i}"]}"] = [params["input_value_#{i}"].to_f]} + (1..size).each{|i| input_pc["#{params["input_key_#{i}"]}"] = [params["input_value_#{i}"].to_f] unless params["input_value_#{i}"] == "-"} + + + # 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 = []) + 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]) @@ -81,9 +172,9 @@ post '/predict/?' do @match = false @nanoparticle = nanoparticle end - # output + # prediction output @input = input_pc @prediction = prediction_model.model.predict_substance nanoparticle - + haml :prediction end -- cgit v1.2.3