stage save for transmission

5 files changed, 167 insertions, 38 deletions

diff --git a/Gemfile b/Gemfile
index a33d28e..7692587 100644
--- a/Gemfile
+++ b/Gemfile
@@ -1,6 +1,7 @@
 source "https://rubygems.org"
 gemspec
 gem "lazar", :path => "../lazar"
+gem "qsar-report", :path => "../qsar-report"
 gem "sinatra"
 gem 'sinatra-reloader', '~> 1.0'
 gem "haml"
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
diff --git a/config.ru b/config.ru
index eec777d..36438a3 100644
--- a/config.ru
+++ b/config.ru
@@ -4,4 +4,10 @@ require 'bundler'
 Bundler.require
 require File.expand_path './application.rb'
 require "sinatra/reloader" if development?
+
+FileUtils.mkdir_p 'log' unless File.exists?('log')
+log = File.new("log/nano-lazar.log", "a")
+$stdout.reopen(log)
+$stderr.reopen(log)
+
 run Sinatra::Application
diff --git a/views/predict.haml b/views/predict.haml
index 1cd2916..0630b2c 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -14,7 +14,7 @@
             = "#{idx+1}. #{m.model.feature_selection_algorithm_parameters[:category].nil? ? "Physchem & Proteomics" : "Physchem" }"
     %div.tab-content
       - @prediction_models.each_with_index do |m, idx|
-        - m[:pc_model] ? (example = @example_pc; type = "pc") : (example = @example_pcp; type = "pcp")
+        - m[:pc_model] ? (example = @example_pc; type = "pc"; relevant_features = @pc_relevant_features) : (example = @example_pcp; type = "pcp"; relevant_features = @pcp_relevant_features)
         #model.tab-pane{:id=>"#{idx}", :class => ("active" if idx == 0)}
           %b Model:
           %br
@@ -38,8 +38,20 @@
           %br
           Unit:
           = m.unit
+          %br
+          Prediction algorithm:
+          = m.model.prediction_algorithm.split(".").last.gsub("_"," ")
+          %br
+          Prediction algorithm parameter:
+          = "random forest" if m.model.prediction_algorithm_parameters["method"] == "rf"
+          %br
+          Neighbor algorithm:
+          = m.model.neighbor_algorithm.gsub("_", " ")
+          %br
+          Neighbor algorithm parameter:
+          = "min sim = #{m.model.neighbor_algorithm_parameters["min_sim"]}"
           %p
-          - cv = OpenTox::CrossValidation.find(m.repeated_crossvalidation_id)
+          -#- cv = OpenTox::CrossValidation.find(m.repeated_crossvalidation_id)
           %b Independent crossvalidations (log2 transformed):
           - crossvalidations =[]
           - m.repeated_crossvalidation.crossvalidation_ids.each{|cv| c = OpenTox::Validation::CrossValidation.find(cv); crossvalidations << c}
@@ -55,18 +67,18 @@
                 = "Num unpredicted"
                 = cv.nr_unpredicted
                 %br
-                = "Root mean squared error:\t"
+                %a.ht5{:href=>"https://en.wikipedia.org/wiki/Root-mean-square_deviation", :rel=>"external"} RMSE:
                 = cv.rmse.round(3) if cv.rmse
                 %br
-                = "Mean absolute error:\t"
+                %a.ht5{:href=>"https://en.wikipedia.org/wiki/Mean_absolute_error", :rel=>"external"} MAE:
                 = cv.mae.round(3) if cv.mae
                 %br 
-                = "R square:\t"
+                %a.ht5{:href=>"https://en.wikipedia.org/wiki/Coefficient_of_determination", :rel=>"external"}= "R"+"<sup>2</sup>"+":"
                 = cv.r_squared.round(3) if cv.r_squared
           %br
-          //%b QSAR report
-          //%br
-          //%a{:href=>to('/qsar-report/'+m.id)} download
+          %b QMRF report
+          %p
+          %a.btn.btn-default{:href=>to('/qmrf-report/'+m.id), :rel=>"external"} download
           %hr
           %form{:id=>idx, :role=>"form", :action=> to("/predict"), :method=>"post"}
             %h3.help-block
@@ -79,13 +91,15 @@
               %input{:id=>"example_core",:type=>"hidden",:name=>"example_core",:value=>"#{example.core}"}
               %input{:id=>"example_coating",:type=>"hidden",:name=>"example_coating",:value=>"#{example.coating}"}
               %input{:id=>"example_pc",:type=>"hidden",:name=>"example_pc",:value=>"#{example.physchem_descriptors}"}
-              - size = example.physchem_descriptors.size
+              -#- size = example.physchem_descriptors.size
+              - size = relevant_features.size
               %input{:id=>"size",:type=>"hidden",:name=>"size",:value=>size}
               %input{:id=>"id",:type=>"hidden",:name=>"example_id",:value=>example.id}
               // input form parameters to transfer
               %div.form-group
                 %label{:for=>"selCore#{idx}"} Core
-                %select.form-control{:id=>"selCore#{idx}", :name=>"input_core",:value=>example.core["name"]}
+                /%p= example.core["name"]
+                %select.form-control{:id=>"selCore#{idx}", :autocomplete=>"off", :name=>"input_core",:value=>example.core["name"]}
                   %option{:selected => ("selected" if example.core["name"] == "Ag")} Ag
                   %option{:selected => ("selected" if example.core["name"] == "Au")} Au
               %input{:id=>"input_core",:type=>"hidden",:name=>"in_core",:value=>"#{example.core}"}
@@ -95,14 +109,20 @@
               %input{:id=>"input_coating",:type=>"hidden",:name=>"in_coating",:value=>example.coating}
               // prediction model id 
               %input{:id=>"prediction_model",:type=>"hidden",:name=>"prediction_model",:value=>m.id}
-            - example.physchem_descriptors.sort_by{|d| OpenTox::Feature.find(d[0]).category}.each_with_index do |v,id|
-              - feature = OpenTox::Feature.find_by(:id => v[0])
+            - relevant_features.sort_by{|d| d.category}.each_with_index do |relf,id|
+              -#- example.physchem_descriptors.sort_by{|d| OpenTox::Feature.find(d[0]).category}.each_with_index do |v,id|
+              - feature = relf
+              /%p= feature.id
+              - v = example.physchem_descriptors.find{|id,v| id == feature.id.to_s  }
+              /%p= v
+              -#- feature = OpenTox::Feature.find_by(:id => v[0])
+              -#- feature = v
               - name = feature.name
               - if feature[:conditions] && !feature[:conditions]["MEDIUM"].blank?
                 - name = feature.name + " / " + feature[:conditions]["MEDIUM"]
               - else
                 - name = feature.name
-              - val = v[1]
+              - val = !v.nil? ? v[1] : "-"
               - id = id + 1
               - if feature.category == "Proteomics"
                 %h5
@@ -113,8 +133,10 @@
                 %h5
                   %a{:href=>$npo_search % string, :rel=>"external"}= name
               // input physchem parameters
-              %input.input-sm.form-control{:id=>id,:type=>"text",:name=>"input_value_#{id}",:value=>val[0]}
-              %input{:id=>id,:type=>"hidden",:name=>"input_key_#{id}",:value=>v[0]}
+              %input.input-sm.form-control{:id=>id,:type=>"text",:name=>"input_value_#{id}",:value=>"#{val[0] if val[0]}", :disabled=>("disabled" if val[0] == "-")}
+              - if val[0] == "-"
+                %input{:id=>id,:type=>"hidden",:name=>"input_value_#{id}",:value=>"-"}
+              %input{:id=>id,:type=>"hidden",:name=>"input_key_#{id}",:value=>feature.id}
             %hr
             #predict
               %button.btn.btn-success{:id=>"submitbutton", :type=>"submit", :onclick=>"showcircle();"} 
diff --git a/views/prediction.haml b/views/prediction.haml
index 8f72a23..e6b4ae4 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -15,6 +15,8 @@
         headerTemplate: '{content} {icon}',
         widgets: ['uitheme', 'staticRow', 'stickyHeaders'],
         widgetOptions: {
+          stickyHeaders_attachTo: 'neighbors',
+          stickyHeaders_offset: 0,
           stickyHeaders_xScroll : null
         },
         sortList: [[1,1]],
@@ -41,7 +43,8 @@
             Net cell association
             %br
             [mL/ug(Mg)]
-          - @input.sort_by{|d| OpenTox::Feature.find(d[0]).category}.each do |key|
+          -#- @input.sort_by{|d| OpenTox::Feature.find(d[0]).category}.each do |key|
+          - @input.each{|d| OpenTox::Feature.find(d[0]).category}.each do |key|
             - feature = OpenTox::Feature.find_by(:id=>key[0])
             - name = feature.name
             - if (feature[:conditions] && !feature[:conditions]["MEDIUM"].blank?)
@@ -88,12 +91,16 @@
               %h5.th5 Prediction:
               = @prediction[:value].round(3)
               %br
-            - if @prediction[:rmse]
+            - if @prediction[:value].blank?
+              %h5.th5 Prediction:
+              = "not available"
+              %br
+            -#- if @prediction[:rmse]
               %h5.th5
                 %a{:href=>"https://en.wikipedia.org/wiki/Root-mean-square_deviation", :rel=>"external"} RMSE:
               = @prediction[:rmse].round(3)
               %br
-            - if @prediction[:r_squared]
+            -#- if @prediction[:r_squared]
               %h5.th5
                 %a{:href=>"https://en.wikipedia.org/wiki/Coefficient_of_determination", :rel=>"external"}= "R"+"<sup>2</sup>"+":"
               = @prediction[:r_squared].round(3)
@@ -111,7 +118,8 @@
             - if !@prediction[:value] && !@prediction[:measurements]
               %h5.th5 not available
           / physchem
-          - @input.sort_by{|d| OpenTox::Feature.find(d[0]).category}.each do |v|
+          -#- @input.sort_by{|d| OpenTox::Feature.find(d[0]).category}.each do |v|
+          - @input.each do |v|
             %td.physchem
               %div{:style=>"display:inline-block;padding-right:20px;"}
                 - if v[1].nil?
@@ -123,7 +131,7 @@
         - if @prediction[:neighbors]
           - @prediction[:neighbors].each_with_index do |neighbor,idx|
             - nano = OpenTox::Nanoparticle.find(neighbor["_id"])
-            - pc_descriptors = nano.physchem_descriptors.delete_if{|id,v| OpenTox::Feature.find(id).category != "P-CHEM"} if @type == "pc"
+            -#- nano.physchem_descriptors.delete_if{|id,v| OpenTox::Feature.find(id).category != "P-CHEM"} if @type == "pc"
             %tr
               / ID
               %td
@@ -144,8 +152,9 @@
                 %h5.th5 Measurement:
                 = neighbor["measurements"][0]
               / Physchem
-              - nano.physchem_descriptors.delete_if{|id,v| @type == "pc" ? !@@pc_relevant_features.include?(OpenTox::Feature.find(id)) : !@@pcp_relevant_features.include?(OpenTox::Feature.find(id))}.sort_by{|id,v| OpenTox::Feature.find(id).category}.each do |k,v|
+              -#- nano.physchem_descriptors.delete_if{|id,v| @type == "pc" ? !@pc_relevant_features.include?(OpenTox::Feature.find(id)) : !@pcp_relevant_features.include?(OpenTox::Feature.find(id))}.sort_by{|id,v| OpenTox::Feature.find(id).category}.each do |k,v|
+              - nano.physchem_descriptors.delete_if{|id,v| @type == "pc" ? !@pc_relevant_features.include?(OpenTox::Feature.find(id)) : !@pcp_relevant_features.include?(OpenTox::Feature.find(id))}.sort_by{|id,v| @pc_relevant_features.index OpenTox::Feature.find(id)}.each do |k,v|
                 %td.physchem
-                  %div
+                  -#%div
                     %div{:style=>"display:inline-block;padding-right:20px;"}
-                      = v[0].round(3) unless v.nil?
+                  = v[0].round(3) unless v.nil?