add mazzatorta

6 files changed, 122 insertions, 17 deletions

diff --git a/Gemfile b/Gemfile
index 7b443e3..9945517 100644
--- a/Gemfile
+++ b/Gemfile
@@ -3,6 +3,7 @@ gemspec
 gem "lazar", :path => "../lazar"
 gem "toxtree", :path => "../toxtree"
 gem "kazius-alerts", :path => "../kazius-alerts"
+gem "loael-mazzatorta", :path => "../loael-mazzatorta"
 gem "gem-path"
 gem "sinatra"
 gem "sinatra-reloader"
diff --git a/application.rb b/application.rb
index ee7837f..fdb7086 100644
--- a/application.rb
+++ b/application.rb
@@ -38,8 +38,11 @@ get '/predict/?' do
   @existing_datasets = dataset_storage
   @models = Model::Validation.all
   @models = @models.delete_if{|m| m.model.name =~ /\b(Net cell association)\b/}
-  @endpoints = @models.collect{|m| m.endpoint}.sort.uniq
-  @endpoints << "Oral toxicity (Cramer rules)"
+  #endpoints = @models.collect{|m| m.endpoint =~ /LOAEL/ ? m.endpoint+" (lazar)" : m.endpoint}
+  endpoints = @models.collect{|m| m.endpoint}
+  endpoints << "Oral toxicity (Cramer rules)"
+  endpoints << "Lowest observed adverse effect level (LOAEL) (Mazzatorta)"
+  @endpoints = endpoints.sort.uniq
   @models.count <= 0 ? (haml :info) : (haml :predict)
 end
 
@@ -63,6 +66,22 @@ get '/task/?' do
       string += "<tr><td>Cramer rules, with extensions:</td><td>#{prediction["Cramer rules, with extensions"][pageNumber.to_i]}</td>"
       string += "</table></td>"
       html += "#{string}</tr></table>"
+    elsif params[:model] == "Mazzatorta"
+      prediction = task.predictions[params[:model]]
+      compound = Compound.find prediction["compounds"][pageNumber]
+      image = compound.svg
+      smiles = compound.smiles
+      html = "<table class=\"table table-bordered single-batch\"><tr>"
+      html += "<td>#{image}</br>#{smiles}</br></td>"
+      string = "<td><table class=\"table\">"
+      if prediction["mazzatorta"][pageNumber.to_i][:prediction]
+        string += "<tr class=\"hide-top\"><td>Prediction:</td><td>#{prediction["mazzatorta"][pageNumber.to_i][:mmol_prediction]} (mmol/kg_bw/day)</td>"
+        string += "<tr class=\"hide-top\"><td></td><td>#{prediction["mazzatorta"][pageNumber.to_i][:prediction]} (mg/kg_bw/day)</td>"
+      else
+        string += "<tr><td>Warnings:</td><td>#{prediction["mazzatorta"][pageNumber.to_i][:warnings]}</td>"
+      end
+      string += "</table></td>"
+      html += "#{string}</tr></table>"
     else
       predictions = task.predictions[params[:model]].collect{|hash| hash.values[0]}
       prediction_object = Prediction.find predictions[pageNumber]
@@ -188,9 +207,13 @@ get '/predict/csv/:task/:model/:filename/?' do
       end
     end
   end
-  endpoint = (params[:model] == "Cramer") ? "Oral_toxicity_(Cramer_rules)" : (m.endpoint =~ /Mutagenicity/i ? "Consensus_mutagenicity" : "#{m.endpoint}_(#{m.species})")
+  if params[:model] == "Mazzatorta"
+    endpoint = "Lowest observed adverse effect level (LOAEL) (Rats) (Mazzatorta)"
+  else
+    endpoint = (params[:model] == "Cramer") ? "Oral_toxicity_(Cramer_rules)" : (m.endpoint =~ /Mutagenicity/i ? "Consensus_mutagenicity" : "#{m.endpoint}_(#{m.species})")
+  end
   tempfile = Tempfile.new
-  if params[:model] == "Cramer"
+  if params[:model] == "Cramer" || params[:model] == "Mazzatorta"
     # add duplicate warning at the end of a line if ID matches
     if @dups
       lines = task.csv.split("\n")
@@ -309,7 +332,7 @@ post '/predict/?' do
     task = Task.run do
       @models.each_with_index do |model,idx|
         t = @tasks[idx]
-        unless model == "Cramer"
+        if model !~ /Cramer|Mazzatorta/
           m = Model::Validation.find model
           type = (m.regression? ? "Regression" : "Classification")
           # add header for regression
@@ -420,6 +443,47 @@ post '/predict/?' do
           t[:csv] = header
           # write predictions
           @predictions["#{model}"] = predictions
+        elsif model == "Mazzatorta"
+          compounds = @compounds.collect{|cid| c = Compound.find cid; c.smiles}
+          prediction = LoaelMazzatorta.predict(compounds)
+          output = {}
+          output["model_name"] = "Lowest observed adverse effect level (LOAEL) (Rats) (Mazzatorta)"
+          output["mazzatorta"] = []
+          #output["mazzatorta"] = prediction
+          # header
+          if @ids.blank?
+            csv = "ID,Input,Endpoint,Unique SMILES,Prediction (mmol/kg_bw/day),Prediction (mg/kg_bw/day),Notes\n"
+          else
+            csv = "ID,Original ID,Input,Endpoint,Unique SMILES,Prediction (mmol/kg_bw/day),Prediction (mg/kg_bw/day),Notes\n"
+          end
+          # content
+          compounds.each_with_index do |smiles, idx|
+            compound = Compound.find @compounds[idx]
+            if prediction[idx]["value"]
+              output["mazzatorta"][idx] = {:mmol_prediction => compound.mg_to_mmol(prediction[idx]["value"].delog10p).signif(3),:prediction => prediction[idx]["value"].delog10p.signif(3)}
+            else
+              output["mazzatorta"][idx] = {:warnings => prediction[idx]["warnings"][0].split("\t").first}
+            end
+            if @ids.blank?
+              csv << "#{idx+1},#{@identifiers[idx]},#{output["model_name"]},#{smiles},"\
+                "#{output["mazzatorta"][idx][:mmol_prediction] if output["mazzatorta"][idx][:mmol_prediction]},"\
+                "#{output["mazzatorta"][idx][:prediction] if output["mazzatorta"][idx][:prediction]},"\
+                "#{output["mazzatorta"][idx][:warnings] if output["mazzatorta"][idx][:warnings]}\n"
+            else
+              csv << "#{idx+1},#{@ids[idx]},#{@identifiers[idx]},#{output["model_name"]},#{smiles},"\
+                "#{output["mazzatorta"][idx][:mmol_prediction] if output["mazzatorta"][idx][:mmol_prediction]},"\
+                "#{output["mazzatorta"][idx][:prediction] if output["mazzatorta"][idx][:prediction]},"\
+                "#{output["mazzatorta"][idx][:warnings] if output["mazzatorta"][idx][:warnings]}\n"
+            end
+          end
+          predictions = {}
+          predictions["mazzatorta"] = output["mazzatorta"]
+          #predictions["compounds"] = @compounds
+          # write csv
+          t[:csv] = csv
+          # write predictions
+          @predictions["#{model}"] = predictions
+          t.update_percent(100)
         else # Cramer model
           compounds = @compounds.collect{|cid| c = Compound.find cid; c.smiles}
           prediction = [Toxtree.predict(compounds, "Cramer rules"), Toxtree.predict(compounds, "Cramer rules with extensions")]
@@ -486,6 +550,16 @@ post '/predict/?' do
       if model_id == "Cramer"
         @toxtree = true
         @predictions << [Toxtree.predict(@compound.smiles, "Cramer rules"), Toxtree.predict(@compound.smiles, "Cramer rules with extensions")]
+      elsif model_id == "Mazzatorta"
+        prediction = LoaelMazzatorta.predict(@compound.smiles)
+        output = {}
+        $logger.debug prediction
+        if prediction["value"]
+          output["mazzatorta"] = {:mmol_prediction => @compound.mg_to_mmol(prediction["value"].delog10p).signif(3),:prediction => prediction["value"].delog10p.signif(3)}
+        else
+          output["mazzatorta"] << {:warnings => prediction["warnings"][0].split("\t").first}
+        end
+        @predictions << output
       else
         model = Model::Validation.find model_id
         @models << model
diff --git a/lazar-gui.gemspec b/lazar-gui.gemspec
index 592d929..34f1aef 100644
--- a/lazar-gui.gemspec
+++ b/lazar-gui.gemspec
@@ -16,11 +16,11 @@ Gem::Specification.new do |s|
   s.add_runtime_dependency "lazar"
   s.add_runtime_dependency "toxtree"
   s.add_runtime_dependency "kazius-alerts"
-  s.add_runtime_dependency "gem-path", "~> 0.6.1", '>= 0.6.1'
-  s.add_runtime_dependency "sinatra", "~> 1.4.0", '>= 1.4.0'
-  s.add_runtime_dependency "rdiscount", "~> 2.1.0", '>= 2.1.0'
-  s.add_runtime_dependency "haml", "~> 4.0.0", '>= 4.0.0'
-  s.add_runtime_dependency "sass", "~> 3.4.0", '>= 3.4.0'
+  s.add_runtime_dependency "gem-path"
+  s.add_runtime_dependency "sinatra"
+  s.add_runtime_dependency "rdiscount"
+  s.add_runtime_dependency "haml"
+  s.add_runtime_dependency "sass"
   s.add_runtime_dependency "unicorn"
 
   s.post_install_message = %q{
diff --git a/views/batch.haml b/views/batch.haml
index 1aa6779..165b64b 100644
--- a/views/batch.haml
+++ b/views/batch.haml
@@ -76,7 +76,7 @@
         callback: function(data, pagination) {
           var html = simpleTemplating(data);
           $('#data-container_'+id).html(html);
-          $('#data-container_'+id).css("min-height", $(window).height() + "px" );
+          //$('#data-container_'+id).css("min-height", $(window).height() + "px" );
         }
       });
     } else if (span.className = "glyphicon glyphicon-menu-down"){
@@ -105,8 +105,12 @@
     #result.panel{:id=>idx}
       %div.row
         %div.col-md-6
-          %h5= (model == "Cramer") ? "Oral toxicity (Cramer rules)" : (m.endpoint =~ /Mutagenicity/i ? "Consensus mutagenicity" : "#{m.endpoint} (#{m.species})")
-          #pager{:id=>idx}
+          - if model =~ /Mazzatorta/
+            %h5= "Lowest observed adverse effect level (LOAEL) (Mazzatorta) Rats"
+            #pager{:id=>idx}
+          - else
+            %h5= (model == "Cramer") ? "Oral toxicity (Cramer rules)" : (m.endpoint =~ /Mutagenicity/i ? "Consensus mutagenicity" : "#{m.endpoint} (#{m.species})")
+            #pager{:id=>idx}
         %div.col-md-6.h5
           %a.btn.btn-default.btn-xs.disabled{:id => "detailsbutton_#{idx}", :data=>{:toggle=>"collapse"}, :href=>"javascript:void(0)", :onclick=>"pagePredictions('#{task}','#{model}','#{idx}')", :style=>"font-size:small;"}
             %span.glyphicon.glyphicon-menu-right
diff --git a/views/predict.haml b/views/predict.haml
index d638451..0afcc99 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -186,8 +186,8 @@
       - @endpoints.each do |endpoint|
         %div{:id=>endpoint.gsub(/\s+/, "_")}
           %h4.head-back=endpoint
-          - unless endpoint =~ /^Oral/
-            - @models.select{|m| m.endpoint == endpoint}.each do |model|
+          - if endpoint !~ /^Oral|Mazzatorta/
+            - @models.select{|m| endpoint = endpoint.gsub("(lazar)","").strip if endpoint =~ /lazar/; m.endpoint == endpoint}.each do |model|
               %div.row{:id => model.id,:style=>"margin-bottom:1em;"}
                 %span.col-lg-4.col-md-4.col-sm-4.col-xs-4
                   %input.check{:type => "checkbox", :name => "selection[#{model.id}]", :id => "selection[#{model.species.gsub(/\s+/, "_")}]", :value => true, :disabled => false}
@@ -223,12 +223,18 @@
                     });
                   }
                 }
-          - else
+          - elsif endpoint =~ /^Oral/
             %div.row{:id => "Cramer",:style=>"margin-bottom:1em;"}
               %span.col-lg-4.col-md-4.col-sm-4.col-xs-4
                 %input.check{:type => "checkbox", :name => "selection[Cramer]", :id => "selection[Cramer]", :value => true, :disabled => false}
                 %label{:for => "selection[Cramer]"}
                   Cramer rules
+          - elsif endpoint =~ /Mazzatorta/
+            %div.row{:id => "Mazzatorta",:style=>"margin-bottom:1em;"}
+              %span.col-lg-4.col-md-4.col-sm-4.col-xs-4
+                %input.check{:type => "checkbox", :name => "selection[Mazzatorta]", :id => "selection[Mazzatorta]", :value => true, :disabled => false}
+                %label{:for => "selection[Mazzatorta]"}
+                  Rats
   %fieldset#bottom.well
     %div.row
       %div.col-md-2
diff --git a/views/prediction.haml b/views/prediction.haml
index b4b51ca..152efc9 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -23,6 +23,8 @@
           - @model_types = {}
           - @dbhit = {}
           - toxtree = @predictions.pop if @toxtree == true
+          - mazzatorta = @predictions.find{|p| p["mazzatorta"]}
+          - @predictions.delete(mazzatorta) if mazzatorta
           - unless @predictions.blank?
             - @predictions.each_with_index do |prediction,i|
               - if prediction["Consensus prediction"]
@@ -138,7 +140,7 @@
                       %br
                       =prediction[:warnings].join("</br>")
 
-          / show Cramer rules if checked
+          / Cramer
           - if @toxtree == true
             %td{:style=>"vertical-align:top;white-space:nowrap;"}
               %b.title Oral toxicity (Cramer rules)
@@ -151,6 +153,24 @@
               %br
               =toxtree.last["Cramer rules, with extensions"]
 
+          / Mazzatorta
+          - if mazzatorta
+            %td{:style=>"vertical-align:top;white-space:nowrap;"}
+              %b.title Lowest observed adverse effect level (LOAEL) (Rats) (Mazzatorta)
+              %p
+              - hash = mazzatorta["mazzatorta"]
+              - unless hash.keys.include?("warnings")
+                %b Prediction:
+                %br
+                = "#{hash[:mmol_prediction]} (mmol/kg_bw/day)"
+                %br
+                = "#{hash[:prediction]} (mg/kg_bw/day)"
+              - else
+                %b Warnings:
+                %br
+                = "#{hash[:warnings]}"
+
+
   / always show the neighbors table, message is given there. Except only Cramer is selected.
   - unless @predictions.blank?
     = haml :neighbors, :layout => false