Initial GUI for Nestec models

6 files changed, 133 insertions, 364 deletions

diff --git a/Gemfile b/Gemfile
index 1b83cff..736527c 100644
--- a/Gemfile
+++ b/Gemfile
@@ -3,12 +3,4 @@ gemspec
 gem "sinatra"
 gem "haml"
 gem "sass"
-gem "opentox-server", :path => "../opentox-server"
-gem "opentox-client", :path => "../opentox-client"
-gem "opentox-algorithm", :path => "../algorithm"
-gem "opentox-compound", :path => "../compound"
-gem "opentox-dataset", :path => "../dataset"
-gem "opentox-feature", :path => "../feature"
-gem "opentox-model", :path => "../model"
-gem "opentox-task", :path => "../task"
-gem "opentox-validation", :path => "../validation"
+gem "lazar", :path => "../lazar"
diff --git a/application.rb b/application.rb
index cff08a2..9b105a4 100644
--- a/application.rb
+++ b/application.rb
@@ -1,16 +1,12 @@
 require_relative 'helper.rb'
-require File.join(ENV["HOME"],".opentox","config","lazar-gui.rb") # until added to ot-tools
+include OpenTox
+#require File.join(ENV["HOME"],".opentox","config","lazar-gui.rb") # until added to ot-tools
 
 # DG: workaround for https://github.com/sinatra/sinatra/issues/808
 # Date: 18/11/2013
 set :protection, :except => :path_traversal
 
 helpers do
-  # models must be edited with RDF.type => (RDF::OT.PredictionModel, EchaEndpoint)
-  @@models = []
-  models = `curl -k GET -H accept:text/uri-list #{$model[:uri]}`.split("\n")
-  .collect{|m| model = OpenTox::Model::Lazar.find m; @@models << model if model.type.flatten.to_s =~ /PredictionModel/}
-  
   class Numeric
     def percent_of(n)
       self.to_f / n.to_f * 100.0
@@ -24,11 +20,9 @@ get '/?' do
 end
 
 get '/predict/?' do
-  # sort models by endpoint alphabetically
-  $size = 0
-  @models = @@models.sort!{|a, b| a.type.select{|e| e =~ /endpoint/i} <=> b.type.select{|e| e =~ /endpoint/i}}
-  @endpoints = @@models.collect{|e| e.type.select{|e| e =~ /endpoint/i}}.sort!.uniq
-  @models.size <= 0 ? (haml :info) : (haml :predict)
+  @models = OpenTox::Model::Prediction.all
+  @endpoints = @models.collect{|m| m.endpoint}.sort.uniq
+  @models.count <= 0 ? (haml :info) : (haml :predict)
 end
 
 get '/jme_help/?' do
@@ -202,68 +196,23 @@ end
 
 post '/predict/?' do
   # validate identifier input
-  task = OpenTox::Task.run("Validate SMILES string.") do
-    # transfered input
-    @identifier = params[:identifier]
-
+  # transfered input
+  @identifier = params[:identifier]
+  begin
     # get compound from SMILES
-    @compound = OpenTox::Compound.from_smiles @identifier.to_s
-    
-    # validate SMILES by converting to INCHI
-    inchi = @compound.inchi
-  end#smiles
-  # necessary to wait for task
-  task.wait
-  # case task fails return message smiles invalid  
-  # case task completed go ahead
-  case task[RDF::OT.hasStatus]
-  when "Error"
+    @compound = Compound.from_smiles @identifier#.to_s
+  rescue
     @error_report = "Attention, '#{params[:identifier]}' is not a valid SMILES string."
     haml :error
-  when "Completed"
-    @identifier = params[:identifier]
-    @compound = OpenTox::Compound.from_smiles @identifier.to_s
-    # init arrays
-    @prediction_models = []
-    @predictions = []
-    @model_type = []
-    # get selected models
-    # compare selected model by uri
-    params[:selection].each do |model|
-      # selected model = model[0]
-      # compare selected with all models
-      @@models.each do |m|
-        @prediction_models << m if m.uri == model[0]
-      end
-    end
-    # predict with selected models
-    # one prediction in 'pa' array = OpenTox::Dataset
-    # all collected predictions in '@predictions' array
-    # add task for progressBar
-    total = @prediction_models.size
-    toptask = OpenTox::Task.find params[:task_uri]
-    toptask.metadata
-    toptask[RDF::OT.hasStatus] = "Running"
-    toptask[RDF::OT.percentageCompleted] = "10"
-    toptask.put
-    @prediction_models.each_with_index do |m, idx|
-      idx = idx+1
-      # define type (classification|regression)
-      m.type.join =~ /classification/i ? (@model_type << "classification") : (@model_type << "regression")
-      
-      # predict against compound
-      @prediction_uri = m.run :compound_uri => "#{@compound.uri}"
-      $logger.debug "prediction dataset:\t#{@prediction_uri}\n"
-      
-      prediction = OpenTox::Dataset.new @prediction_uri
-      pa = []
-      pa << prediction
-      @predictions << pa
-      toptask[RDF::OT.percentageCompleted] = idx.percent_of(total).round(1)
-      toptask.put
-    end
-    haml :prediction
   end
+  @models = []
+  @predictions = []
+  params[:selection].keys.each do |model_id|
+    model = Model::Prediction.find model_id
+    @models << model
+    @predictions << model.predict(@compound)
+  end
+  haml :prediction
 end
 
 get '/style.css' do
diff --git a/lazar-gui.gemspec b/lazar-gui.gemspec
index 8b07ab2..dd852a0 100644
--- a/lazar-gui.gemspec
+++ b/lazar-gui.gemspec
@@ -15,18 +15,10 @@ Gem::Specification.new do |s|
   s.files       = `git ls-files`.split("\n")
   s.required_ruby_version = '>= 1.9.2'
 
-  s.add_runtime_dependency "opentox-server"
-  s.add_runtime_dependency "opentox-client"
-  s.add_runtime_dependency "opentox-algorithm"
-  s.add_runtime_dependency "opentox-compound"
-  s.add_runtime_dependency "opentox-dataset"
-  s.add_runtime_dependency "opentox-feature"
-  s.add_runtime_dependency "opentox-model"
-  s.add_runtime_dependency "opentox-task"
-  s.add_runtime_dependency "opentox-validation"
+  #s.add_runtime_dependency "opentox-server"
+  s.add_runtime_dependency "lazar"
   s.add_runtime_dependency "sinatra"
   s.add_runtime_dependency "haml"
   s.add_runtime_dependency "sass"
   s.add_runtime_dependency "unicorn"
-  s.post_install_message = "Please configure your service in ~/.opentox/config/lazar-gui.rb"
 end
diff --git a/views/neighbors.haml b/views/neighbors.haml
index 22dff56..9f60e7c 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -4,110 +4,74 @@
 / display preordered in table view ;
 
 %div.results{:style=>"display:none"}
-  - count_m = 0
   %h3 Neighbors:
   / tabs div
   #tabs
     %ul.nav.nav-tabs.nav-justified{:id=>"neighborTabs", :role=>"tablist"}
       / each model a tab head ;
-      - @prediction_models.each do |m|
-        - count_m += 1
-        - m_title = m.title.split("_").last(2)[0]
+      - @models.each_with_index do |model,i|
         %li
-          %a{:href => "#results_#{count_m}", :id => "linkTab#{count_m}", data: {toggle:"tab"}}
-            = m_title
-    - count_rs = 0
+          %a{:href => "#results_#{i+1}", :id => "linkTab#{i+1}", data: {toggle:"tab"}}
+            = "#{model.endpoint} (#{model.species})"
     %div.tab-content
       / unpack to single arrays
-      - @predictions.each do |pa|
+      - @predictions.each_with_index do |prediction,j|
         / pass model type for significant fragments view
-        - @type = @model_type[count_rs]
-        - count_rs += 1
-        #results.tab-pane.fade{:id=>"#{count_rs}"}
-          - pa.each do |p|
-            / prepare dataset for neighbors table ;
-            / delete first array which contains prediction ;
-            / following arrays are the neighbor predictions ;
-            - @model_uri = p.metadata[RDF::OT.hasSource][0]
-            - p.data_entries.shift
-            - p.compounds.shift
-            
-            / call the tablesorter plugin ;
-            / presort by similarity ;
-            :javascript
-              $(document).ready(function(){
-                $("table##{count_rs}").tablesorter({
-                  debug: false,
-                  //table: 'ui-widget ui-widget-content ui-corner-all',
-                  //header: 'ui-widget-header ui-corner-all ui-state-default',
-                  theme: "bootstrap",
-                  //widthFixed: true,
-                  //hover: 'ui-state-hover',
-                  //even: 'ui-widget-content',
-                  //odd: 'ui-state-default',
-                  headerTemplate: '{content} {icon}',
-                  widgets: ['zebra', 'columns', 'uitheme'],
-                  headers: {0: {sorter: false}, 3: {sorter: false}},
-                  sortList: [[2,1]]
-                });
+        #results.tab-pane.fade{:id=>"#{j+1}"}
+          / prepare dataset for neighbors table ;
+          / delete first array which contains prediction ;
+          / following arrays are the neighbor predictions ;
+          / call the tablesorter plugin ;
+          / presort by similarity ;
+          :javascript
+            $(document).ready(function(){
+              $("table##{j+1}").tablesorter({
+                debug: false,
+                theme: "bootstrap",
+                headerTemplate: '{content} {icon}',
+                widgets: ['zebra', 'columns', 'uitheme'],
+                headers: {0: {sorter: false}, 3: {sorter: false}},
+                sortList: [[2,1]]
               });
-            - $logger.debug "neighbors compounds:\t#{p.data_entries[0]}\n"
-            - if p.data_entries[0][2] != nil && p.data_entries[0].size != 3
-              -#%h2= "Neighbors: "
-                  
-              %div.table-responsive
-                %table.tablesorter{:id=>"#{count_rs}", :style=>"border-style: solid;"}
-                  %thead
-                    %tr
-                      %th{:style =>"vertical-align:middle;"}
-                        Compound
-                      %th{:style =>"vertical-align:middle;"}
-                        Measured Activity
-                      %th{:style =>"vertical-align:middle;"}
-                        Similarity
-                      %th{:style =>"vertical-align:middle;"}
-                        Supporting Information
-                  %info
-                    %tr
-                      %td
-                      %td{:style=>"font-size:x-small;padding:0px;"}
-                        %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Measured Activity", data: {toggle:"popover", placement:"auto", html:"true", content:"Experimental result(s) from the training dataset."}, :style=>"z-index:auto+10;"}
-                      %td{:style=>"font-size:x-small;padding:0px;"}
-                        %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Similarity", data: {toggle:"popover", placement:"auto", html:"true", content:"LAZAR calculates activity specific similarities based on the presence of statistically significant fragments. This procedure will <ul><li>consider only those parts of a chemical structure that are relevant for a particular endpoint</li><li>ignore inert parts of the structure</li><li>lead to different similarities, depending on the toxic endpoint Similarities of 1 may be encountered even for structurally dissimilar compounds, because inert parts are ignored.</li></ul>"}, :style=>"z-index:auto+10;"}
-                  %tbody
-                  - count = 0
-                  - p.compounds.each do |neighbor_compound|
-                    / prevent conversion of nil
-                    - c = p.data_entries[count][2] != nil ? p.data_entries[count][2] : '' 
-                    - case c
-                    - when /(false|true|inactive|active)/i
-                      - c = c
-                    - else
-                      /- c = Array.new
-                      - c = p.data_entries[count][2].to_f.round(3)
-                    %tr
-                      %td{:style =>"vertical-align:middle;padding-left:1em;"}
-                        %a.btn.btn-link{:href => "#details#{count_rs}", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(neighbor_compound.uri)}/details"), :id=>"link#{count_rs}#{count}"}}
-                          %img.blind{:src=>"#{neighbor_compound.uri}/image", :alt=>"no image", :onError=>"this.onerror=null;", :title=>"#{neighbor_compound.smiles}", :width=>"150px"}
-                      %td{:style =>"vertical-align:middle;padding-left:1em;"}
-                        - if c.class == String
-                          = c
-                        - else
-                          = c
-                      %td{:style =>"vertical-align:middle;padding-left:1em;"}
-                        = p.data_entries[count][3] != nil ? p.data_entries[count][3].round(3) : "Not enough similar compounds in training dataset." 
-                      %td{:style =>"vertical-align:middle;padding-left:1em;"}
-                        - if @type =~ /classification/i
-                          - if p.data_entries[count][3] != nil 
-                            %a.btn.btn-default{:href => "#details#{count_rs}", :id=>"link#{count_rs}#{count}sf", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@type}/#{CGI.escape(neighbor_compound.uri)}/significant_fragments")}} Significant Fragments
-                        - if @type =~ /regression/i
-                          - if p.data_entries[count][3] != nil
-                            %a.btn.btn-default{:href => "#details#{count_rs}", :id=>"link#{count_rs}#{count}sf", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@type}/#{CGI.escape(neighbor_compound.uri)}/significant_fragments")}} Descriptors
-                      - count += 1
-            - else
-              %span.btn.btn-default.disabled Not enough similar compounds in training dataset
+            });
+          - if prediction[:neighbors].size > 0
+                
+            %div.table-responsive
+              %table.tablesorter{:id=>"#{j+1}", :style=>"border-style: solid;"}
+                %thead
+                  %tr
+                    %th{:style =>"vertical-align:middle;"}
+                      Compound
+                    %th{:style =>"vertical-align:middle;"}
+                      Measured Activity
+                    %th{:style =>"vertical-align:middle;"}
+                      Similarity
+                    / %th{:style =>"vertical-align:middle;"}
+                    / Supporting Information
+                %info
+                  %tr
+                    %td
+                    %td{:style=>"font-size:x-small;padding:0px;"}
+                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Measured Activity", data: {toggle:"popover", placement:"auto", html:"true", content:"Experimental result(s) from the training dataset."}, :style=>"z-index:auto+10;"}
+                    %td{:style=>"font-size:x-small;padding:0px;"}
+                      %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Similarity", data: {toggle:"popover", placement:"auto", html:"true", content:"LAZAR calculates activity specific similarities based on the presence of statistically significant fragments. This procedure will <ul><li>consider only those parts of a chemical structure that are relevant for a particular endpoint</li><li>ignore inert parts of the structure</li><li>lead to different similarities, depending on the toxic endpoint Similarities of 1 may be encountered even for structurally dissimilar compounds, because inert parts are ignored.</li></ul>"}, :style=>"z-index:auto+10;"}
+                    / %td
+                %tbody
+                - prediction[:neighbors].each_with_index do |neighbor,count|
+                  %tr
+                    %td{:style =>"vertical-align:middle;padding-left:1em;"}
+                      %a.btn.btn-link{:href => "#details#{j+1}", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(neighbor[0].to_s)}/details"), :id=>"link#{j+1}#{count}"}}
+                        = Compound.find(neighbor[0]).svg
+                    %td{:style =>"vertical-align:middle;padding-left:1em;"}
+                      = neighbor[2].collect{|n| '%.2e' % n}.join ", "
+                    %td{:style =>"vertical-align:middle;padding-left:1em;"}
+                      / TODO differentiate between no neighbors found and compound found in dataset, display neighbors for compounds in dataset?
+                      = neighbor[1] != nil ? neighbor[1] : "Not enough similar compounds in training dataset." 
 
-          %div.modal.fade{:id=>"details#{count_rs}", :role=>"dialog"}
+          - else
+            %span.btn.btn-default.disabled Not enough similar compounds in training dataset
+
+          %div.modal.fade{:id=>"details#{j+1}", :role=>"dialog"}
             %div.modal-dialog.modal-lg
               %div.modal-content
 
diff --git a/views/predict.haml b/views/predict.haml
index bd430a6..118c4d4 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -1,35 +1,6 @@
 %link{ :href=>"/jsme/jsa.css", :rel=>"stylesheet"}
 %script{:src=>"/jsme/jsme.nocache.js"}
 :javascript
-  function callTask(url) {
-    var result="";
-    $.ajax({
-      url: url,
-      async: false,
-      success:function(data) {
-        var response = data.match(/Completed\s.*\./)[0];
-        var arr = response.split(" ");
-        result = arr[1].replace(/"/g, "");
-      }
-    });
-    return result;
-  };
-  // form function
-  function progress($element, url) {
-    $element.width("2%");
-    $element.show();
-    var timer = setInterval(function(){
-      var percent = callTask(url);
-      if(percent == 100.0){
-        var next = percent;
-        clearInterval(timer);
-      }
-      else {
-        var next = percent;
-      }
-      $element.width(next+"%");
-    }, 3000);
-  };
   function checksmiles () {
     if (document.form.identifier.value == "") {
       alert("Please draw or insert a chemical structure.");
@@ -48,7 +19,6 @@
     });
     if (checked == false){
       alert("Please select an endpoint.");
-      $('.progress-bar').hide();
       return false;
     };
     return true;
@@ -67,8 +37,6 @@
   };
 
 // init task for progress
-- task_uri = OpenTox::Task.task_uri
-- OpenTox::Task.run("Predict compound.", "#{$lazar[:uri]}", task_uri)do;end
 
 // whole site content needs to be in one form. Input and checkboxes are proofed by js functions. 
 %form{:name => "form", :action => to('/predict'), :method => "post", :enctype => "multipart/form-data", :onsubmit => "return  !!(checksmiles() & checkboxes())" }
@@ -102,74 +70,14 @@
       });
       
     #models
-      - @detail_count = 0
       - @endpoints.each do |endpoint|
         %div
-          %b= endpoint[0].split("#").last.gsub("_", " ").gsub(/\"|\]/, "")+" :"
-          - @models.each do |model|
-            - if endpoint == model.type.select{|e| e =~ /Endpoint/}
-              - model_title = model.title.split("_").last(2)[0]
-              - model_t = model.title.gsub("_", " ")
-              - @detail_count +=1
-              %div{:id => model_title}
-                %input{:type => "checkbox", :name => "selection[#{model.uri}]", :id => "selection[#{model_title}]", :value => true, :disabled => false}
-                %label{:for => "selection[#{model_title}]"}
-                  = model_t
-                %a.btn.btn-default.btn-xs{:href=>"#details", :id => "linkDetails#{model_title}", :title=>"#{model_title} details", :style=>"font-size:small;"}
-                  Details | Validation
-            
-                :javascript
-                  $("a#linkDetails#{model_title}").click(function () {
-                    $("#details_#{@detail_count}").toggle();
-                    //document.location = document.location + "#" + "details";
-                  });
-              #details{:id => "#{@detail_count}", :style => "display:none;"}
-                %div.panel{:style=>"padding:0.5em;"}
-                  %div.row
-                    %div.col-md-6
-                      %h3 Model Details:
-                      %p
-                        Algorithm: LAZAR
-                        - model.type.to_s =~ /regression/i ? type = "regression" : type = "classification"
-                        - @model_type = type
-                      %p
-                        = "Type: "+type
-                      - training_dataset = OpenTox::Dataset.new "#{model[RDF::OT.trainingDataset]}"
-                      - training_compounds = training_dataset.compounds.size.to_s
-                      %p
-                        Training compounds:
-                        = training_compounds
-                      %p
-                        Descriptors:
-                        - if type == "regression"
-                          %a{:href=>"https://services.in-silico.ch/algorithm/descriptor/physchem/list", :title=>"link opens in new window.", :target=>"_blank"} Physico-chemical (PC) properties
-                        - else
-                          %a{:href=>"http://www.maunz.de/libfminer2-bbrc-doc/", :title=>"link opens in new window.", :target=>"_blank"} Fminer backbone refinement classes
-                      %p
-                        Model:
-                        %a.btn{:href=>"#{to("/predict/#{CGI.escape(model.uri)}")}", :title=>"download"}
-                          rdf
-                          %span.glyphicon.glyphicon-download-alt
-                      %p
-                        Feature Dataset:
-                        %a.btn{:href=>"#{to("/predict/#{CGI.escape(model[RDF::OT.featureDataset])}")}", :title=>"download"}
-                          rdf
-                          %span.glyphicon.glyphicon-download-alt
-                        -#%a{:href=>"#{to("/predict/#{CGI.escape(model[RDF::OT.featureDataset])}")}/sdf", :title=>"download"} sdf
-                      %p
-                        Training Dataset:
-                        %a.btn{:href=>"#{to("/predict/#{CGI.escape(model[RDF::OT.trainingDataset])}")}", :title=>"link opens in new window."}
-                          rdf
-                          %span.glyphicon.glyphicon-download-alt
-                        -#%a{:href=>"#{to("/predict/#{CGI.escape(model[RDF::OT.trainingDataset])}/sdf")}", :title=>"link opens in new window."} sdf
-                    - unless model.metadata[RDF::OT.crossValidation].nil?
-                      %div.col-md-6
-                        %h3 Validation:
-                        %a.btn.btn-info.btn-xs{:href => "#{model.metadata[RDF::OT.crossValidation][0]}", :title=>"link opens in new window.", :target=>"_blank"} 
-                          Detailed report link
-                        %p
-                        - @cv = OpenTox::Validation.find "#{model.metadata[RDF::OT.crossValidation][0]+"/statistics"}"
-                        = haml :validation, :layout => false, :validation => @cv, :model_type => @model_type
+          %b= endpoint
+          - @models.select{|m| m.endpoint == endpoint}.each do |model|
+            %div{:id => model.id}
+              %input{:type => "checkbox", :name => "selection[#{model.id}]", :id => "selection[#{model.id}]", :value => true, :disabled => false}
+                %label{:for => "selection[#{model.id}]"}
+                  = model.species
             %p
 
   
@@ -179,9 +87,4 @@
         %h2
           3. Predict
       %div.col-md-10
-        %input.btn.btn-warning.h2{ :type => "submit", :id => "submit", :value=>">>", :onclick => "(progress($('.progress-bar'),'#{task_uri}') & getsmiles())"}
-        %input{:type => "hidden", :name => "task_uri", :value => "#{task_uri}"}
-    %div.row
-      %div.col-md-12
-        %div.progress
-          %div.progress-bar.progress-bar-striped.active{:role=>"progressbar", aria: { valuemin: 0, valuemax: 100}, :style=>"width:0;"}
+        %input.btn.btn-warning.h2{ :type => "submit", :id => "submit", :value=>">>", :onclick => "getsmiles()"}
diff --git a/views/prediction.haml b/views/prediction.haml
index dfc11fc..91f7024 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -18,89 +18,58 @@
       %tbody
         %tr
           %td{:id=>"compound", :style=>"vertical-align:top;"}
-            %a.btn.btn-link{:href => "#detailsTop", :id=>"linkCompound", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@compound.uri)}/details")}}
-              %img.img-responsive{:src=>"#{@compound.uri}/image", :alt=>"no image", :title=>"#{@compound.smiles}", :width=>"150", :height=>"150"}
-          - count=0
-          - @predictions.each do |pa|
-            / unpack to single array/prediction
-            / if p.data_entries array[0].size == 3 -> database hit
-            / change 'result' if database hit
-            / change 'confidence' if database hit
-            - pa.each do |p|
-              / prevent conversion of nil
-              /- $logger.debug "data entries in prediction array:\t#{p.data_entries}\n"
-              - database_hit = 0
-              - if p.data_entries[0].size == 3
-                - database_hit = 1
-              - c = p.data_entries[0][0] != nil ? p.data_entries[0][0] : ''
-              - case c
-              - when /(false|true|inactive|active)/i
-                - c = c
-              - else
-                /- c = Array.new
-                - c = (p.data_entries[0][0].class == Float) ? p.data_entries[0][0].round(3) : (p.data_entries[0][0] != nil ? p.data_entries[0][0] : "no prediction")
-              %td{:style=>"vertical-align:top;"}
-                %b{:class => "title"}
-                  = @prediction_models[count].title.gsub("_", " ")
-                - @model_uri = @prediction_models[count].uri
+            %a.btn.btn-link{:href => "#detailsTop", :id=>"linkCompound", data: { toggle: "modal", remote: to("/prediction/#{@compound.id.to_s}/details")}}
+              / %img.img-responsive{:src=>"#{@compound.id}/image", :alt=>"no image", :title=>"#{@compound.smiles}", :width=>"150", :height=>"150"}
+              = @compound.svg
+          - @predictions.each_with_index do |prediction,i|
+            %td{:style=>"vertical-align:top;"}
+              %b{:class => "title"}
+                = "#{@models[i].endpoint.gsub('_', ' ')} (#{@models[i].species})"
+              %p
+              - if prediction[:confidence] == "measured"
+                %p
+                / TODO fix scientific notation from database
+                %b Measured activity:
+                = prediction[:value].numeric? ? "#{prediction[:value].round(3)} (#{@models[i].unit})" : prediction[:value]
+                %p Compound is part of the training dataset
+              - elsif prediction[:neighbors].size > 0
                 %p
                 / model type (classification|regression)
                 %b Type:
-                = @model_type[count]
+                = @models[i].model.class.to_s.match("Classification") ? "Classification" : "Regression"
+                %br
+                %b Prediction:
+                / TODO scientific notation
+                = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} #{@models[i].unit}" : prediction[:value]
+                / TODO update description
+                %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", data: {toggle:"popover", placement:"left", html:"true", content:"LAZAR calculates searches the training dataset for similar compounds (neighbors) and calculates the prediction from their measured activities. LAZAR calculates predictions using <ul><li>a majority vote (weighted by compound similarity) for<br /><b>classification</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'>original publication</a>) </li><li>a local QSAR model based on neighbors for<br /><b>regression</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'</h>original publication</a>) </li></ul>Please keep in mind that predictions are based on the measured activities of neighbors."}}
+                %br
+                / TODO probability
+                %b Confidence:
+                = prediction[:confidence].round(3)
+                %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Confidence", data: {toggle:"popover", placement:"left", html:"true", content:"Indicates the applicability domain of a model. Predictions with a high confidence can be expected to be more reliable than predictions with low confidence. Confidence values may take any value between 0 and 1. For most models confidence > 0.025 is a sensible (hard) cutoff to distinguish between reliable and unreliable predictions."}}
+                %p
+                /TODO add tooltip for significant ftagments and descriptors
+                / - if @model_type[i] =~ /classification/i && (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0)
+                / Significant fragments:
+                / %a.btn.btn-default.btn-sm{:id=>"linkSigFragments", :href => "#detailsTop", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[i]}/#{CGI.escape(@compound.uri)}/fingerprints")}} Significant fragments
+                / - if @model_type[i] =~ /regression/i && (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0)
+                / Descriptors
+                / %a.btn.btn-default.btn-sm{:id=>"linkDescriptors", :href => "#detailsTop", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[i]}/#{CGI.escape(@compound.uri)}/fingerprints")}} Descriptors
+                / %p
+                %a.btn.btn-default.btn-sm{:href=> "#tabs", :id=>"link#{i+1}"}
+                  Neighbors
+                :javascript
+                  $("a#link#{i}").click(function () {
+                    $(".results").show();
+                    //document.getElementById('tabs').focus();
+                    $('#neighborTabs a[href="#results_#{i+1}"]').tab('show');
+                    //$("#tabs").tabs({ active: "#{i}" });
+                  });
+                %p
+              - else
                 %p
-                - unless database_hit > 0
-                  %b Result:
-                  %b
-                    - if c.class == String
-                      - result = (c != '' ? c : "No prediction result.")
-                      = result
-                    - else
-                      - result = (c != '' ? c.round(3) : "No prediction result.")
-                      = result
-                    - confidence = (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0) ? p.data_entries[0][1].round(2) : "--"
-                  %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Result", data: {toggle:"popover", placement:"left", html:"true", content:"LAZAR calculates searches the training dataset for similar compounds (neighbors) and calculates the prediction from their measured activities. LAZAR calculates predictions using <ul><li>a majority vote (weighted by compound similarity) for<br /><b>classification</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'>original publication</a>) </li><li>a local QSAR model based on neighbors for<br /><b>regression</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'</h>original publication</a>) </li></ul>Please keep in mind that predictions are based on the measured activities of neighbors."}}
-                  - @cv = OpenTox::Validation.find @prediction_models[count].metadata[RDF::OT.crossValidation][0]+"/statistics" #unless @prediction_models[count].title.include?("Mutagenicity")
-                    - unless @model_type[count] == "regression"
-                    %br  
-                    %b
-                      = "Probability: "
-                    - unless result == "No prediction result." or confidence == "--"
-                      - prob = @cv.probabilities( confidence, result )[:probs][result]*100
-                      = "#{prob.round(1)} %"
-                  %p
-                  %b Confidence:
-                  = confidence
-                  %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Confidence", data: {toggle:"popover", placement:"left", html:"true", content:"Indicates the applicability domain of a model. Predictions with a high confidence can be expected to be more reliable than predictions with low confidence. Confidence values may take any value between 0 and 1. For most models confidence > 0.025 is a sensible (hard) cutoff to distinguish between reliable and unreliable predictions."}}
-                  %p
-                  /TODO add tooltip for significant ftagments and descriptors
-                  - if @model_type[count] =~ /classification/i && (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0)
-                    / Significant fragments:
-                    %a.btn.btn-default.btn-sm{:id=>"linkSigFragments", :href => "#detailsTop", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[count]}/#{CGI.escape(@compound.uri)}/fingerprints")}} Significant fragments
-                  - if @model_type[count] =~ /regression/i && (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0)
-                    / Descriptors
-                    %a.btn.btn-default.btn-sm{:id=>"linkDescriptors", :href => "#detailsTop", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[count]}/#{CGI.escape(@compound.uri)}/fingerprints")}} Descriptors
-                  %p
-                  - if c != ''
-                    %a.btn.btn-default.btn-sm{:href=> "#tabs", :id=>"link#{count}"}
-                      Neighbors
-                    :javascript
-                      $("a#link#{count}").click(function () {
-                        $(".results").show();
-                        //document.getElementById('tabs').focus();
-                        $('#neighborTabs a[href="#results_#{count+1}"]').tab('show');
-                        //$("#tabs").tabs({ active: "#{count}" });
-                      });
-                  %p
-                  - count+=1
-                - else # database hit
-                  %b Database hit: 
-                  %br Compound found in training dataset
-                  %p
-                  %b Measured activity:
-                  = p.data_entries[0][2]
-                  %p
-                    
-                  - count+=1
+                Not enough similar compounds in training dataset.
 
   / always show the neighbors table, message is given there  
   = haml :neighbors, :layout => false, :model_type => @model_type