add additional files

14 files changed, 469 insertions, 204 deletions

diff --git a/.bundle/config b/.bundle/config
new file mode 100644
index 0000000..601c76b
--- /dev/null
+++ b/.bundle/config
@@ -0,0 +1,2 @@
+---
+BUNDLE_PATH: "/home/ist/.gem"
diff --git a/.gitignore b/.gitignore
index 49b161f..0dace87 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,3 @@
 Gemfile.lock
 .sass-cache/
+login.rb
diff --git a/VERSION b/VERSION
index f0bb29e..3a3cd8c 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-1.3.0
+1.3.1
diff --git a/application.rb b/application.rb
index 895b0c2..af78b05 100644
--- a/application.rb
+++ b/application.rb
@@ -1,7 +1,19 @@
-require 'rdiscount'
-require_relative 'qmrf_report.rb'
+[
+  'batch.rb',
+  'helper.rb',
+  'login.rb',
+  'prediction.rb',
+  'qmrf_report.rb',
+  'task.rb'
+].each do |lib|
+  require_relative lib
+end
+
 include OpenTox
 
+use Rack::Auth::Basic, "Please enter your login credentials." do |username, password|
+  [username, password] == [$user, $pass]
+end
 
 configure :production do
   $logger = Logger.new(STDOUT)
diff --git a/batch.rb b/batch.rb
new file mode 100644
index 0000000..0002279
--- /dev/null
+++ b/batch.rb
@@ -0,0 +1,91 @@
+require 'csv'
+require 'tempfile'
+
+module OpenTox
+
+  class Batch
+
+    include OpenTox
+    include Mongoid::Document
+    include Mongoid::Timestamps
+    store_in collection: "batch"
+    field :name,  type: String
+    field :source,  type: String
+    field :identifiers, type: Array
+    field :compounds, type: Array
+    field :warnings, type: Array, default: []
+
+    def self.from_csv_file file
+      source = file
+      name = File.basename(file,".*")
+      batch = self.find_by(:source => source, :name => name)
+      if batch
+        $logger.debug "Skipping import of #{file}, it is already in the database (id: #{batch.id})."
+      else
+        $logger.debug "Parsing #{file}."
+        table = CSV.read file, :skip_blanks => true, :encoding => 'windows-1251:utf-8'
+        batch = self.new(:source => source, :name => name, :identifiers => [], :compounds => [])
+        
+        # features
+        feature_names = table.shift.collect{|f| f.strip}
+        warnings << "Duplicated features in table header." unless feature_names.size == feature_names.uniq.size
+        compound_format = feature_names.shift.strip
+        bad_request_error "#{compound_format} is not a supported compound format. Accepted formats: SMILES, InChI." unless compound_format =~ /SMILES|InChI/i
+        numeric = []
+        features = []
+        # guess feature types
+        feature_names.each_with_index do |f,i|
+          metadata = {:name => f}
+          values = table.collect{|row| val=row[i+1].to_s.strip; val.blank? ? nil : val }.uniq.compact
+          types = values.collect{|v| v.numeric? ? true : false}.uniq
+          feature = nil
+          if values.size == 0 # empty feature
+          elsif  values.size > 5 and types.size == 1 and types.first == true # 5 max classes
+            numeric[i] = true
+            feature = NumericFeature.find_or_create_by(metadata)
+          else
+            metadata["accept_values"] = values
+            numeric[i] = false
+            feature = NominalFeature.find_or_create_by(metadata)
+          end
+          features << feature if feature
+        end
+        
+        table.each_with_index do |vals,i|
+          identifier = vals.shift.strip
+          batch.identifiers << identifier
+          begin
+            case compound_format
+            when /SMILES/i
+              compound = OpenTox::Compound.from_smiles(identifier)
+            when /InChI/i
+              compound = OpenTox::Compound.from_inchi(identifier)
+            end
+          rescue 
+            compound = nil
+          end
+          if compound.nil? # compound parsers may return nil
+            batch.warnings << "Cannot parse #{compound_format} compound '#{identifier}' at line #{i+2} of #{source}."
+            next
+          end
+          batch.compounds << compound.id
+        end
+        batch.compounds.duplicates.each do |duplicate|
+          dup = Compound.find duplicate
+          positions = []
+          batch.compounds.each_with_index do |co,i|
+            c = Compound.find co
+            if !c.blank? and c.inchi and c.inchi == dup.inchi
+              positions << i+1
+            end
+          end
+          batch.warnings << "Duplicate compound at ID #{positions.join(' and ')}."
+        end
+        batch.save
+      end
+      batch
+    end
+
+  end
+
+end
diff --git a/helper.rb b/helper.rb
index 54dbd5e..06b1517 100644
--- a/helper.rb
+++ b/helper.rb
@@ -1,3 +1,138 @@
 helpers do
-  
+
+  def embedded_svg image, options={}
+    doc = Nokogiri::HTML::DocumentFragment.parse image
+    svg = doc.at_css 'svg'
+    title = doc.at_css 'title'
+    if options[:class].present?
+      svg['class'] = options[:class]
+    end
+    if options[:title].present?
+      title.children.remove
+      text_node = Nokogiri::XML::Text.new(options[:title], doc)
+      title.add_child(text_node)
+    end
+    doc.to_html.html_safe
+  end
+
+  def prediction_to_csv(m,c,p)
+    model = m
+    model_name = "#{model.endpoint.gsub('_', ' ')} (#{model.species})"
+    model_unit = model.regression? ? "(#{model.unit})" : ""
+    converted_model_unit = model.regression? ? "#{model.unit =~ /\b(mmol\/L)\b/ ? "(mg/L)" : "(mg/kg_bw/day)"}" : ""
+
+    csv = ""
+    compound = c
+    prediction = p
+    output = {}
+    line = ""
+    output["model_name"] = model_name
+    output["model_unit"] = model_unit
+    output["converted_model_unit"] = converted_model_unit
+
+    if prediction[:value]
+      inApp = (prediction[:warnings].join(" ") =~ /Cannot/ ? "no" : (prediction[:warnings].join(" ") =~ /may|Insufficient|Weighted/ ? "maybe" : "yes"))
+      if prediction[:info] =~ /\b(identical)\b/i
+        prediction[:info] = "This compound was part of the training dataset. All information "\
+          "from this compound was removed from the training data before the "\
+          "prediction to obtain unbiased results."
+      end
+      note = "\"#{prediction[:warnings].uniq.join(" ")}\""
+
+      output["prediction_value"] = model.regression? ? "#{prediction[:value].delog10.signif(3)}" : "#{prediction[:value]}"
+      output["converted_value"] = model.regression? ? "#{compound.mmol_to_mg(prediction[:value].delog10).signif(3)}" : nil
+
+      if prediction[:measurements].is_a?(Array)
+        output["measurements"] = model.regression? ? prediction[:measurements].collect{|value| "#{value.delog10.signif(3)}"} : prediction[:measurements].collect{|value| "#{value}"}
+        output["converted_measurements"] = model.regression? ? prediction[:measurements].collect{|value| "#{compound.mmol_to_mg(value.delog10).signif(3)}"} : false
+      else
+        output["measurements"] = model.regression? ? "#{prediction[:measurements].delog10.signif(3)}" : "#{prediction[:measurements]}"
+        output["converted_measurements"] = model.regression? ? "#{compound.mmol_to_mg(prediction[:measurements].delog10).signif(3)}" : false
+
+      end #db_hit
+
+      if model.regression?
+
+        if !prediction[:prediction_interval].blank?
+          interval = prediction[:prediction_interval]
+          output['interval'] = []
+          output['converted_interval'] = []
+          output['interval'] << interval[1].delog10.signif(3)
+          output['interval'] << interval[0].delog10.signif(3)
+          output['converted_interval'] << compound.mmol_to_mg(interval[1].delog10).signif(3)
+          output['converted_interval'] << compound.mmol_to_mg(interval[0].delog10).signif(3)
+        end #prediction interval
+
+        line += "#{output['model_name']},#{compound.smiles},"\
+          "\"#{prediction[:info] ? prediction[:info] : "no"}\",\"#{output['measurements'].join("; ") if prediction[:info]}\","\
+          "#{!output['prediction_value'].blank? ? output['prediction_value'] : ""},"\
+          "#{!output['converted_value'].blank? ? output['converted_value'] : ""},"\
+          "#{!prediction[:prediction_interval].blank? ? output['interval'].first : ""},"\
+          "#{!prediction[:prediction_interval].blank? ? output['interval'].last : ""},"\
+          "#{!prediction[:prediction_interval].blank? ? output['converted_interval'].first : ""},"\
+          "#{!prediction[:prediction_interval].blank? ? output['converted_interval'].last : ""},"\
+          "#{inApp},#{note.nil? ? "" : note.chomp}\n"
+      else # Classification
+
+        if !prediction[:probabilities].blank?
+          output['probabilities'] = []
+          prediction[:probabilities].each{|k,v| output['probabilities'] << v.signif(3)}
+        end
+
+        line += "Consensus mutagenicity,#{compound.smiles},"\
+          "\"#{prediction[:info] ? prediction[:info] : "no"}\",\"#{output['measurements'].join("; ") if prediction[:info]}\","\
+          "#{prediction['Consensus prediction']},"\
+          "#{prediction['Consensus confidence']},"\
+          "#{prediction['Structural alerts for mutagenicity']},"\
+          "#{output['prediction_value']},"\
+          "#{!prediction[:probabilities].blank? ? output['probabilities'].first : ""},"\
+          "#{!prediction[:probabilities].blank? ? output['probabilities'].last : ""},"\
+          "#{inApp},#{note.nil? ? "" : note}\n"
+
+      end
+      
+      output['warnings'] = prediction[:warnings] if prediction[:warnings]
+
+    else #no prediction value
+      inApp = "no"
+      if prediction[:info] =~ /\b(identical)\b/i
+        prediction[:info] = "This compound was part of the training dataset. All information "\
+          "from this compound was removed from the training data before the "\
+          "prediction to obtain unbiased results."
+      end
+      note = "\"#{prediction[:warnings].join(" ")}\""
+
+      output['warnings'] = prediction[:warnings]
+      output['info'] = prediction[:info] if prediction[:info]
+
+      if model.regression?
+        line += "#{output['model_name']},#{compound.smiles},#{prediction[:info] ? prediction[:info] : "no"},"\
+          "#{prediction[:measurements].collect{|m| m.delog10.signif(3)}.join("; ") if prediction[:info]},,,,,,,"+ [inApp,note].join(",")+"\n"
+      else
+        #line += "Consensus mutagenicity,#{compound.smiles},#{prediction[:info] ? prediction[:info] : "no"},"\
+        #  "#{prediction[:measurements].join("; ") if prediction[:info]},,,,,,,"+ [inApp,note].join(",")+"\n"
+        line += "Consensus mutagenicity,#{compound.smiles},"\
+          "\"#{prediction[:info] ? prediction[:info] : "no"}\",\"#{output['measurements'].join("; ") if prediction[:info]}\","\
+          "#{prediction['Consensus prediction']},"\
+          "#{prediction['Consensus confidence']},"\
+          "#{prediction['Structural alerts for mutagenicity']},"\
+          "#{output['prediction_value']},"\
+          "#{!prediction[:probabilities].blank? ? output['probabilities'].first : ""},"\
+          "#{!prediction[:probabilities].blank? ? output['probabilities'].last : ""},"\
+          "#{inApp},#{note.nil? ? "" : note}\n"
+      end
+
+    end
+    csv += line
+    # output
+    csv
+  end
+
+  def dataset_storage
+    all = Batch.where(:source => /^tmp/)
+    out = Hash.new
+    all.reverse.each{|d| out[d.id] = [d.name, d.created_at]}
+    out
+  end  
+
 end
diff --git a/prediction.rb b/prediction.rb
new file mode 100644
index 0000000..afceb08
--- /dev/null
+++ b/prediction.rb
@@ -0,0 +1,35 @@
+module OpenTox
+
+  class Prediction
+
+    include OpenTox
+    include Mongoid::Document
+    include Mongoid::Timestamps
+    store_in collection: "predictions"
+    field :compound, type: BSON::ObjectId
+    field :model, type: BSON::ObjectId
+    field :prediction, type: Hash, default:{}
+    field :csv, type: String
+
+    attr_accessor :compound, :model, :prediction, :csv
+
+    def compound
+      self[:compound]
+    end
+    
+    def model
+      self[:model]
+    end
+    
+    def prediction
+      self[:prediction]
+    end
+
+    def csv
+      self[:csv]
+    end
+
+  end
+
+end
+
diff --git a/task.rb b/task.rb
new file mode 100644
index 0000000..9b9ca26
--- /dev/null
+++ b/task.rb
@@ -0,0 +1,53 @@
+DEFAULT_TASK_MAX_DURATION = 36000
+
+module OpenTox
+
+  class Task
+
+    include OpenTox
+    include Mongoid::Document
+    include Mongoid::Timestamps
+    store_in collection: "tasks"
+    field :pid, type: Integer
+    field :percent, type: Float, default: 0
+    field :predictions, type: Hash, default:{}
+    field :csv, type: String
+
+    attr_accessor :pid, :percent, :predictions, :csv
+
+    def pid
+      self[:pid]
+    end
+    
+    def percent
+      self[:percent]
+    end
+    
+    def predictions
+      self[:predictions]
+    end
+
+    def csv
+      self[:csv]
+    end
+    
+    def update_percent(percent)
+      self[:percent] = percent
+      save
+    end
+
+    def self.run
+      task = Task.new #uri
+      pid = fork do
+        yield
+      end
+      Process.detach(pid)
+      task[:pid] = pid
+      task.save
+      task
+    end
+
+  end
+
+end
+
diff --git a/views/batch.haml b/views/batch.haml
index 0e7efc7..7f6ddb7 100644
--- a/views/batch.haml
+++ b/views/batch.haml
@@ -1,10 +1,94 @@
+:javascript
+
+  function progress(value,id) {
+    var percent = Math.round(value);
+    var bar = document.getElementById("bar_"+id);
+    var prog = document.getElementById("progress_"+id);
+    bar.style.width = value + '%';
+    if (percent == 100){
+      prog.style.display = "none";
+    };
+  };
+
+  var HttpClient = function() {
+    this.get = function(aUrl, aCallback) {
+    var anHttpRequest = new XMLHttpRequest();
+    anHttpRequest.onreadystatechange = function() {
+    if (anHttpRequest.readyState == 4 && anHttpRequest.status == 200)
+      aCallback(anHttpRequest.responseText);
+    }
+      anHttpRequest.open( "GET", aUrl, true );
+      anHttpRequest.send( null );
+    }
+  };  
+
+  var markers = [];
+
+  function renderTask(task_id,model_id,id) {
+    var uri = "#{to("/")}" + 'task/?turi=' + task_id;
+    var aClient = new HttpClient();
+    aClient.get(uri, function(res) {
+      var response = JSON.parse(res);
+      if (model_id == "Cramer"){
+        $("img.circle").show();
+      }else{
+        progress(response['percent'],id);
+      }
+      if (response['percent'] == 100){
+        window.clearInterval(markers[id]);
+        $("a#downbutton_"+id).removeClass("disabled");
+        $("a#detailsbutton_"+id).removeClass("disabled");
+        $("img.circle").hide();
+      };
+    });
+  };
+  function simpleTemplating(data) {
+    var html = '<ul class=pagination>';
+    $.each(data, function(index, item){
+      html += '<li>'+ item +'</li>'+'</br>';
+    });
+    html += '</ul>';
+    return html;
+  };
+  function pagePredictions(task_id,model_id,id){
+    button = document.getElementById("detailsbutton_"+id);
+    span = button.childNodes[1];
+    if (span.className == "glyphicon glyphicon-menu-right"){
+      span.className = "glyphicon glyphicon-menu-down";
+      $('#data-container_'+id).show();
+      $('#pager_'+id).show();
+      $('#pager_'+id).pagination({
+        dataSource: '#{to("/")}' + 'task/?predictions=' + task_id + '&model=' + model_id ,
+        locator: 'prediction',
+        totalNumber: #{@compounds.size},
+        pageSize: 1,
+        showPageNumbers: true,
+        showGoInput: true,
+        formatGoInput: 'go to <%= input %>',
+        formatAjaxError: function(jqXHR, textStatus, errorThrown) {
+          $('#data-container_'+id).html(errorThrown);
+        },
+        /*ajax: {
+          beforeSend: function() {
+            $('#data-container_'+id).html('Loading content ...');
+          }
+        },*/
+        callback: function(data, pagination) {
+          var html = simpleTemplating(data);
+          $('#data-container_'+id).html(html);
+          $('#data-container_'+id).css("min-height", $(window).height() + "px" );
+        }
+      });
+    } else if (span.className = "glyphicon glyphicon-menu-down"){
+      span.className = "glyphicon glyphicon-menu-right";
+      $('#data-container_'+id).hide();
+      $('#pager_'+id).hide();
+    };
+  };
 %div.well
-  %a.btn.btn-warning{:href => to('/predict')}
+  %a.btn.btn-warning{:href => to("/predict?tpid=#{@pid}")}
     %span.glyphicon.glyphicon-menu-left{:aria=>{:hidden=>"true"}}
     New Prediction
-  %a.btn.btn-success{:id => "downbutton", :href=>"#{to("/predict/#{@tmppath}/#{@filename}")}", :title=>"download"}
-    %span.glyphicon.glyphicon-download-alt
-    Download CSV
 
   / show file name
   %topline
@@ -13,97 +97,46 @@
         %h3 Batch Prediction Results:
       %div.col-md-8
         %h3= @filename
-  
-  / displays all prediction result in one table
-  %div.table-responsive
-    %table.table.table-bordered{:id=>"batch", :style=>"background-color:white;"}
-      %tbody
-        - if @warnings
-          - @warnings.each do |warning|
-            %tr
-              %td
-                %b Warning
-              %td
-                = warning.sub(/\b(tmp\/)\b/,"")
-        - @view.each do |compound, array|
-          %tr
-            %td{:style=>"vertical-align:top;"}
-              %p= compound.svg
-              %p= compound.smiles
-            - array.each do |model,prediction|
-              %td{:style=>"vertical-align:top;white-space:nowrap;"}
-                - model.model.class.to_s.match("Classification") ? type = "Classification" : type = "Regression"
-                - unit = model.unit
-                
-                %b{:class => "title"}
-                  = "#{model.endpoint.gsub('_', ' ')} (#{model.species})"
-                    
-                / check for prediction
-                - if prediction[:value]
-                  %p
-                  / show model type (classification|regression)
-                  %b Type:
-                  = type
-                  %p 
-                  / check for database hit
-                  - if prediction[:info] =~ /\b(identical)\b/i
-                    
-                    / show message about dbhit and measurements
-                    %p
-                      %b Compound is part of the training dataset
-                      %p
-                      %b Measured activity:
-                      %br
-                      - if prediction[:measurements].is_a?(Array)
-                        = (type == "Regression") ? prediction[:measurements].collect{|value| "#{value.delog10.signif(3)} (#{unit})</br>#{compound.mmol_to_mg(value.delog10).signif(3)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : prediction[:measurements].join(", ")
-                      - else
-                        = (type == "Regression") ? "#{prediction[:measurements].delog10.signif(3)} (#{unit})</br>#{compound.mmol_to_mg(prediction[:measurements].delog10).signif(3)} #{(unit =~ /\b(mmol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:measurements]
-                    
-                    
-                  / show prediction
-                  %p
-                    %b Prediction:
-                    %br
-                    = (type == "Regression") ? "#{prediction[:value].delog10.signif(3)} (#{unit})</br>#{compound.mmol_to_mg(prediction[:value].delog10).signif(3)} #{(unit =~ /\b(mmol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value]
-                    
-                    / show prediction interval or probability
-                    %p
-                    - if type == "Regression"
-                      %b 95% Prediction interval:
-                      - interval = (prediction[:prediction_interval].nil? ? nil : prediction[:prediction_interval])
-                      %br
-                      = interval.nil? ? "" : "#{interval[1].delog10.signif(3)} - #{interval[0].delog10.signif(3)} (#{unit})"
-                      %br
-                      = "#{compound.mmol_to_mg(interval[1].delog10).signif(3)} - #{compound.mmol_to_mg(interval[0].delog10).signif(3)} #{(unit =~ /\b(mmol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" if !prediction[:prediction_interval].nil?
-                    - else
-                      %b Probability:
-                      - unless prediction[:probabilities].nil?
-                        - probabilities = ""
-                        - prediction[:probabilities].each{|k,v| probabilities += "#{k}: #{v.signif(3)}<br>"}
-                        %br
-                        = probabilities
-                  / show warnings
-                  %p
-                  - if !prediction[:info].blank?
-                    %b Info:
-                    %br
-                    %p=prediction[:info].sub(/\'.*\'/,"").sub(/,/, ",<br>")
-                  - if !prediction[:warnings].blank?
-                    %b Warnings:
-                    - prediction[:warnings].uniq.each do |warning|
-                      %br
-                      %p=warning.sub(/substances/, "substances<br>").sub(/prediction\:/, "prediction\:<br>")
-                        
-                  / no prediction  
-                - else
-                  %br
-                  - if !prediction[:info].blank?
-                    %b Info:
-                    %br
-                    %p=prediction[:info].sub(/\'.*\'/,"").sub(/,/, ",<br>")
-                  - if !prediction[:warnings].blank?
-                    %b Warnings:
-                    - prediction[:warnings].uniq.each do |warning|
-                      %br
-                      %p=warning.sub(/substances/, "substances<br>").sub(/prediction\:/, "prediction\:<br>")
-            %tr
+
+
+  - @models.each_with_index do |model,idx|
+    - m = Model::Validation.find model
+    - task = @tasks[idx].id
+    #result.panel{:id=>idx}
+      %div.row
+        %div.col-md-6
+          %h5= "#{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
+            Details
+          %a.btn.btn-default.btn-xs.disabled{:id => "downbutton_#{idx}", :href=>"#{to("/predict/csv/#{task}/#{model}/#{@filename}")}", :title=>"download", :style=>"font-size:small;"}
+            %span.glyphicon.glyphicon-download-alt
+            CSV
+      - if model == "Cramer"
+        %img.h2{:src=>"/images/wait30trans.gif", :id=>"circle", :class=>"circle", :alt=>"wait", :style=>"display:none;"}
+      - if model != "Cramer"
+        %div{:id=>"progress_#{idx}", :style=>"width:100%;height:3px;position:relative;background-color:#ccc;"}
+          %div{:id=>"bar_#{idx}", :style=>"background-color: #4CAF50;width:10px;height:3px;position:absolute;"}
+      - # increase interval timer for large datasets 
+      - ctimer = ((@compounds.size/1000) == 0 ? 1000 : ((@compounds.size/1000)*1000))
+      :javascript
+        var timer = #{ctimer};
+        $(document).ready(function(){
+          // check button class before execute a task
+          if (#{idx} > 0){
+            markers[#{idx}] = setInterval(function(){
+              var button = document.getElementById("detailsbutton_#{idx-1}");
+              if(!button.classList.contains('disabled')){
+                renderTask('#{task}','#{model}',#{idx});
+              }
+            }, timer );
+          }else{
+            markers[#{idx}] = setInterval(function(){
+              renderTask('#{task}','#{model}',#{idx});
+            }, timer );
+          };
+        });
+      #data-container{:id=>idx,:style=>"width:100%;"}
+      -#pager{:id=>idx}
diff --git a/views/details.haml b/views/details.haml
deleted file mode 100644
index be4948a..0000000
--- a/views/details.haml
+++ /dev/null
@@ -1,28 +0,0 @@
-:javascript
-  $(document).ready(function(){
-    addExternalLinks();
-  });
-%div.modal-body{:style=>"padding:10px;"}
-  %button.close{ :type=>" button", data: { dismiss:"modal"}} &times;
-  %h3
-    Names and synonyms:
-  %p= @compound.svg
-  %p
-  %b="SMILES:"
-  %p= @smiles
-  %br
-  %b="InChI:"
-  %p= @inchi
-  %br
-  %b="Names:"
-  %p{:style=>"padding-left:0.5em;"}
-  - if @names !~ /^no names/i
-    = @names.join("; ")
-  - else
-    = @names
-  %hr
-  %p{:style=>"padding-left:0.5em;"}
-    / pubchem link
-    %a.btn.btn-primary{:href=>"http://aop.in-silico.ch/", :title=>"Link opens in new window.", :alt=>"pubchem read across", :rel=>"external"} PubChem read across 
-    %i (experimental)
-  %br
diff --git a/views/faq.haml b/views/faq.haml
deleted file mode 100644
index 818b96a..0000000
--- a/views/faq.haml
+++ /dev/null
@@ -1,2 +0,0 @@
-%div.well.faq
-  = @faq
diff --git a/views/license.haml b/views/license.haml
deleted file mode 100644
index 2813220..0000000
--- a/views/license.haml
+++ /dev/null
@@ -1 +0,0 @@
-= @license
diff --git a/views/predict.haml b/views/predict.haml
index 2308911..1c995e9 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -125,12 +125,12 @@
       %br
       %input{:type => 'text', :name => 'identifier', :id => 'identifier', :size => '60'}
       %p
-      -#%label{:for=>"fileselect"}
+      %label{:for=>"fileselect"}
         or upload a CSV file for batch predictions:
-      -#%a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"File format", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"auto", html:"true", content:"One column with compounds and keyword SMILES or InChI in the first row."}}
-      -#%br
-      %span.btn.btn-default.btn-file{:style=>"display:none;"}
-        %input{:type=>"file", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv", :disabled=>"disabled", :type=>"hidden"}
+      %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"File format", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"auto", html:"true", content:"One column with compounds and keyword SMILES or InChI in the first row."}}
+      %br
+      %span.btn.btn-default.btn-file
+        %input{:type=>"file", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv"}
 
   %fieldset#middle.well
     %h2 2. Select one or more endpoints
diff --git a/views/significant_fragments.haml b/views/significant_fragments.haml
deleted file mode 100644
index bd3598d..0000000
--- a/views/significant_fragments.haml
+++ /dev/null
@@ -1,66 +0,0 @@
-%div.modal-body{:style=>"padding:10px;"}
-  %button.close{ :type=>" button", data: { dismiss:"modal"}} &times;
-  - if @type =~ /classification/i
-    %div.row
-      %div.col-md-4
-        %h3{:style=>"margin-left:8px;"}
-          Significant fragments:
-        %img{:src=>"#{@compound.uri}/image", :alt=>"#{@compound.smiles}", :title=>"#{@compound.smiles}", :width=>"300px", :heigth=>"300px"}
-      - if !@significant_fragments.empty?
-        %div.col-md-8
-          %table{:id => "sf"}
-            %tr
-              / @value_map => hash; interpret the effect
-              %th{:style=>"border:2px solid #E6E6E6;"}
-                Predominantly in compounds with activity "inactive"
-              %th{:style=>"border:2px solid #E6E6E6;"}
-                p value
-              - @significant_fragments.each do |fragments|
-                / fragments == [effect, smarts, pValue]
-                / fragments[0] = effect
-                /- $logger.debug "effect:\t#{fragments[0]}\n"
-                - if fragments[0] == @value_map.index("inactive")
-                  %tr
-                    %td
-                      / fragments[1] = smarts 
-                      = fragments[1]
-                      -#%img{:src => "http://smartsview.de/smartsview/auto/png/1/both/#{CGI.escape(fragments[1])}", :class => "smarts"}
-                    %td
-                      /fragments[2] = pValue
-                      = fragments[2]
-            %tr
-              %th{:style=>"border:2px solid #E6E6E6;"}
-                Predominantly in compounds with activity "active"   
-              %th{:style=>"border:2px solid #E6E6E6;"}
-                p value
-              - @significant_fragments.each do |fragments|
-                / fragments == [effect, smarts, pValue]
-                - if fragments[0] == @value_map.index("active")
-                  %tr
-                    %td
-                      -#%img{:src => "http://smartsview.de/smartsview/auto/png/1/both/#{CGI.escape(fragments[1])}", :class => "smarts"}
-                      = fragments[1]
-                    %td
-                      = fragments[2]
-    %br
-  - if @type =~ /regression/i
-    %div.row
-      %div.col-md-4
-        %h3
-          Descriptors:
-        %img{:src=>"#{@compound.uri}/image", :alt=>"#{@compound.smiles}", :title=>"#{@compound.smiles}", :width=>"300px", :heigth=>"300px"}
-      - if !@significant_fragments.empty?
-        %div.col-md-8
-          %table{:id =>"de"}
-            %tr
-              %th{:style=>"border:2px solid #E6E6E6;"}
-                Descriptor
-              %th{:style=>"border:2px solid #E6E6E6;"}
-                value
-              - @significant_fragments.each do |fragments|
-                %tr
-                  %td
-                    = fragments[0]
-                  %td
-                    = fragments[1][0].round(3)
-    %br