save stadium

5 files changed, 286 insertions, 278 deletions

diff --git a/application.rb b/application.rb
index acf3c73..0214db4 100644
--- a/application.rb
+++ b/application.rb
@@ -6,6 +6,10 @@ include OpenTox
 # Date: 18/11/2013
 set :protection, :except => :path_traversal
 
+configure :development do
+  $logger = Logger.new(STDOUT)
+end
+
 helpers do
   class Numeric
     def percent_of(n)
@@ -195,24 +199,49 @@ get '/predict/:dataset/?' do
 end
 
 post '/predict/?' do
+
+  # process batch prediction
+  if !params[:fileselect].blank?
+    File.open('tmp/' + params[:fileselect][:filename], "w") do |f|
+      f.write(params[:fileselect][:tempfile].read)
+    end
+    input = OpenTox::Dataset.from_csv_file File.join "tmp", params[:fileselect][:filename]
+    dataset = OpenTox::Dataset.find input.id 
+    @compounds = dataset.compounds
+    @models = []
+    @predictions = []
+    @compounds.each do |compound|
+      params[:selection].keys.each do |model_id|
+        model = Model::Prediction.find model_id
+        @models << model
+        @predictions << model.predict(compound)
+      end
+    end
+    input.delete
+    return haml :batch
+  end
+
   # validate identifier input
   # transfered input
-  @identifier = params[:identifier]
-  begin
-    # get compound from SMILES
-    @compound = Compound.from_smiles @identifier
-  rescue
-    @error_report = "Attention, '#{params[:identifier]}' is not a valid SMILES string."
-    return haml :error
-  end
-  @models = []
-  @predictions = []
-  params[:selection].keys.each do |model_id|
-    model = Model::Prediction.find model_id
-    @models << model
-    @predictions << model.predict(@compound)
+  if !params[:identifier].blank?
+    @identifier = params[:identifier]
+    begin
+      # get compound from SMILES
+      @compound = Compound.from_smiles @identifier
+    rescue
+      @error_report = "Attention, '#{params[:identifier]}' is not a valid SMILES string."
+      return haml :error
+    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
-  haml :prediction
 end
 
 get '/style.css' do
diff --git a/views/batch.haml b/views/batch.haml
new file mode 100644
index 0000000..5bae411
--- /dev/null
+++ b/views/batch.haml
@@ -0,0 +1,39 @@
+/ displays all prediction result in first table
+%div.table-responsive
+  %table.table.table-bordered{:id=>"batch", :style=>"background-color:white;"}
+    %thead
+      %tr
+        %h3 Batch Prediction Results:
+
+    %tbody
+    - @compounds.each_with_index do |compound,i|
+      %tr
+        %td{:id=>"compound", :style=>"vertical-align:top;"}
+          %p= compound.svg
+          %p= compound.smiles
+        - @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:
+              = @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]
+              %br
+              / TODO probability
+              %b Confidence:
+              = prediction[:confidence].round(3)
+              %p
+              %p
diff --git a/views/layout.haml b/views/layout.haml
index 974a8ed..60f2bb3 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -9,6 +9,7 @@
     %link{:rel=>'stylesheet', :href=>"#{'/css/bootstrap.min.css'}"}
     %link{:rel=>'stylesheet', :href=>"#{'/css/theme.default.min.css'}"}
     %link{:rel=>'stylesheet', :href=>"#{'/css/theme.bootstrap.min.css'}"}
+    %link{ :href=>"/style.css", :rel=>"stylesheet"}
     %link{ :href=>"/stylesheets/jquery-ui.css", :rel=>"stylesheet"}
     %script{:src=>"/javascripts/jquery-1.11.2.min.js"}
     %script{:src=>"/javascripts/bootstrap.min.js"}
diff --git a/views/predict.haml b/views/predict.haml
index 77f16bc..917a04a 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -1,21 +1,58 @@
 %link{ :href=>"/jsme/jsa.css", :rel=>"stylesheet"}
 %script{:src=>"/jsme/jsme.nocache.js"}
 :javascript
+  function getTab(){
+    t = $('.nav-tabs li.active').text();
+    return t.trim();
+  };
   function showcircle() {
-    if (checksmiles() && checkboxes()){
+    /*if (checksmiles() && checkboxes()){
       button = document.getElementById("submit");
       image = document.getElementById("circle");
       button.parentNode.replaceChild(image, button);
       $("img.circle").show();
       return true;
     };
+    return false;*/
+    switch (getTab()){
+      case "single":
+        if (checksmiles() && checkboxes()){
+          button = document.getElementById("submit");
+          image = document.getElementById("circle");
+          button.parentNode.replaceChild(image, button);
+          $("img.circle").show();
+          return true;
+        };
+        return false;
+        break;
+      case "batch":
+        if (checkfile() && checkboxes()){
+          button = document.getElementById("submit");
+          image = document.getElementById("circle");
+          button.parentNode.replaceChild(image, button);
+          $("img.circle").show();
+          return true;
+        };
+        return false;
+        break;
+      default: false;
+    };
+    return false;
+  };
+  function checkfile() {
+    var fileinput = document.getElementById("fileselect");
+    if(fileinput.value != "") {
+      //TODO check file type is csv
+      return true;
+    };
+    alert("Please select a file (csv).");
     return false;
   };
   function checksmiles () {
+    getsmiles();
     if (document.form.identifier.value == "") {
       alert("Please draw or insert a chemical structure.");
       document.form.identifier.focus();
-      //$('.progress-bar').hide();
       $("img.circle").hide();
       return false;
     };
@@ -48,49 +85,171 @@
     };
   };
 
-// init task for progress
-
 // 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  !!(showcircle())" }
   %fieldset#top.well
-    %h2 1. Draw a chemical structure
-    :javascript
-      $("a#linkInsert").click(function () {
-        $("#insert").toggle();
-        document.location = document.location + "#" + "insert";
-      });
-    #insert
-      %p
-      %label &nbsp;
-      #appletContainer
-      %br
-      %label{:for => 'identifier'}
-        or enter the
-        %a{:href => "http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification", :rel => "external"} SMILES
-        string:
-      %br
-      %input{:type => 'text', :name => 'identifier', :id => 'identifier', :size => '60'}
+    // tabs to select single prediction or batch prediction
+    %ul.nav.nav-tabs{:role=>"tablist"}
+      - ["single", "batch"].each do |select|  
+        %li{:class => ("active" if select == "single")}
+          %a{:href => "div##{select}", :id => "linkTab#{select}", :data=> {:toggle=>"tab"}} 
+            = select
+
+    %div.tab-content
+      #single.tab-pane.fade-in.active
+        %h2 1. Draw a chemical structure
+        #insert
+          %p
+          %label &nbsp;
+          #appletContainer
+          %br
+          %label{:for => 'identifier'}
+            or enter the
+            %a{:href => "http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification", :rel => "external"} SMILES
+            string:
+          %br
+          %input{:type => 'text', :name => 'identifier', :id => 'identifier', :size => '60'}
+
+      #batch.tab-pane.fade-in
+        %h2 1. Select a file to upload
+        Browse (csv):
+        %span.btn.btn-default.btn-file
+          %input{:type=>"file", :name=> "fileselect", :id=>"fileselect"}
     
    
   %fieldset#middle.well
     %h2 2. Select one or more endpoints
-    
-    :javascript
-      $("a#linkModels").click(function () {
-        $("#models").toggle();
-        document.location = document.location + "#" + "models";
-      });
-      
     #models
       - @endpoints.each do |endpoint|
-        %div
-          %b= endpoint
+        %div{:id=>endpoint}
+          %h4.head-back=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}
+            %div.row{:id => model.id}
+              %span.col-sm-4
+                %input{:type => "checkbox", :name => "selection[#{model.id}]", :id => "selection[#{model.id}]", :value => true, :disabled => false}
                 %label{:for => "selection[#{model.id}]"}
                   = model.species
-            %p
+              %span.col-sm-8
+                %a.btn.btn-default.btn-xs{:data=>{:toggle=>"collapse"}, :href=>"#details#{model.id}", :id => "link#{model.id}", :style=>"font-size:small;"}
+                  Details | Validation
+            %div.panel-collapse.collapse{:id=>"details#{model.id}", :style=>"margin-left:1em;"}
+              %b Model:
+              = model.id
+              %br
+              = "Algorithm:\tLAZAR"
+              %br
+              - model.classification? ? type = "classification" : type = "regression"
+              = "Type:\t"
+              = type
+              %br
+              - training_dataset = OpenTox::Dataset.find model.training_dataset.id
+              = "Training dataset:\t"
+              = training_dataset.source.split("/").last
+              %br
+              = "Training compounds:\t"
+              = training_dataset.compounds.size
+
+
+              %p
+              %b Validation:
+              %br
+              - cv = OpenTox::CrossValidation.find model.crossvalidation.id
+              = "Num folds:\t"
+              = cv.folds
+              %br
+              = "Num instances:\t"
+              = cv.nr_instances
+              %br
+              = "Num unpredicted"
+              = cv.nr_unpredicted
+              - if model.classification? 
+                %br
+                = "Accuracy:\t"
+                = cv.accuracy.round(3)
+                %br
+                = "Weighted Accuracy:\t"
+                = cv.weighted_accuracy.round(3)
+                %br
+                = "True positive rate:\t"
+                = cv.true_rate["active"].round(3)
+                %br
+                = "True negative rate:\t"
+                = cv.true_rate["inactive"].round(3)
+                %br 
+                = "Positive predictive value:\t"
+                = cv.predictivity["active"].round(3)
+                %br
+                = "Negative predictive value:\t"
+                = cv.predictivity["inactive"].round(3)
+                %p
+                %b Confusion Matrix:
+                %table.table.table-condensed.table-borderless{:style=>"width:20%;"}
+                  %tbody
+                    %tr
+                      %td
+                      %td
+                      %td 
+                        %b actual
+                      %td
+                      %td
+                    %tr
+                      %td
+                      %td
+                      %td active
+                      %td inactive
+                      %td total
+                    %tr
+                      %td 
+                        %b predicted
+                      %td active
+                      %td 
+                        =cv.confusion_matrix[0][0]
+                      %td 
+                        =cv.confusion_matrix[0][1]
+                      %td 
+                        =cv.confusion_matrix[0][0]+cv.confusion_matrix[0][1]
+                    %tr
+                      %td
+                      %td inactive
+                      %td 
+                        =cv.confusion_matrix[1][0]
+                      %td 
+                        =cv.confusion_matrix[1][1]
+                      %td 
+                        =cv.confusion_matrix[1][0]+cv.confusion_matrix[1][1]
+                    %tr
+                      %td
+                      %td total
+                      %td
+                        =cv.confusion_matrix[0][0]+cv.confusion_matrix[1][0]
+                      %td
+                        =cv.confusion_matrix[0][1]+cv.confusion_matrix[1][1]
+                      %td
+                -#= "Confusion Matrix:\t"
+                -#= cv.confusion_matrix
+              - if model.regression? 
+                %br
+                = "Root mean squared error:\t"
+                = cv.rmse.round(3)
+                %br
+                = "Weighted root mean squared error:\t"
+                = cv.weighted_rmse.round(3)
+                %br
+                = "Mean absolute error:\t"
+                = cv.mae.round(3)
+                %br
+                = "Weighted mean absolute error:\t"
+                = cv.weighted_mae.round(3)
+                %br 
+                = "R square:\t"
+                = cv.r_squared.round(3)
+                %br
+                -#= "Correlation plot"
+                -#= cv.correlation_plot
+                %br
+                -#= "Confidence plot:"
+                -#= cv.confidence_plot
+              %hr
 
   
   %fieldset#bottom.well
diff --git a/views/style.scss b/views/style.scss
index 0802545..fd05c3e 100644
--- a/views/style.scss
+++ b/views/style.scss
@@ -1,230 +1,10 @@
-$ist-color: rgba(200, 194, 200, 0.4);
-$black: #2b2b2b;
-$orange: #f76700;
-
-body {
-  background-image: url("/images/gray_jean.png");
-  overflow: scroll;
-  font-family: sans-serif; }
-  body a {
-    &:hover {
-    color: $orange; }
-    text-decoration: none;
-    font-weight: bold;
-    color: $black; }
-  body img {
-    border: 0; }
-  body h1 {
-    color: $black; }
-  body h2 {
-    padding-top: 12px;
-    font-size: x-large;
-    color: $orange; }
-
-.logo {
-  top: 0;
-  position: fixed;
-  background-color: #efefef;
-  width: 100%;
-  z-index: 40; }
-  .logo img {
-    float: left;
-    display: inline;
-    margin-right: 1em;
-    padding: 1em; }
-  .logo h1 {
-    width: 80%; }
-  .logo img.ote {
-    width: 100px;
-    height: 50px;
-    display: inline;
-    float: right; }
-
-.content {
-  background-image: url("/images/gray_jean.png");
-  margin-top: 6em; }
-  .content h1 {
-    text-shadow: white 1px 1px 0;
-    font-size: x-large;
-    display: inline; }
-  .content .arrow {
-    margin: 8px 0px 5px 20px; }
-  .content .back {
-    display: inline; }
-  .content fieldset#top {
-    border: 0;
-    padding: 10px;
-    background-color: $ist-color; }
-    .content fieldset#top a#linkInsert {
-      display: block;
-      width: 100%;
-      height: 2em; }
-    .content fieldset#top #appletContainer {
-      padding: 10px; }
-  .content fieldset#middle {
-    border: 0;
-    padding: 10px;
-    background-color: $ist-color; }
-    .content fieldset#middle a#linkModels {
-      display: block;
-      width: 100%;
-      height: 2em; }
-    .content fieldset#middle #models {
-      padding-left: 1em; }
-    .content fieldset#middle #model a {
-      display: inline;
-      font-weight: normal; }
-  .content fieldset#bottom {
-    border: 0;
-    background-color: $ist-color;
-    padding: 10px;
-    margin-bottom: 5em; }
-    .content fieldset#bottom input#predict {
-      margin-left: 1em; }
-  .content .predictions {
-    background-color: $ist-color;
-    padding: 10px;
-    text-align: justify; }
-  .content .overview {
-    padding: 12px;
-    margin-top: 1em;
-    margin-bottom: 1em;
-    text-align: left; }
-    .content .overview a:hover {
-      color: $orange; }
-    .content .overview caption {
-      text-align: left; }
-    .content .overview #overview tr td {
-      background-color: white;
-      border: 1px solid #dad9c7;
-      padding-left: 1em;
-      padding-top: 0.5em; }
-      .content .overview #overview tr td#compound {
-        width: 250px; }
-      .content .overview #overview tr td b.c {
-        color: #d42200; }
-      .content .overview #overview tr td b.n {
-        color: #5c8533; }
-      .content .overview #overview tr td .confidence {
-        display: inline; }
-  .content .error {
-    background-color: $ist-color;
-    box-shadow: (1px 1px 1px rgba(white, 1) inset, -1px -1px 5px rgba($black, 0.3) inset);
-    padding: 15px; }
-    .content .error .message {
-      margin: 2em;
-      padding: 1em;
-      border: 2px solid $orange;
-      background-color: white;
-      color: $black; }
-  .content #closebutton {
-    color: $orange;
-    margin-left: 98%; }
-
-.details {
-  width: 98%;
-  box-shadow: (1px 1px 1px rgba(white, 1) inset, -1px -1px 5px rgba($black, 0.3) inset);
-  background-color: $ist-color; }
-  .details a:hover {
-    color: $orange; }
-  .details img {
-    display: inline;
-    float: left;
-    margin: 0.5em; }
-
-.significant_fragments {
-  width: 98%;
-  margin-bottom: 2em;
-  box-shadow: (1px 1px 1px rgba(white, 1) inset, -1px -1px 5px rgba($black, 0.3) inset);
-  background-color: $ist-color; }
-  .significant_fragments img {
-    display: inline;
-    float: left;
-    margin: 0.5em; }
-  .significant_fragments table#sf1 {
-    text-align: left; }
-    .significant_fragments table#sf1 td {
-      padding: 0.2em; }
-
-  img.smarts{
-    width: 100px;
-    //float: left;
-  }
-  img.smarts:hover{
-    transform: scale(4);
-    border: solid 1px black;
-  }
-
-.descriptors {
-  width: 98%;
-  margin-bottom: 2em;
-  box-shadow: (1px 1px 1px rgba(white, 1) inset, -1px -1px 5px rgba($black, 0.3) inset);
-  background-color: $ist-color; }
-  .descriptors img {
-    display: inline;
-    float: left;
-    margin: 0.5em; }
-  .descriptors table#sf2 {
-    text-align: left; }
-    .descriptors table#sf2 td {
-      padding: 0.2em; }
-
-.results {
-  overflow-x: auto;
-  overflow-y: hidden;
-  margin-top: 2em;
-  margin-bottom: 2em; }
-  .results a:hover {
-    color: $orange; }
-  .results .tablesorter {
-    width: 100%;
-    text-align: left; }
-    .results .tablesorter thead {
-      background-color: $ist-color; }
-      .results .tablesorter thead tr th.header {
-        background-image: url("/images/bg.gif");
-        background-repeat: no-repeat;
-        background-position: center left;
-        cursor: pointer;
-        padding-left: 20px;
-        border: 1px solid #dad9c7;
-        margin-left: -1px; }
-      .results .tablesorter thead tr th.headerSortDown {
-        background-image: url("/images/desc.gif");
-        background-color: $ist-color; }
-      table.tablesorter .tablesorter-default thead tr .tablesorter-headerRow th .tablesorter-header .tablesorter-headerAsc {
-        background-image: url("/images/asc.gif");
-        background-color: $ist-color; }
-    .results .tablesorter tbody tr td {
-      border-spacing: 1px;
-      padding-left: 1em; }
-    .results .tablesorter tbody .compound {
-      width: 250px;
-      padding: 0.2em; }
-    .results .tablesorter tbody .n {
-      color: #5c8533; }
-    .results .tablesorter tbody .c {
-      color: #d42200; }
-
-input#predict {
-  border: 0px;
-  background-color: $ist-color;
-  margin: 0;
-  padding: 0; }
-
-.tooltip {
-  background-color: white;
-  border: 2px solid $orange;
-  font-size: 0.5em;
-  padding: 1em;
-  display: none;
-  z-index: 50; }
-
-.footer {
-  margin: 20px 0 20px 0; }
-  .footer a {
-    text-decoration: none;
-    color: black; }
-    .footer a:hover {
-      color: $orange; }
-
+table.table-borderless tbody tr td{
+  border-top: none;
+}
+
+h4.head-back, h5.head-back{
+  background-color: #E7E7E7;
+}
+//.btn:focus{
+  //background: #f0ad4e;
+//}