new batch mode with single calls

4 files changed, 360 insertions, 129 deletions

diff --git a/views/batch.haml b/views/batch.haml
index 0e7efc7..aaa09bf 100644
--- a/views/batch.haml
+++ b/views/batch.haml
@@ -1,10 +1,273 @@
+:javascript
+  function progress(model,idx,total) {
+    var p = 100/total;
+    var percent = Math.round((idx+1)*p);
+    var bar = document.getElementById("bar_"+model);
+    var prog = document.getElementById("progress_"+model);
+    bar.style.width = percent + '%';
+    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 );
+    }
+  };  
+
+  function renderResponse(model,idx,compound,last,total,tmppath) {
+    // create request
+    if (model == "Cramer"){
+      var dataset = '#{@dataset.id}';
+      var uri = "#{to("/batch/")}" + model + '/?dataset=' + escape(dataset) + '&tmppath=' + tmppath + '&last=' + last;
+    } else {
+      var dataset = '#{@dataset.id}';
+      var uri = "#{to("/batch/")}" + model + '/?compound=' + escape(compound) + '&dataset=' + dataset + '&idx=' + idx + '&tmppath=' + tmppath + '&last=' + last;
+    };
+    var aClient = new HttpClient();
+    aClient.get(uri, function(res) {
+      // progress bar function
+      progress(model,idx,total);
+
+      var response = JSON.parse(res);
+      var td = document.getElementById("prediction_"+compound+'_'+model+'_'+idx);
+      //td.innerHTML = "";
+      if (model != "Cramer"){
+        // init general structure
+        a = ["title", "type", "db_hit", "measurements", "prediction", "interval", "probability", "warnings", "info"];
+        
+        // handles consesus mutagenicity
+        if (response['sa_prediction'] != false){
+          var p = document.createElement("p");
+          var h = document.createElement("h5");
+          p.id = "sa";
+          // Consensus mutagenicity
+          var t = document.createTextNode("Consensus mutagenicity");
+          h.appendChild(t);
+          p.appendChild(h);
+          // handle db_hit first
+          if (response['db_hit'] != false){
+            var value = document.createTextNode(response['db_hit']);
+            p.appendChild(value);
+          };
+          // Structural alerts
+          var h2 = document.createElement("h5");
+          var t = document.createTextNode("Structural alerts:");
+          h2.appendChild(t);
+          p.appendChild(h2);
+          // prediction
+          var h3 = document.createElement("h5");
+          var t = document.createTextNode("Prediction:");
+          if (response['sa_prediction']['prediction'] == false){
+            var value = document.createTextNode("non-mutagenic");
+          };
+          if (response['sa_prediction']['prediction'] == true){
+            var value = document.createTextNode("mutagenic");
+          };
+          h3.appendChild(t);
+          p.appendChild(h3);
+          p.appendChild(value);
+          // confidence
+          var h4 = document.createElement("h5");
+          var t = document.createTextNode("Confidence:");
+          var value = document.createTextNode(response['confidence']);
+          h4.appendChild(t);
+          p.appendChild(h4);
+          p.appendChild(value);
+          // Structural alerts for mutagenicity
+          var h5 = document.createElement("h5");
+          var t = document.createTextNode("Structural alerts for mutagenicity:");
+          h5.appendChild(t);
+          p.appendChild(h5);
+          if (response['sa_matches'] != false){
+            var value = document.createTextNode(response['sa_matches']);
+            p.appendChild(value);
+          } else {
+            var span = document.createElement("span");
+            var value = document.createTextNode("none");
+            span.style.fontStyle = "italic";
+            span.appendChild(value);
+            p.appendChild(span);
+          };
+          
+          // append to td
+          td.appendChild(p);
+        };
+
+        // proceed to general structure
+        for (val of a){
+          var p = document.createElement("p");
+          var h = document.createElement("h5");
+          p.id = val;
+          if (val == "title") {
+            var value = document.createTextNode(response['model_name']);
+            h.appendChild(value);
+            p.appendChild(h);
+          } else if (val == "type") {
+            var t = document.createTextNode("Type: ");
+            var value = document.createTextNode(response['model_type']);
+            h.appendChild(t);
+            p.appendChild(h);
+            p.appendChild(value);
+            h.style.display = "inline";
+          } else if (val == "db_hit" && response['db_hit'] != false && response['sa_prediction'] == false) {
+            var value = document.createTextNode(response['db_hit']);
+            p.appendChild(value);
+          } else if (val == "measurements" && response['measurements'] != false) {
+            var t = document.createTextNode("Measurements:");
+            h.appendChild(t);
+            p.appendChild(h);
+            if (response['model_type'] == "Regression"){
+              for (var i=0; i<response['measurements'].length; i++){
+                var value = document.createTextNode(response['measurements'][i]);
+                var br = document.createElement("br");
+                p.appendChild(value);
+                p.appendChild(br);
+                if (response['converted_measurements'] != false) {
+                  var value = document.createTextNode(response['converted_measurements'][i]);
+                  var br = document.createElement("br");
+                  p.appendChild(value);
+                  p.appendChild(br);
+                  if (i+1 != response['measurements'].length){
+                    var br2 = document.createElement("br");
+                    p.appendChild(br2);
+                  };
+                };
+              };
+            } else if (response['model_type'] == "Classification"){
+              for (var i=0; i<response['measurements'].length; i++){
+                var value = document.createTextNode(response['measurements'][i]);
+                var br = document.createElement("br");
+                p.appendChild(value);
+                p.appendChild(br);
+              };
+            };
+          } else if (val == "prediction" && response['prediction_value'] != false) {
+            var t = document.createTextNode("Prediction:");
+            var value = document.createTextNode(response['prediction_value']+" "+response['model_unit']);
+            h.appendChild(t);
+            p.appendChild(h);
+            p.appendChild(value);
+            if (response['converted_value'] != false) {
+              var br = document.createElement("br");
+              var value = document.createTextNode(response['converted_value']+" "+response['converted_model_unit']);
+              p.appendChild(br);
+              p.appendChild(value);
+            };
+            if (response['model_type'] == "Classification" && response['probability'] != false){
+              var h = document.createElement("h5");
+              var t = document.createTextNode("Probability:");
+              h.appendChild(t);
+              p.appendChild(h);
+              for (var i=0; i<response['probability'].length; i++){
+                var value = document.createTextNode(response['probability'][i]);
+                var br = document.createElement("br");
+                p.appendChild(value);
+                p.appendChild(br);
+              };
+            };
+          } else if (val == "interval" && response['interval'] != false) {
+            var t = document.createTextNode("95% Prediction interval:");
+            var value = document.createTextNode(response['interval']+" "+response['model_unit']);
+            h.appendChild(t);
+            p.appendChild(h);
+            p.appendChild(value);
+            if (response['converted_interval'] != false) {
+              var br = document.createElement("br");
+              var value = document.createTextNode(response['converted_interval']+" "+response['converted_model_unit']);
+              p.appendChild(br);
+              p.appendChild(value);
+            };
+          } else if (val == "warnings" && response['warnings'] != false && response['db_hit'] == false) {
+            var t = document.createTextNode("Warnings: ");
+            h.appendChild(t);
+            p.appendChild(h);
+            for (var i=0; i<response['warnings'].length; i++){
+              var value = document.createTextNode(response['warnings'][i]);
+              var br = document.createElement("br");
+              p.appendChild(value);
+              p.appendChild(br);
+            };
+          } else if (val == "info" && response['info'] != false) {
+            var t = document.createTextNode("Info: ");
+            var value = document.createTextNode(response['info']);
+            h.appendChild(t);
+            p.appendChild(h);
+            p.appendChild(value);
+          };
+
+          // append to td
+          td.appendChild(p);
+        };
+      };// if model != Cramer
+      if (model == "Cramer"){
+        for(i=0; i < response['tds'].length; i++){
+          progress('Cramer',i,response['tds'].length);
+          var td = document.getElementById(response['tds'][i]);
+          var p = document.createElement("p");
+          var h = document.createElement("h5");
+          var t = document.createTextNode("Oral toxicity (Cramer rules)");
+          p.id = "cramer";
+          h.appendChild(t);
+          p.appendChild(h);
+          var h2 = document.createElement("h5");
+          var t = document.createTextNode("Cramer rules:");
+          h2.appendChild(t);
+          p.appendChild(h2);
+          if (response['cramer_rules'][i] != "nil"){
+            var value = document.createTextNode(response['cramer_rules'][i]);
+            p.appendChild(value);
+          } else {
+            var span = document.createElement("span");
+            var value = document.createTextNode("none");
+            span.style.fontStyle = "italic";
+            span.appendChild(value);
+            p.appendChild(span);
+          };
+          var h3 = document.createElement("h5");
+          var t = document.createTextNode("Cramer rules, with extensions:");
+          h3.appendChild(t);
+          p.appendChild(h3);
+          if (response['cramer_rules_extensions'][i] != "nil"){
+            var value = document.createTextNode(response['cramer_rules_extensions'][i]);
+            p.appendChild(value);
+          } else {
+            var span = document.createElement("span");
+            var value = document.createTextNode("none");
+            span.style.fontStyle = "italic";
+            span.appendChild(value);
+            p.appendChild(span);
+          };
+
+          // append to td
+          td.appendChild(p);
+          if (i === response['tds'].length-1) {
+            $("img#circle_Cramer").hide();
+            $("a#downbutton_Cramer").show();
+          };
+
+        };
+      };// if model == Cramer
+      // if last compound change progress to download;
+      if (last == true) {
+        $("img#circle_"+model).hide();
+        $("a#downbutton_"+model).show();
+      };
+    });
+  };
+
+
 %div.well
   %a.btn.btn-warning{:href => to('/predict')}
     %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
@@ -14,96 +277,62 @@
       %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
+  / displays prediction result in table tabs
+  #tabs
+    %ul.nav.nav-tabs.nav-justified{:id=>"batchTabs", :role=>"tablist"}
+      - @models.each_with_index do |model,i|
+        - m = Model::Validation.find model unless model == "Cramer"
+        %li{:class => ("active" if i == 0)}
+          %a{:href => "#results_#{i+1}", :id => "linkTab#{i+1}", data: {toggle:"tab"}}
+            = (model == "Cramer") ? "Oral toxicity (Cramer rules)" : "#{m.endpoint} (#{m.species})"
+          %img.dlwait{:src=>"/images/wait30trans.gif", :id=>"circle_#{model}", :class=>"circle", :alt=>"wait", :style=>"display:none;"}
+          %a.csv.btn{:id => "downbutton_#{model}", :href=>"#{to("/predict/#{@tmppaths[model]}/#{model}/#{@filename}")}", :title=>"download", :style=>"display:none;"}
+            %span.glyphicon.glyphicon-download-alt
+            CSV
+
+    %div.tab-content
+      - csize = @compounds.size
+      - msize = @models.size
+      - timer = 0
+      - @models.each_with_index do |model,j|
+        #results.tab-pane{:id=>"#{j+1}", :class => ("active" if j == 0)}
+          %div{:id=>"progress_"+model, :style=>"width:100%;height:2px;position:relative;background-color:#ccc;"}
+            %div{:id=>"bar_"+model, :style=>"background-color: #4CAF50;width:10px;height:2px;position:absolute;"}
+          %table.table.table-bordered
+            %tbody
+              - @compounds.each_with_index do |compound,cidx|
+                - timer += 800
+                :javascript
+                  $(document).ready(function() {
+                    $("img.circle").show();
+                    var model = '#{model}',
+                        msize = #{msize},
+                        idx = #{j+1},
+                        last = false,
+                        compound = '#{compound.id}',
+                        csize = #{csize},
+                        cidx = #{cidx},
+                        timer = #{timer},
+                        tmppath = '#{@tmppaths[model]}';
+                    // check for last request;
+                    if (cidx+1 == csize) {
+                      last = true;
+                    };
+                    setTimeout(function(){
+                      if (model != "Cramer"){
+                        renderResponse(model,cidx,compound,last,csize,tmppath);
+                      } else if (model == "Cramer" && cidx == 0){
+                        renderResponse(model,cidx,compound,last,csize,tmppath);
+                      };
+                    }, timer );
+                  });
+                // table layout:
+                // one row per prediction;
+                // first col compound; sec col results
+                %tr{:id=>model}
+                  // compound
+                  %td.col-md-6{:id=>"compound"}
+                    %p=embedded_svg(compound.svg, title: compound.smiles)
+                    %p=compound.smiles
+                  // prediction values from js function
+                  %td.col-md-6{:id=>"prediction_#{compound.id}_#{model}_#{cidx}", :style => "vertical-align:top;"}
diff --git a/views/neighbors.haml b/views/neighbors.haml
index 9c12be9..37c99d0 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -60,7 +60,7 @@
                     / Compound
                     - c = Compound.find(neighbor)
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:50%;"}
-                      = c.svg
+                      = embedded_svg(c.svg, title: c.smiles)
                       %p= c.smiles
                     
                     / Measured Activity
diff --git a/views/prediction.haml b/views/prediction.haml
index 62bed8b..b5a7e82 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -4,12 +4,6 @@
     $('.modal').on('hidden.bs.modal', function () {
       $(this).removeData('bs.modal');
     });
-    /*TableExport.prototype.bootstrap = ["btn", "btn-default", "btn-toolbar"];
-    var BootstrapTable = document.getElementById('overview');
-    new TableExport(BootstrapTable, {
-      ignoreCSS: ".ignore",
-      bootstrap: true,
-    });*/
   });
 
 %div.well
@@ -24,7 +18,7 @@
         %tr
           %td{:id=>"compound"}
             %b.title Compound
-            %p= embedded_svg @compound.svg, class: '.ignore', title: "#{@compound.smiles}"
+            %p= embedded_svg(@compound.svg, title: @compound.smiles)
             %p= @compound.smiles
           - @model_types = {}
           - @dbhit = {}
@@ -47,6 +41,16 @@
                   %p
                   %b Structural alerts:
                   %p
+                  / check for database hit
+                  - if prediction[:info] =~ /\b(identical)\b/i
+                    - @dbhit[i] = true
+                    / show message about dbhit and measurements
+                    %p
+                      :plain
+                        This compound was part of the training dataset. <i>All</i> information </br>
+                        from this compound was removed from the training data before the </br>
+                        prediction, to obtain unbiased results.
+                      %p
                   %b Prediction:
                   %br
                   =(hash[:prediction] == true ? "mutagenic" : "non-mutagenic")
@@ -71,19 +75,20 @@
                   - if prediction[:info] =~ /\b(identical)\b/i
                     - @dbhit[i] = true
                     / show message about dbhit and measurements
-                    %p
-                      :plain
-                        This compound was part of the training dataset. <i>All</i> information </br>
-                        from this compound was removed from the training data before the </br>
-                        prediction, to obtain unbiased results.
+                    - unless sa_prediction
                       %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]
-                  
+                        :plain
+                          This compound was part of the training dataset. <i>All</i> information </br>
+                          from this compound was removed from the training data before the </br>
+                          prediction, to obtain unbiased results.
+                        %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]
+                    
                   - else
                     - @dbhit[i] = false
                   
@@ -111,17 +116,6 @@
                           %br
                           = "#{prediction[:probabilities].keys[1]}: #{prediction[:probabilities].values[1].signif(3)}"
                   
-                  / show warnings and info
-                  -#%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(/,/, ",<br>")
                 - else
                   %p
                   - if !prediction[:info].blank?
@@ -148,6 +142,6 @@
 
   / always show the neighbors table, message is given there. Except only Cramer is selected.
   - unless @predictions.blank?
-    = haml :neighbors, :layout => false, :model_type => @model_types, :dbhit => @dbhit
+    = haml :neighbors, :layout => false
     
 
diff --git a/views/style.scss b/views/style.scss
index ac070a1..2a8f9d4 100644
--- a/views/style.scss
+++ b/views/style.scss
@@ -89,7 +89,15 @@ supporters{
     margin: 1em;
   }
 }
-
+.csv.btn{
+  width: 100%;
+  height: 30px;
+}
+.dlwait{
+  display: block;
+  margin-left: auto;
+  margin-right: auto;
+}
 .footer{
   margin-top:3em;
 }