bumped version;adjustments for updated lazar library

7 files changed, 39 insertions, 38 deletions

diff --git a/VERSION b/VERSION
index 45a1b3f..26aaba0 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-1.1.2
+1.2.0
diff --git a/application.rb b/application.rb
index fa5df0a..911965f 100644
--- a/application.rb
+++ b/application.rb
@@ -19,6 +19,10 @@ before do
   @version = File.read("VERSION").chomp
 end
 
+not_found do
+  redirect to('/predict')
+end
+
 get '/?' do
   redirect to('/predict') 
 end
diff --git a/public/css/bootstrap.vertical-tabs.min.css b/public/css/bootstrap.vertical-tabs.min.css
new file mode 100644
index 0000000..d711daa
--- /dev/null
+++ b/public/css/bootstrap.vertical-tabs.min.css
@@ -0,0 +1 @@
+.tabs-left,.tabs-right{border-bottom:none;padding-top:2px}.tabs-left{border-right:1px solid #ddd}.tabs-right{border-left:1px solid #ddd}.tabs-left>li,.tabs-right>li{float:none;margin-bottom:2px}.tabs-left>li{margin-right:-1px}.tabs-right>li{margin-left:-1px}.tabs-left>li.active>a,.tabs-left>li.active>a:focus,.tabs-left>li.active>a:hover{border-bottom-color:#ddd;border-right-color:transparent}.tabs-right>li.active>a,.tabs-right>li.active>a:focus,.tabs-right>li.active>a:hover{border-bottom:1px solid #ddd;border-left-color:transparent}.tabs-left>li>a{border-radius:4px 0 0 4px;margin-right:0;display:block}.tabs-right>li>a{border-radius:0 4px 4px 0;margin-right:0}.sideways{margin-top:50px;border:none;position:relative}.sideways>li{height:20px;width:120px;margin-bottom:100px}.sideways>li>a{border-bottom:1px solid #ddd;border-right-color:transparent;text-align:center;border-radius:4px 4px 0 0}.sideways>li.active>a,.sideways>li.active>a:focus,.sideways>li.active>a:hover{border-bottom-color:transparent;border-right-color:#ddd;border-left-color:#ddd}.sideways.tabs-left{left:-50px}.sideways.tabs-right{right:-50px}.sideways.tabs-right>li{-webkit-transform:rotate(90deg);-moz-transform:rotate(90deg);-ms-transform:rotate(90deg);-o-transform:rotate(90deg);transform:rotate(90deg)}.sideways.tabs-left>li{-webkit-transform:rotate(-90deg);-moz-transform:rotate(-90deg);-ms-transform:rotate(-90deg);-o-transform:rotate(-90deg);transform:rotate(-90deg)}
diff --git a/views/batch.haml b/views/batch.haml
index 6c37a2b..c1b45f6 100644
--- a/views/batch.haml
+++ b/views/batch.haml
@@ -53,7 +53,7 @@
                 = type
                 %p 
                 / check for database hit
-                - if prediction[:warning] =~ /\b(identical)\b/i
+                - if prediction[:info] =~ /\b(identical)\b/i
                   
                   / show message about dbhit and measurements
                   %p
diff --git a/views/neighbors.haml b/views/neighbors.haml
index 2d7c4a5..7c814dc 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -1,38 +1,17 @@
-/ unpacks multi prediction array ;
-/ prepare it for neighbors ;
-/ align single prediction to endpoint ;
-/ display preordered in table view ;
-
 %div.results
   %h3 Neighbors:
   / tabs div
   #tabs
     %ul.nav.nav-tabs.nav-justified{:id=>"neighborTabs", :role=>"tablist"}
-      / each model a tab head ;
-      / hash for predictionFeature
-      - predictionFeature = {}
       - @models.each_with_index do |model,i|
         / get predictionFeature type
         - m = Model::Lazar.find model.model_id.to_s
-        - predFeature = Feature.find m.prediction_feature_id.to_s
-        / define feature type (numeric : nominal)
-        - predFeatureType = (predFeature.numeric? ? "numeric" : "nominal")
-        / use prediction feature id for neighbor compound features
-        - predFeatureId = m.prediction_feature_id.to_s
-        - predictionFeature[i] = {"id" => predFeatureId, "type" => predFeatureType}
         %li{:class => ("active" if i == 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_with_index do |prediction,j|
-        / pass model type for significant fragments view
         #results.tab-pane{:id=>"#{j+1}", :class => ("active" if j == 0)}
-          / 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({
@@ -58,7 +37,7 @@
                 widthFixed: false
               });
             });
-          - if prediction[:neighbors].size > 0
+          - if prediction[:neighbors]
             %div.table-responsive
               %table{:id=>"#{j+1}", :style=>"border-style: solid;"}
                 %thead
@@ -71,8 +50,6 @@
                     %th.sorter-false{:style =>"vertical-align:middle;"}
                       Similarity
                       %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Similarity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"auto", html:"true", content:"<a alt=\"Link opens in new window.\" title=\"Link opens in new window.\" target=\"_blank\" href=\"https://en.wikipedia.org/wiki/Jaccard_index\">Tanimoto/Jaccard</a> similarity based on <a alt=\"Link opens in new window.\" title=\"Link opens in new window.\" target=\"_blank\" href=\"https://openbabel.org/docs/dev/FileFormats/MolPrint2D_format.html\">Molprint2D</a> fingerprints."}, :style=>"z-index:auto+10;"}
-                    / %th{:style =>"vertical-align:middle;"}
-                    / Supporting Information
                 %tbody
                   - type = @model_types[j]
                   - unit = @models[j].unit
@@ -90,8 +67,8 @@
                       - if neighbor[:measurement].is_a?(Array)
                         = (type == "Regression") ? neighbor[:measurement].collect{|value| "#{value.delog10.signif(3)} (#{unit})</br>#{c.mmol_to_mg(value.delog10).signif(3)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : neighbor[:measurement].join(", ")
                       - else
-                        = (type == "Regression") ? "#{neighbor[:measurement].delog10.signif(3)} (#{unit})</br>#{c.mmol_to_mg(neighbor[:measurement].delog10).signif(3)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : neighbor[:measurement]
-                    
+                        - if !neighbor[:measurement].nil?
+                          = (type == "Regression") ? "#{neighbor[:measurement].delog10.signif(3)} (#{unit})</br>#{c.mmol_to_mg(neighbor[:measurement].delog10).signif(3)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : neighbor[:measurement]
                     / Similarity = tanimoto
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"}
                       = neighbor[:similarity].round(3)
diff --git a/views/prediction.haml b/views/prediction.haml
index 77d7524..12a1fde 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -23,14 +23,15 @@
                 = "#{@models[i].endpoint.gsub('_', ' ')} (#{@models[i].species})"
               
               / check for prediction
-              - if prediction[:neighbors].size > 0
+              /- if prediction[:neighbors].size > 0
+              - if prediction[:neighbors] and !prediction[:value].nil?
                 %p
                 / show model type (classification|regression)
                 %b Type:
                 = type
                 %p 
                 / check for database hit
-                - if prediction[:warning] =~ /\b(identical)\b/i
+                - if prediction[:info] =~ /\b(identical)\b/i
                   - @dbhit[i] = true
                   
                   / show message about dbhit and measurements
@@ -77,15 +78,30 @@
                         %br
                         = "#{prediction[:probabilities].keys[1]}: #{prediction[:probabilities].values[1].signif(3)}"
                 
-                / show warnings
+                / show warnings and info
                 %p
-                - if !prediction[:warning].nil?
-                  %b Warnings:
-                  %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Warnings", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"auto", html:"true", content:"#{prediction[:warning]}"}}
+                - if !prediction[:info].blank?
+                  %b info:
+                  %br
+                  %p=prediction[:info].sub(/excluded/, "excluded<br>")
+                - if !prediction[:warnings].blank?
+                  %b warnings:
+                  - prediction[:warnings].each do |warning|
+                    %br
+                    %p=warning
+                    %p=warning.sub(/substances/, "substances<br>").sub(/prediction\:/, "prediction\:<br>")
               - else
+                %br
                 - @dbhit[i] = false
-                %p
-                  = "Not enough similar compounds </br>in training dataset."
+                - if !prediction[:info].blank?
+                  %b info:
+                  %br
+                  %p=prediction[:info].sub(/excluded/, "excluded<br>")
+                - if !prediction[:warnings].blank?
+                  %b warnings:
+                  - prediction[:warnings].each do |warning|
+                    %br
+                    %p=warning.sub(/substances/, "substances<br>").sub(/prediction\:/, "prediction\:<br>")
 
   / always show the neighbors table, message is given there  
   = haml :neighbors, :layout => false, :model_type => @model_types, :dbhit => @dbhit
diff --git a/views/style.scss b/views/style.scss
index 2c84781..5c56d14 100644
--- a/views/style.scss
+++ b/views/style.scss
@@ -9,14 +9,14 @@ h4.head-back, h5.head-back{
 }
 .nav-tabs {
   background-color: #E7E7E7;
-  margin-bottom: 0;
+  //margin-bottom: 0;
 
   li.active a:hover {
     background-color: #f5f5f5;
   }
 
   li a {
-    height: 5em;
+    height: 7em;
   }
 }
 img {
@@ -40,6 +40,9 @@ img {
 .tablesorter-bootstrap thead .sorter-false {
   cursor: default;
 }
+.tablesorter-bootstrap thead {
+  background-color: #E7E7E7;
+}
 ul.share-buttons{
   list-style: none;
 }