batch merge

5 files changed, 54 insertions, 20 deletions

diff --git a/application.rb b/application.rb
index 229f3a1..fc7e415 100644
--- a/application.rb
+++ b/application.rb
@@ -202,21 +202,34 @@ get '/predict/?:csv?' do
       model = array[0]
       prediction = array[1]
       compound = key.smiles
+      mw = key.molecular_weight
       endpoint = "#{model.endpoint.gsub('_', ' ')} (#{model.species})"
       if prediction[:confidence] == "measured"
-        type = ""
-        pred = prediction[:value].numeric? ? "#{prediction[:value].round(3)} (#{model.unit})" : prediction[:value]
-        confidence = "measured activity"
+        if prediction[:value].is_a?(Array)
+          prediction[:value].each do |value|
+            type = ""
+            weight = Compound.from_smiles(compound).mmol_to_mg(value, mw)
+            pred = value.numeric? ? "#{'%.2e' % value} (#{model.unit}) | #{'%.2e' % weight} (mg/kg_bw/day)" : value
+            confidence = "measured activity"
+            @csv += "\"#{compound}\",\"#{endpoint}\",\"#{type}\",\"#{pred}\",\"#{confidence}\"\n"
+          end
+        else
+          type = ""
+          weight = Compound.from_smiles(compound).mmol_to_mg(prediction[:value], mw)
+          pred = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % weight} (mg/kg_bw/day)" : prediction[:value]
+          confidence = "measured activity"
+        end
       elsif prediction[:neighbors].size > 0
+        weight = Compound.from_smiles(compound).mmol_to_mg(prediction[:value], mw)
         type = model.model.class.to_s.match("Classification") ? "Classification" : "Regression"
-        pred = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} #{model.unit}" : prediction[:value]
+        pred = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % weight} (mg/kg_bw/day)" : prediction[:value]
         confidence = prediction[:confidence]
       else
         type = ""
         pred = "Not enough similar compounds in training dataset."
         confidence = ""
       end
-      @csv += "\"#{compound}\",\"#{endpoint}\",\"#{type}\",\"#{pred}\",\"#{confidence}\"\n"
+      @csv += "\"#{compound}\",\"#{endpoint}\",\"#{type}\",\"#{pred}\",\"#{confidence}\"\n" unless prediction[:value].is_a?(Array)
     end
   end
   @csv
diff --git a/views/batch.haml b/views/batch.haml
index ec987c4..9bfa67e 100644
--- a/views/batch.haml
+++ b/views/batch.haml
@@ -18,6 +18,7 @@
       / key = compound, values = array of arrays with model, prediction
       - @batch.each do |key, values|
         - compound = key
+        - mw = compound.molecular_weight
         %tr
           %td{:style=>"vertical-align:top;"}
             %p= compound.svg
@@ -32,10 +33,13 @@
               %p
               - if prediction[:confidence] == "measured"
                 %p
-                / TODO fix scientific notation from database
-                %b Measured activity:
-                = prediction[:value].numeric? ? "#{prediction[:value].round(3)} (#{model.unit})" : prediction[:value]
-                %p Compound is part of the training dataset
+                  %b Measured activity:
+                - if prediction[:value].is_a?(Array)
+                  = prediction[:value][0].numeric? ? prediction[:value].collect{|v| weight = compound.mmol_to_mg(v, mw); '%.2e' % v + " (#{model.unit})"+" | #{'%.2e' % weight} (mg/kg_bw/day)"}.join("</br>") : prediction[:value].join(", ")
+                - else
+                  = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value]
+                %p 
+                %b Compound is part of the training dataset
               - elsif prediction[:neighbors].size > 0
                 %p
                 / model type (classification|regression)
@@ -43,8 +47,7 @@
                 = model.model.class.to_s.match("Classification") ? "Classification" : "Regression"
                 %br
                 %b Prediction:
-                / TODO scientific notation
-                = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit})" : prediction[:value]
+                = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value]
                 %br
                 / TODO probability
                 %b Confidence:
diff --git a/views/neighbors.haml b/views/neighbors.haml
index a741b45..6001605 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -29,7 +29,20 @@
                 debug: false,
                 theme: "bootstrap",
                 headerTemplate: '{content} {icon}',
-                widgets: ['zebra', 'columns', 'uitheme'],
+                widgets: ['zebra', 'columns', 'uitheme', 'stickyHeaders'],
+                widgetOptions: {
+                  stickyHeaders_attachTo : '.tab-content',
+                  stickyHeaders : '',
+                  stickyHeaders_offset : 0,
+                  stickyHeaders_cloneId : '-sticky',
+                  stickyHeaders_addResizeEvent : true,
+                  stickyHeaders_includeCaption : true,
+                  stickyHeaders_zIndex : 2,
+                  stickyHeaders_attachTo : null,
+                  stickyHeaders_xScroll : null,
+                  stickyHeaders_yScroll : null,
+                  stickyHeaders_filteredToTop: true
+                },
                 headers: {0: {sorter: false}, 3: {sorter: false}},
                 sortList: [[2,1]],
                 widthFixed: false
@@ -65,9 +78,11 @@
                       /%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}"}}
                       %p= Compound.find(neighbor[0]).svg
                       %p= Compound.find(neighbor[0]).smiles
+                    - c = Compound.find(neighbor[0])
+                    //- mw = c.molecular_weight
                     / Measured Activity
-                    %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"}
-                      = (type == "Regression") ? neighbor[2].collect{|n| '%.2e' % n + " (#{@models[j].unit})"}.join("</br>") : neighbor[2].join(", ")
+                    %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;white-space:nowrap;"}
+                      = (type == "Regression") ? neighbor[2].collect{|n| weight = c.mmol_to_mg(n); '%.2e' % n + " (#{@models[j].unit})"+"|#{'%.2e' % weight} (mg/kg_bw/day)"}.join("</br>") : neighbor[2].join(", ")
                     / Similarity
                     %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"}
                       / TODO differentiate between no neighbors found and compound found in dataset, display neighbors for compounds in dataset?
diff --git a/views/predict.haml b/views/predict.haml
index 8ab9ee0..010ed12 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -125,7 +125,6 @@
       %br
       %input{:type => 'text', :name => 'identifier', :id => 'identifier', :size => '60'}
       %p
-      // disable for public version
       %label{:for=>"fileselect"}
         or upload a CSV file for batch predictions (disabled in public version)
       %br
diff --git a/views/prediction.haml b/views/prediction.haml
index ef0c5db..33e9ec5 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -18,6 +18,7 @@
           %td{:id=>"compound", :style=>"vertical-align:top;"}
             %p= @compound.svg
             %p= @compound.smiles
+          -#- mw = @compound.molecular_weight
           - @model_types = {}
           - @dbhit = {}
           - @predictions.each_with_index do |prediction,i|
@@ -30,10 +31,14 @@
               - if prediction[:confidence] == "measured"
                 - @dbhit[i] = true
                 %p
-                / TODO fix scientific notation from database
                 %b Measured activity:
-                = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{@models[i].unit})" : prediction[:value]
-                %p Compound is part of the training dataset
+                - p prediction[:value]
+                - if prediction[:value].is_a?(Array)
+                  = (type == "Regression") ? prediction[:value].collect{|v| weight = Compound.from_smiles(@compound.smiles).mmol_to_mg(v); '%.2e' % v + " (#{@models[i].unit})"+"|#{'%.2e' % weight} (mg/kg_bw/day)"}.join("</br>") : prediction[:value].join(", ")
+                - else
+                  = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} (mg/kg_bw/day)" : prediction[:value]
+                %p
+                  %b Compound is part of the training dataset
               - elsif prediction[:neighbors].size > 0
                 %p
                 / model type (classification|regression)
@@ -41,8 +46,7 @@
                 = type
                 %br
                 %b Prediction:
-                / TODO scientific notation
-                = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{@models[i].unit})" : prediction[:value]
+                = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} (mg/kg_bw/day)" : 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