version bump;units;general class update;sort by

2 files changed, 34 insertions, 26 deletions

diff --git a/views/predict.haml b/views/predict.haml
index 5d5d6f0..7819698 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -11,7 +11,7 @@
       - @prediction_models.each_with_index do |m, idx|
         %li{:class => ("active" if idx == 0)}
           %a{:href => "#model_#{idx}", :id => "linkTab#{idx}", data: {toggle:"tab"}}
-            = "#{idx+1}. #{m.model.feature_selection_algorithm_parameters[:category].nil? ? "Physchem & Proteomics" : "Physchem" }"
+            = "#{idx+1}. #{m[:pcp_model] ? "Physchem & Proteomics" : "Physchem" }"
     %div.tab-content
       - @prediction_models.each_with_index do |m, idx|
         - m[:pc_model] ? (example = @example_pc; type = "pc"; relevant_features = @pc_relevant_features) : (example = @example_pcp; type = "pcp"; relevant_features = @pcp_relevant_features)
@@ -39,17 +39,23 @@
           Unit:
           = m.unit
           %br
-          Prediction algorithm:
-          = m.model.prediction_algorithm.split(".").last.gsub("_"," ")
+          %b Algorithms:
           %br
-          Prediction algorithm parameter:
-          = "random forest" if m.model.prediction_algorithm_parameters["method"] == "rf"
+          Similarity:
+          %a{:href=> "http://www.rubydoc.info/gems/lazar/OpenTox%2F#{m.model.algorithms["similarity"]["method"].sub("::", "%2F")}", :rel=>"external"}
+            = m.model.algorithms["similarity"]["method"]
+          = ", min: #{m.model.algorithms["similarity"]["min"]}"
           %br
-          Neighbor algorithm:
-          = m.model.neighbor_algorithm.gsub("_", " ")
+          Prediction:
+          %a{:href=>"http://www.rubydoc.info/gems/lazar/OpenTox%2F#{m.model.algorithms["prediction"]["method"].sub("::","%2f")}", :rel=>"external"}
+            = m.model.algorithms["prediction"]["method"]
           %br
-          Neighbor algorithm parameter:
-          = "min sim = #{m.model.neighbor_algorithm_parameters["min_sim"]}"
+          Feature selection:
+          = m.model.algorithms["feature_selection"]["method"].split(".").last
+          %br
+          Descriptors:
+          = m.model.algorithms["descriptors"]["method"]+","
+          = m.model.algorithms["descriptors"]["categories"]
           %p
           %b Independent crossvalidations (log2 transformed):
           - crossvalidations =[]
@@ -89,7 +95,7 @@
               // example data to compare
               %input{:id=>"example_core",:type=>"hidden",:name=>"example_core",:value=>"#{example.core}"}
               %input{:id=>"example_coating",:type=>"hidden",:name=>"example_coating",:value=>"#{example.coating}"}
-              %input{:id=>"example_pc",:type=>"hidden",:name=>"example_pc",:value=>"#{example.physchem_descriptors}"}
+              %input{:id=>"example_pc",:type=>"hidden",:name=>"example_pc",:value=>"#{example.properties}"}
               - size = relevant_features.size
               %input{:id=>"size",:type=>"hidden",:name=>"size",:value=>size}
               %input{:id=>"id",:type=>"hidden",:name=>"example_id",:value=>example.id}
@@ -107,9 +113,13 @@
               %input{:id=>"input_coating",:type=>"hidden",:name=>"in_coating",:value=>example.coating}
               // prediction model id 
               %input{:id=>"prediction_model",:type=>"hidden",:name=>"prediction_model",:value=>m.id}
-            - relevant_features.sort_by{|d| d.category}.each_with_index do |relf,id|
+            //sort the relevant features
+            - pc = relevant_features.collect{|f| f if f.category == "P-CHEM"}.compact
+            - pcp = relevant_features.collect{|f| f if f.category == "Proteomics"}.compact
+            - relevant_features = pc.sort_by{|f| f.name} + pcp.sort_by{|f| f.name}
+            - relevant_features.each_with_index do |relf,id|
               - feature = relf
-              - v = example.physchem_descriptors.find{|id,v| id == feature.id.to_s  }
+              - v = example.properties.find{|id,v| id == feature.id.to_s  }
               - name = feature.name
               - if feature[:conditions] && !feature[:conditions]["MEDIUM"].blank?
                 - name = feature.name + " / " + feature[:conditions]["MEDIUM"]
@@ -119,12 +129,10 @@
               - id = id + 1
               - if feature.category == "Proteomics"
                 %h5
-                  %a{:href=>"http://www.uniprot.org/uniprot/#{name}", :rel=>"external"}= name
-              - else
-                / prepare name string for npo_search
-                - string = name.split("/").first.downcase.gsub(/%s/, "%20")
+                  %a{:href=>"http://www.uniprot.org/uniprot/#{name}", :rel=>"external"}= name + (feature.unit.blank? ? "" : " (#{feature.unit})")
+              - if feature.category == "P-CHEM"
                 %h5
-                  %a{:href=>$npo_search % string, :rel=>"external"}= name
+                  %a.descriptor{:href=>$npo[feature.name], :rel=>"external"}= name + (feature.unit.blank? ? "" : " (#{feature.unit})")
               // input physchem parameters
               %input.input-sm.form-control{:id=>id,:type=>"text",:name=>"input_value_#{id}",:value=>"#{val[0] if val[0]}", :disabled=>("disabled" if val[0] == "-")}
               - if val[0] == "-"
diff --git a/views/prediction.haml b/views/prediction.haml
index 53a9cfd..e451c5f 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -12,7 +12,7 @@
       $(".tablesorter").tablesorter({
         debug: false,
         theme: "bootstrap",
-        headerTemplate: '{content} {icon}',
+        //headerTemplate: '{content} {icon}',
         widgets: ['uitheme', 'staticRow', 'stickyHeaders'],
         widgetOptions: {
           stickyHeaders_attachTo: 'neighbors',
@@ -43,15 +43,15 @@
             Net cell association
             %br
             [mL/ug(Mg)]
-          - @input.each{|d| OpenTox::Feature.find(d[0]).category}.each do |key|
-            - feature = OpenTox::Feature.find_by(:id=>key[0])
+          - @input.each{|d| Feature.find(d[0]).category}.each do |key|
+            - feature = Feature.find_by(:id=>key[0])
             - name = feature.name
             - if (feature[:conditions] && !feature[:conditions]["MEDIUM"].blank?)
               - name = feature.name + " / " + feature[:conditions]["MEDIUM"]
             - else
               - name = feature.name
-            %th.physchem
-              = name
+            %th.physchem.sorter-false
+              %a.descriptor{:href=>$npo[feature.name], :rel=>"external"}= name + (feature.unit.blank? ? "" : " (#{feature.unit})")
       %tbody
         / query and match combined
         %tr.static
@@ -118,7 +118,7 @@
         / neighbors
         - if @prediction[:neighbors]
           - @prediction[:neighbors].each_with_index do |neighbor,idx|
-            - nano = OpenTox::Nanoparticle.find(neighbor["_id"])
+            - nano = Nanoparticle.find(neighbor[:id])
             %tr
               / ID
               %td
@@ -126,7 +126,7 @@
                   %h5.th5= nano.name
               / Similarity
               %td
-                %h5.th5= neighbor["similarity"].round(3)
+                %h5.th5= neighbor[:similarity].round(3)
               / Composition
               %td
                 %h5.th5 Core:
@@ -137,8 +137,8 @@
               / Tox
               %td.tox
                 %h5.th5 Measurement:
-                = neighbor["measurements"][0]
+                = neighbor[:measurement]
               / Physchem
-              - nano.physchem_descriptors.delete_if{|id,v| @type == "pc" ? !@pc_relevant_features.include?(OpenTox::Feature.find(id)) : !@pcp_relevant_features.include?(OpenTox::Feature.find(id))}.sort_by{|id,v| @pc_relevant_features.index OpenTox::Feature.find(id)}.each do |k,v|
+              - nano.properties.delete_if{|id,v| @type == "pc" ? !@pc_relevant_features.include?(Feature.find(id)) : !@pcp_relevant_features.include?(Feature.find(id))}.sort_by{|id,v| @pc_relevant_features.index Feature.find(id)}.each do |k,v|
                 %td.physchem
                   = v[0].round(3) unless v.nil?