serveral minor changes;pass values active/inactive

6 files changed, 59 insertions, 41 deletions

diff --git a/application.rb b/application.rb
index 13d98cb..0bbf18a 100644
--- a/application.rb
+++ b/application.rb
@@ -77,8 +77,17 @@ get '/prediction/:model_uri/:type/:compound_uri/fingerprints/?' do
         feature_calc_algo = p[RDF::OT.paramValue].object
       end
     }
+
+    @desc = []
     fingerprints = OpenTox::Algorithm::Descriptor.send( feature_calc_algo, [ @compound ], feature_dataset.features.collect{ |f| f[RDF::DC.title] } )
-    fingerprints.each{|x, h| h.each{|descriptor, value| @significant_fragments << [descriptor, [value]]}}
+    fingerprints.each{|x, h| h.each{|descriptor, value| @desc << [descriptor, [value]]}}
+    
+    pc_descriptor_titles_descriptions = {}
+    feature_dataset.features.collect{ |f|
+      pc_descriptor_titles_descriptions[f[RDF::DC.title]]= f[RDF::DC.description]
+    }
+
+    @desc.each{|d, v| @significant_fragments << [pc_descriptor_titles_descriptions[d], v] }
   end
 
   haml :significant_fragments, :layout => false
diff --git a/views/details.haml b/views/details.haml
index b69f1af..9f6915f 100644
--- a/views/details.haml
+++ b/views/details.haml
@@ -17,7 +17,10 @@
     %br
     %b="Names:"
     %p{:style=>"padding-left:0.5em;"}
+    - if @names !~ /^no names/i
       = @names.join("; ")
+    - else
+      = @names
     %p{:style=>"padding-left:0.5em;"}
       / pubchem link
       %a{:href=>"http://aop.in-silico.ch/", :title=>"link opens in new tab", :alt=>"pubchem link", :target=>"_blank"} PubChem read across 
diff --git a/views/neighbors.haml b/views/neighbors.haml
index df03b85..7785eaa 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -42,9 +42,10 @@
                 sortList: [[2,1]]
               });
             });
-          %h2= "Neighbors: "
+          /%h2= "Neighbors: "
           - $logger.debug "neighbors compounds:\t#{p.data_entries[0]}\n"
           - if p.data_entries[0][2] != nil && p.data_entries[0].size != 3
+            %h2= "Neighbors: "
             %table{:id=>"#{count_rs}", :class=>"tablesorter", :cellspacing=>"1"}
               %thead
                 %tr
@@ -90,22 +91,24 @@
                 / prevent conversion of nil
                 - c = p.data_entries[count][2] != nil ? p.data_entries[count][2] : '' 
                 - case c
-                - when /(0|false|inactive)/
+                - when /(false|true|inactive|active)/i
+                  - c = c
+                -#- when /(0|false|inactive)/
                   - c = "non-carcinogen"
-                - when /(1|true|active)/
+                -#- when /(1|true|active)/
                   - c = "carcinogen"
                 - else
-                  - c = Array.new
-                  - c[0] = p.data_entries[count][2]
+                  /- c = Array.new
+                  - c = p.data_entries[count][2].round(3)
                 %tr
                   %td.compound
                     %img{:src=>"#{neighbor_compound.uri}/image", :alt=>"Compound image not available", :title=>"#{neighbor_compound.smiles}", :width=>"150px"}
-                  %td{:class => c[0]}
+                  %td
                     - if c.class == String
                       = c
                     - else
-                      = c[0]
-                  %td{:class => c[0]}
+                      = c
+                  %td
                     = p.data_entries[count][3] != nil ? p.data_entries[count][3].round(3) : "Not enough similar compounds in training dataset." 
                   %td
                     -#- if p.data_entries[count][3] != nil
@@ -129,7 +132,7 @@
                           });
                       });
                   - count += 1
-          - else
+          -#- else
             %h3
               Not enough similar compounds in training dataset
 
diff --git a/views/predict.haml b/views/predict.haml
index 6340def..d515902 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -79,7 +79,7 @@
           %div{:id => model_title}
             %input{:type => "checkbox", :name => "selection[#{model_title}]", :id => "selection[#{model_title}]", :value => true, :disabled => false}
             %label{:for => "selection[#{model_title}]"}
-              = model.title
+              = model.title.gsub("_", " ")
             %a{:href=>"#details", :id => "linkDetails#{model_title}", :title=>"#{model_title} details", :style=>"font-size:small;"}
               [Details]
         
@@ -112,7 +112,7 @@
           %div{:id => model_title}
             %input{:type => "checkbox", :name => "selection[#{model_title}]", :id => "selection[#{model_title}]", :value => true, :disabled => false}
             %label{:for => "selection[#{model_title}]"}
-              = model.title
+              = model.title.gsub("_", " ")
             %a{:href=>"#details", :id => "linkDetails#{@detail_count}", :title=>"#{model_title} details", :style=>"font-size:small;"}
               [Details]
 
@@ -146,7 +146,7 @@
           %div{:id => model_title}
             %input{:type => "checkbox", :name => "selection[#{model_title}]", :id => "selection[#{model_title}]", :value => true, :disabled => false}
             %label{:for => "selection[#{model_title}]"}
-              = model.title
+              = model.title.gsub("_", " ")
             %a{:href=>"#details", :id => "linkDetails#{model_title}", :title=>"#{model_title} details", :style=>"font-size:small;"}
               [Details]
         
diff --git a/views/prediction.haml b/views/prediction.haml
index 5de0564..16101d3 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -16,7 +16,7 @@
         %tr
           %td{:id=>"compound", :style=>"align:center;"}
             %a{:href => to("/prediction/#{CGI.escape(@compound.uri)}/details"), :id=>"linkCompound", :target=>"details_overview"}
-              %img{:src=>"#{@compound.uri}/image", :alt=>"Compound image not available", :width=>"150", :height=>"150"}
+              %img{:src=>"#{@compound.uri}/image", :alt=>"Compound image not available", :title=>"#{@compound.smiles}", :width=>"150", :height=>"150"}
             %p
             %a{:href => to("/prediction/#{CGI.escape(@compound.uri)}/details"), :id=>"linkCompound", :target=>"details_overview"} Names and synonyms
             %p
@@ -40,14 +40,16 @@
                 - database_hit = 1
               - c = p.data_entries[0][0] != nil ? p.data_entries[0][0] : ''
               - case c
-              - when /(0|false|inactive)/
+              - when /(false|true|inactive|active)/i
+                - c = c
+              -#- when /(0|false|inactive)/
                 - c = "non-carcinogen"
-              - when /(1|true|active)/
+              -#- when /(1|true|active)/
                 - c = "carcinogen"
               - else
-                - c = Array.new
-                - c[0] = (p.data_entries[0][0].class == Float) ? p.data_entries[0][0].round(3) : (p.data_entries[0][0] != nil ? p.data_entries[0][0] : "no prediction")
-              %td{:style=>"valign:top;"}
+                /- c = Array.new
+                - c = (p.data_entries[0][0].class == Float) ? p.data_entries[0][0].round(3) : (p.data_entries[0][0] != nil ? p.data_entries[0][0] : "no prediction")
+              %td{:style=>"vertical-align:top;"}
                 %b{:class => "title"}
                   = @prediction_models[count].title.gsub("_", " ")
                 - @model_uri = @prediction_models[count].uri
@@ -58,11 +60,11 @@
                 %p
                 - unless database_hit > 0
                   %b Result:
-                  %b{:class => c[0]}
+                  %b
                     - if c.class == String
                       = (c != '' ? c : "No prediction result.")
                     - else
-                      = (c[0] != '' ? c[0] : "No prediction result.")
+                      = (c != '' ? c.round(3) : "No prediction result.")
                   / title must be empty for tooltip
                   %a{:href=>"#result", :title=>"", :id=>"result"}
                     %img{:src=>"/images/info_white.png"}
@@ -89,7 +91,7 @@
                   %p
                   .confidence
                     %b Confidence:
-                    = p.data_entries[0][1] != nil ? p.data_entries[0][1].round(3) : "-"
+                    = (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0) ? p.data_entries[0][1].round(3) : "--"
                     / title must be empty for tooltip
                     %a{:href=>"#confidence", :title=>"", :id=>"confidence"}
                       %img{:src=>"/images/info_white.png"}
@@ -105,7 +107,7 @@
                         reliable and unreliable predictions.
                   %p
                   /TODO add tooltip for significant ftagments and descriptors
-                  - if @model_type[count] =~ /classification/i
+                  - if @model_type[count] =~ /classification/i && (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0)
                     / Significant fragments:
                     %a{:href => to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[count]}/#{CGI.escape(@compound.uri)}/fingerprints"), :id=>"linkPredictionSf", :target=>"details_overview"}Significant fragments
                     :javascript
@@ -114,7 +116,7 @@
                           $('#iframe_overview').bPopup();
                         });
                       });
-                  - if @model_type[count] =~ /regression/i
+                  - if @model_type[count] =~ /regression/i && (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0)
                     / Descriptors
                     %a{:href => to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[count]}/#{CGI.escape(@compound.uri)}/fingerprints"), :id=>"linkPredictionSf", :target=>"details_overview"} Descriptors
                     :javascript
@@ -132,15 +134,16 @@
                     %dd
                       Significant fragments are solely used to determine activity specific similarities of neighbors.
                   %p
-                  %b Neighbors:
-                  %a{:href=> "#tabs", :id=>"link#{count}"}
-                    %img{:src=>"/images/arrow_down_float.png", :alt=>"v"}
-                    :javascript
-                      $("a#link#{count}").click(function () {
-                        $(".results").show();
-                        document.getElementById('tabs').focus();
-                        $("#tabs").tabs({ active: "#{count}" });
-                      });
+                  - if c != ''
+                    %b Neighbors:
+                    %a{:href=> "#tabs", :id=>"link#{count}"}
+                      %img{:src=>"/images/arrow_down_float.png", :alt=>"v"}
+                      :javascript
+                        $("a#link#{count}").click(function () {
+                          $(".results").show();
+                          document.getElementById('tabs').focus();
+                          $("#tabs").tabs({ active: "#{count}" });
+                        });
                   %p
                   - count+=1
                 - else # database hit
diff --git a/views/significant_fragments.haml b/views/significant_fragments.haml
index 46cca5f..5bb4c31 100644
--- a/views/significant_fragments.haml
+++ b/views/significant_fragments.haml
@@ -12,9 +12,9 @@
     - if !@significant_fragments.empty?
       %table{:id => "sf1"}
         %tr
-          %th{:style=>"border:2px solid #C0C0C0;"}
-            Predominantly in compounds with activity "non-carcinogen"
-          %th{:style=>"border:2px solid #C0C0C0;"}
+          %th{:style=>"border:2px solid #E6E6E6;"}
+            Predominantly in compounds with activity "non-active"
+          %th{:style=>"border:2px solid #E6E6E6;"}
             p value
           - @significant_fragments.each do |fragments|
             / fragments == [1||2, smarts, pValue]
@@ -28,9 +28,9 @@
           %td
             %br
         %tr
-          %th{:style=>"border:2px solid #C0C0C0;"}
-            Predominantly in compounds with activity "carcinogen"   
-          %th{:style=>"border:2px solid #C0C0C0;"}
+          %th{:style=>"border:2px solid #E6E6E6;"}
+            Predominantly in compounds with activity "active"   
+          %th{:style=>"border:2px solid #E6E6E6;"}
             p value
           - @significant_fragments.each do |fragments|
             / fragments == [1||2, smarts, pValue]
@@ -50,9 +50,9 @@
     - if !@significant_fragments.empty?
       %table{:id => "sf2"}
         %tr
-          %th{:style=>"border:2px solid #C0C0C0;"}
+          %th{:style=>"border:2px solid #E6E6E6;"}
             Descriptor
-          %th{:style=>"border:2px solid #C0C0C0;"}
+          %th{:style=>"border:2px solid #E6E6E6;"}
             value
           - @significant_fragments.each do |fragments|
             %tr