use value map for sf

5 files changed, 79 insertions, 41 deletions

diff --git a/application.rb b/application.rb
index 0bbf18a..5ac5186 100644
--- a/application.rb
+++ b/application.rb
@@ -68,8 +68,19 @@ get '/prediction/:model_uri/:type/:compound_uri/fingerprints/?' do
     # collect all features from feature_dataset
     @features = feature_dataset.features.collect{|f| f }
     
-    # search for each fingerprint in all features and collect feature values(smarts, pValue, effect)
+    # search for each fingerprint in all features and collect feature values( effect, smarts, pValue )
     @fingerprint_values.each{ |fi, v| @features.each{ |f| @significant_fragments << [f[RDF::OT.effect].to_i, f[RDF::OT.smarts], f[RDF::OT.pValue]] if fi == f[RDF::OT.smarts] } }
+    
+    # pass value_map, important to interprete effect value
+    prediction_feature_uri = ""
+    model.parameters.each {|p|
+      if p[RDF::DC.title].to_s == "prediction_feature_uri"
+        prediction_feature_uri = p[RDF::OT.paramValue].object
+      end
+    }
+    prediction_feature = OpenTox::Feature.find prediction_feature_uri
+    @value_map = prediction_feature.value_map
+
   else #regression
     feature_calc_algo = ""
     model.parameters.each {|p|
@@ -128,11 +139,23 @@ get '/prediction/:model_uri/:type/:neighbor/significant_fragments/?' do
 
     # pass feature uris if value > 0
     @feat.each do |f|
+      # search relevant features
       if f[0] > 0
         f = OpenTox::Feature.find f[1]
+        # pass relevant features with [ effect, smarts, pValue ] 
         @significant_fragments << [f[RDF::OT.effect].to_i, f[RDF::OT.smarts], f[RDF::OT.pValue].to_f.round(3)]
       end
     end
+    # pass value_map, important to interprete effect value
+    prediction_feature_uri = ""
+    model.parameters.each {|p|
+      if p[RDF::DC.title].to_s == "prediction_feature_uri"
+        prediction_feature_uri = p[RDF::OT.paramValue].object
+      end
+    }
+    prediction_feature = OpenTox::Feature.find prediction_feature_uri
+    @value_map = prediction_feature.value_map
+
   else # regression
     # find a value in feature dataset by compound and feature
     @values = []
diff --git a/public/stylesheets/screen.css b/public/stylesheets/screen.css
index 6850732..afd55d7 100644
--- a/public/stylesheets/screen.css
+++ b/public/stylesheets/screen.css
@@ -1 +1 @@
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#f55;background-color:#fff;color:#f55;-moz-border-radius-topleft:25px;-webkit-border-top-left-radius:25px;border-top-left-radius:25px;-moz-border-radius-bottomleft:25px;-webkit-border-bottom-left-radius:25px;border-bottom-left-radius:25px;-moz-border-radius-topright:25px;-webkit-border-top-right-radius:25px;border-top-right-radius:25px;-moz-border-radius-bottomright:25px;-webkit-border-bottom-right-radius:25px;border-bottom-right-radius:25px;-webkit-background-clip:border;-moz-background-clip:border;background-clip:border-box}.content #closebutton{color:#f55;margin-left:98%;padding:0}.details{width:98%;background-color:#c5c1e4;-moz-border-radius-bottomleft:5px;-webkit-border-bottom-left-radius:5px;border-bottom-left-radius:5px;-moz-border-radius-bottomright:5px;-webkit-border-bottom-right-radius:5px;border-bottom-right-radius:5px;-webkit-background-clip:border;-moz-background-clip:border;background-clip:border-box;-webkit-box-shadow:1px 1px 1px #fff inset,0px -1px 2px rgba(0,0,0,0.3) inset;-moz-box-shadow:1px 1px 1px #fff inset,0px -1px 2px rgba(0,0,0,0.3) inset;box-shadow:1px 1px 1px #fff inset,0px -1px 2px rgba(0,0,0,0.3) inset}.details a:hover{color:#f55}.details img{display:inline;float:left;margin:0.5em}.significant_fragments{width:98%;margin-bottom:2em;background-color:#c5c1e4;-moz-border-radius-bottomleft:5px;-webkit-border-bottom-left-radius:5px;border-bottom-left-radius:5px;-moz-border-radius-bottomright:5px;-webkit-border-bottom-right-radius:5px;border-bottom-right-radius:5px;-webkit-background-clip:border;-moz-background-clip:border;background-clip:border-box;-webkit-box-shadow:1px 1px 1px #fff inset,0px -1px 2px rgba(0,0,0,0.3) inset;-moz-box-shadow:1px 1px 1px #fff inset,0px -1px 2px rgba(0,0,0,0.3) inset;box-shadow:1px 1px 1px #fff inset,0px -1px 2px rgba(0,0,0,0.3) inset}.significant_fragments img{display:inline;float:left;margin:0.5em}.significant_fragments table#sf1{text-align:left}.significant_fragments table#sf1 td{padding:0.2em}.descriptors{width:98%;margin-bottom:2em;background-color:#c5c1e4;-moz-border-radius-bottomleft:5px;-webkit-border-bottom-left-radius:5px;border-bottom-left-radius:5px;-moz-border-radius-bottomright:5px;-webkit-border-bottom-right-radius:5px;border-bottom-right-radius:5px;-webkit-background-clip:border;-moz-background-clip:border;background-clip:border-box;-webkit-box-shadow:1px 1px 1px #fff inset,0px -1px 2px rgba(0,0,0,0.3) inset;-moz-box-shadow:1px 1px 1px #fff inset,0px -1px 2px rgba(0,0,0,0.3) inset;box-shadow:1px 1px 1px #fff inset,0px -1px 2px rgba(0,0,0,0.3) inset}.descriptors img{display:inline;float:left;margin:0.5em}.descriptors table#sf2{text-align:left}.descriptors table#sf2 td{padding:0.2em}.results{background-image:url("/images/gray_jean.png");overflow-x:auto;overflow-y:hidden;margin-top:2em;margin-bottom:2em;-webkit-box-shadow:1px 1px 1px #fff inset,0px -1px 2px rgba(0,0,0,0.3) inset;-moz-box-shadow:1px 1px 1px #fff inset,0px -1px 2px rgba(0,0,0,0.3) inset;box-shadow:1px 1px 1px #fff inset,0px -1px 2px rgba(0,0,0,0.3) inset}.results a:hover{color:#f55}.results .tablesorter{width:100%;text-align:left}.results .tablesorter thead{background-color:#e6e5f3}.results .tablesorter thead tr th.header{background-image:url("/images/bg.gif");background-repeat:no-repeat;background-position:center left;cursor:pointer;padding-left:20px;border:1px solid #dad9c7;margin-left:-1px}.results .tablesorter thead tr th.headerSortDown{background-image:url("/images/desc.gif");background-color:#c5c1e4}.results .tablesorter thead tr th.headerSortUp{background-image:url("/images/asc.gif");background-color:#c5c1e4}.results .tablesorter tbody tr td{padding-left:1em;-webkit-box-shadow:1px 1px 1px #fff inset,0px -1px 2px rgba(0,0,0,0.3) inset;-moz-box-shadow:1px 1px 1px #fff inset,0px -1px 2px rgba(0,0,0,0.3) inset;box-shadow:1px 1px 1px #fff inset,0px -1px 2px rgba(0,0,0,0.3) inset}.results .tablesorter tbody .compound{width:200px;padding:0.2em}.results .tablesorter tbody .n{color:#5c8533}.results .tablesorter tbody .c{color:#d42200}input#predict{border:0px;background-color:#c5c1e4;margin:0;padding:0}.tooltip{background-color:#fff;border:2px solid #ccc;font-size:0.5em;padding:1em;display:none;z-index:50}.footer{margin:20px 0 20px 0}
diff --git a/public/stylesheets/screen.sass b/public/stylesheets/screen.sass
index 9af4cdb..bce863d 100644
--- a/public/stylesheets/screen.sass
+++ b/public/stylesheets/screen.sass
@@ -92,27 +92,36 @@ body
       //background-image: url("/images/gray_jean.png")
       +box-shadow(1px 1px 1px rgba(white, 1) inset, -1px -1px 5px rgba(black, 0.3) inset)
       padding: 1em
+      a:hover
+        color: #FF5555
     #details_1
       background-color: adjust-lightness($ist-color, 10%)
       //background-image: url("/images/gray_jean.png")
       +box-shadow(1px 1px 1px rgba(white, 1) inset, -1px -1px 5px rgba(black, 0.3) inset)
       padding: 1em
+      a:hover
+        color: #FF5555
     #details_2
       background-color: adjust-lightness($ist-color, 10%)
       //background-image: url("/images/gray_jean.png")
       +box-shadow(1px 1px 1px rgba(white, 1) inset, -1px -1px 5px rgba(black, 0.3) inset)
       padding: 1em
+      a:hover
+        color: #FF5555
     #details_3
       background-color: adjust-lightness($ist-color, 10%)
       //background-image: url("/images/gray_jean.png")
       +box-shadow(1px 1px 1px rgba(white, 1) inset, -1px -1px 5px rgba(black, 0.3) inset)
       padding: 1em
+      a:hover
+        color: #FF5555
     #details_4
       background-color: adjust-lightness($ist-color, 10%)
       //background-image: url("/images/gray_jean.png")
       +box-shadow(1px 1px 1px rgba(white, 1) inset, -1px -1px 5px rgba(black, 0.3) inset)
       padding: 1em
-
+      a:hover
+        color: #FF5555
   fieldset#bottom
     border: 0
     background-color: $ist-color
diff --git a/views/predict.haml b/views/predict.haml
index d515902..8831c56 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -71,20 +71,22 @@
       - @detail_count = 0
       // TODO order models by echa endpoint
       #endpoint
-      %b Acute toxicity to fish (lethality):
       - @models.each do |model|
         - model_title = model.title.split("_").last(2)[0]
-        - if model_title =~ /LC50/i
+        - model_t = model.title.gsub("_", " ")
+        - case model_title
+        - when /LC50/i
+          %b Acute toxicity to fish (lethality):
           - @detail_count +=1
           %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.gsub("_", " ")
+              = model_t
             %a{:href=>"#details", :id => "linkDetails#{model_title}", :title=>"#{model_title} details", :style=>"font-size:small;"}
               [Details]
         
             :javascript
-              $("a#linkDetails#{@detail_count}").click(function () {
+              $("a#linkDetails#{model_title}").click(function () {
                 $("#details_#{@detail_count}").toggle();
                 //document.location = document.location + "#" + "details";
               });
@@ -94,30 +96,29 @@
             //%p= "Training Dataset:\t#{model[RDF::OT.trainingDataset]}"
             %p Algorithm: Lazar
             %p Type: regression
-            %p Training compounds: integer
-            %p Descriptors: Fminer
+            %p Training compounds: 580
+            %p{:style=>"display:inline;"} Descriptors:
+            %a{:href=>"https://services.in-silico.ch/algorithm/descriptor/physchem", :title=>"link opens in new window.", :target=>"_blank"} Physico-chemical (PC)properties
             //%p= "Training Dataset:\t#{model[RDF::OT.trainingDataset]}"
             //%p= "Feature Dataset:\t#{model[RDF::OT.featureDataset]}"
-            %h3 Validation: 
-            %a{:href => "#"} 
+            /%h3 Validation: 
+            -#%a{:href => "#"} 
               Detailed report link
-            %p Number of predictions: integer
-            %p Correct predictions: %
-      %br
-      %b Carcinogenicity:
-      - @models.each do |model|
-        - model_title = model.title.split("_").last(2)[0]
-        - if model_title =~ /hamster|rodent/i
+            /%p Number of predictions: integer
+            /%p Correct predictions: %
+        - when /hamster/i
+          %br
+          %b Carcinogenicity:
           - @detail_count +=1
           %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.gsub("_", " ")
-            %a{:href=>"#details", :id => "linkDetails#{@detail_count}", :title=>"#{model_title} details", :style=>"font-size:small;"}
+            %a{:href=>"#details", :id => "linkDetails#{model_title}", :title=>"#{model_title} details", :style=>"font-size:small;"}
               [Details]
 
             :javascript
-              $("a#linkDetails#{@detail_count}").click(function () {
+              $("a#linkDetails#{model_title}").click(function () {
                 $("#details_#{@detail_count}").toggle();
                 //document.location = document.location + "#" + "details";
               });
@@ -127,21 +128,20 @@
             //%p= "Training Dataset:\t#{model[RDF::OT.trainingDataset]}"
             %p Algorithm: Lazar
             %p Type: classification
-            %p Training compounds: integer
-            %p Descriptors: Fminer
+            %p Training compounds: 86
+            %p{:style=>"display:inline;"} Descriptors:
+            %a{:href=>"http://www.maunz.de/libfminer2-bbrc-doc/", :title=>"link opens in new window.", :target=>"_blank"} Fminer backbone refinement classes
             //%p= "Training Dataset:\t#{model[RDF::OT.trainingDataset]}"
             //%p= "Feature Dataset:\t#{model[RDF::OT.featureDataset]}"
             %h3 Validation: 
-            %a{:href => "#"} 
+            %a{:href => "http://lazar-services.in-silico.ch/validation/report/crossvalidation/22", :title=>"Link opens in new window.", :target=>"_blank"} 
               Detailed report link
-            %p Number of predictions: integer
-            %p Correct predictions: %
+            /%p Number of predictions: integer
+            /%p Correct predictions: %
             %br
-      %br
-      %b Mutagenicity:
-      - @models.each do |model|
-        - model_title = model.title.split("_").last(2)[0]
-        - if model_title =~ /Mutagenicity/i
+        - when /mutagenicity/i
+          %br
+          %b Mutagenicity:
           - @detail_count +=1
           %div{:id => model_title}
             %input{:type => "checkbox", :name => "selection[#{model_title}]", :id => "selection[#{model_title}]", :value => true, :disabled => false}
@@ -151,7 +151,7 @@
               [Details]
         
             :javascript
-              $("a#linkDetails#{@detail_count}").click(function () {
+              $("a#linkDetails#{model_title}").click(function () {
                 $("#details_#{@detail_count}").toggle();
                 //document.location = document.location + "#" + "details";
               });
@@ -161,15 +161,16 @@
             //%p= "Training Dataset:\t#{model[RDF::OT.trainingDataset]}"
             %p Algorithm: Lazar
             %p Type: classification
-            %p Training compounds: integer
-            %p Descriptors: Fminer
+            %p Training compounds: 828
+            %p{:style=>"display:inline;"} Descriptors:
+            %a{:href=>"http://www.maunz.de/libfminer2-bbrc-doc/", :title=>"link opens in new window.", :target=>"_blank"} Fminer backbone refinement classes
             //%p= "Training Dataset:\t#{model[RDF::OT.trainingDataset]}"
             //%p= "Feature Dataset:\t#{model[RDF::OT.featureDataset]}"
             %h3 Validation: 
-            %a{:href => "#"} 
+            %a{:href => "http://lazar-services.in-silico.ch/validation/report/crossvalidation/25", :title=>"Link opens in new window.", :target=>"_blank"} 
               Detailed report link
-            %p Number of predictions: integer
-            %p Correct predictions: %
+            /%p Number of predictions: integer
+            /%p Correct predictions: %
 
 
       %br
diff --git a/views/significant_fragments.haml b/views/significant_fragments.haml
index 5bb4c31..7301f53 100644
--- a/views/significant_fragments.haml
+++ b/views/significant_fragments.haml
@@ -12,17 +12,22 @@
     - if !@significant_fragments.empty?
       %table{:id => "sf1"}
         %tr
+          / @value_map => hash; interpret the effect
           %th{:style=>"border:2px solid #E6E6E6;"}
-            Predominantly in compounds with activity "non-active"
+            Predominantly in compounds with activity "inactive"
           %th{:style=>"border:2px solid #E6E6E6;"}
             p value
           - @significant_fragments.each do |fragments|
-            / fragments == [1||2, smarts, pValue]
-            - if fragments[0] == 1
+            / fragments == [effect, smarts, pValue]
+            / fragments[0] = effect
+            /- $logger.debug "effect:\t#{fragments[0]}\n"
+            - if fragments[0] == @value_map.index("inactive")
               %tr
                 %td
+                  / fragments[1] = smarts 
                   = fragments[1]
                 %td
+                  /fragments[2] = pValue
                   = fragments[2]
         %tr
           %td
@@ -33,8 +38,8 @@
           %th{:style=>"border:2px solid #E6E6E6;"}
             p value
           - @significant_fragments.each do |fragments|
-            / fragments == [1||2, smarts, pValue]
-            - if fragments[0] == 2
+            / fragments == [effect, smarts, pValue]
+            - if fragments[0] == @value_map.index("active")
               %tr
                 %td
                   = fragments[1]