small edits for new model names

9 files changed, 95 insertions, 55 deletions

diff --git a/application.rb b/application.rb
index 5cd5093..13d98cb 100644
--- a/application.rb
+++ b/application.rb
@@ -12,7 +12,7 @@ helpers do
   # model uris must be manually added
   @@models = []
   CSV.foreach("./prediction_models.csv"){|uri| m = OpenTox::Model::Lazar.find uri[0]; @@models << m}
-  #$logger.debug "model uris from csv file:\t#{@@models}\n"
+  $logger.debug "model uris from csv file:\t#{@@models}\n"
 end
 
 get '/?' do
@@ -55,7 +55,7 @@ get '/prediction/:model_uri/:type/:compound_uri/fingerprints/?' do
   model = OpenTox::Model::Lazar.find params[:model_uri]
   feature_dataset = OpenTox::Dataset.find model[RDF::OT.featureDataset]
   @compound = OpenTox::Compound.new params[:compound_uri]
-
+  @significant_fragments = []
   if @type =~ /classification/i
     # collect all feature values with fingerprint
     fingerprints = OpenTox::Algorithm::Descriptor.send("smarts_match", [@compound], feature_dataset.features.collect{ |f| f[RDF::DC.title]})[@compound.uri]
@@ -69,10 +69,16 @@ get '/prediction/:model_uri/:type/:compound_uri/fingerprints/?' do
     @features = feature_dataset.features.collect{|f| f }
     
     # search for each fingerprint in all features and collect feature values(smarts, pValue, effect)
-    @significant_fragments = []
     @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] } }
   else #regression
-    @significant_fragments = []
+    feature_calc_algo = ""
+    model.parameters.each {|p|
+      if p[RDF::DC.title].to_s == "feature_calculation_algorithm"
+        feature_calc_algo = p[RDF::OT.paramValue].object
+      end
+    }
+    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]]}}
   end
 
   haml :significant_fragments, :layout => false
@@ -169,7 +175,7 @@ post '/predict/?' do
       # selected model = model[0]
       # compare selected with all models
       @@models.each do |m|
-        @prediction_models << m if m.title =~ /#{model[0]}/
+        @prediction_models << m if m.title =~ /#{model[0]}/i
       end
     end
 
@@ -205,4 +211,3 @@ get '/predict/stylesheets/:name.css' do
   sass(:"stylesheets/#{params[:name]}", Compass.sass_engine_options )
 end
 
-
diff --git a/prediction_models.csv b/prediction_models.csv
index e69de29..df45768 100644
--- a/prediction_models.csv
+++ b/prediction_models.csv
@@ -0,0 +1,3 @@
+https://dg.in-silico.ch/model/c939adda-a6ed-425e-8c39-5b679d9138a2,
+https://dg.in-silico.ch/model/885a138a-3011-47a9-9279-fd472141b9de,
+https://dg.in-silico.ch/model/7e1dda67-3bb7-4a97-b82b-136090faf4e0,
diff --git a/public/stylesheets/screen.css b/public/stylesheets/screen.css
index a81705c..6850732 100644
--- a/public/stylesheets/screen.css
+++ b/public/stylesheets/screen.css
@@ -1 +1 @@
-body{background-image:url("/images/gray_jean.png");overflow:scroll;font-family:sans-serif}body a{text-decoration:none;font-weight:bold;color:#000}body img{border:0}body h2{padding-top:12px;text-shadow:#fff 1px 1px 0;font-size:x-large;color:#f55}.logo img{float:left;display:inline;margin-right:1em}.logo h1{display:inline;width:80%}.logo img.ote{width:100px;height:50px;display:inline;float:right}.logo hr{margin:0.5em}.content{background-image:url("/images/gray_jean.png")}.content h1{margin:0.3em;text-shadow:#fff 1px 1px 0;font-size:x-large;font-family:Verdana;display:inline}.content .arrow{margin:8px 0px 5px 20px}.content .back{display:inline}.content #back-top{z-index:100;position:fixed;bottom:3%;margin-left:91%}.content #back-top a:hover{color:#bbb}.content fieldset#top{border:0;padding:10px;background-color:#c5c1e4;-moz-border-radius-topleft:25px;-webkit-border-top-left-radius:25px;border-top-left-radius:25px;-moz-border-radius-topright:25px;-webkit-border-top-right-radius:25px;border-top-right-radius:25px;-webkit-background-clip:border;-moz-background-clip:border;background-clip:border-box;-webkit-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;-moz-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset}.content fieldset#top a#linkInsert{display:block;width:100%;height:2em}.content fieldset#top #appletContainer{padding:10px}.content fieldset#middle{border:0;padding:10px;background-color:#c5c1e4;-webkit-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;-moz-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset}.content 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inset;-moz-border-radius-topleft:25px;-webkit-border-top-left-radius:25px;border-top-left-radius:25px;-moz-border-radius-topright:25px;-webkit-border-top-right-radius:25px;border-top-right-radius:25px;-webkit-background-clip:border;-moz-background-clip:border;background-clip:border-box}.content .overview a:hover{color:#f55}.content .overview caption{text-align:left}.content .overview #overview tr td{background-color:#fff;border:1px solid #dad9c7;padding-left:1em;padding-top:0.5em}.content .overview #overview tr td #compound{width:200px}.content .overview #overview tr td b.c{color:#d42200}.content .overview #overview tr td b.n{color:#5c8533}.content .overview #overview tr td .confidence{display:inline}.content .error{background-color:#c5c1e4;padding:15px;-webkit-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;-moz-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;-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 .error .message{margin-top:1em;padding:1em;border:2px solid #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 bfbedc6..9af4cdb 100644
--- a/public/stylesheets/screen.sass
+++ b/public/stylesheets/screen.sass
@@ -87,23 +87,27 @@ body
     #model a
       display: inline
       font-weight: normal
-    a#linkDetailsLC50_mmol
-      font-size: small
-    a#linkDetailsHamster
-      font-size: small
-    a#linkDetailsRodent
-      font-size: small
-    #details_LC50_mmol
+    #details_0
       background-color: adjust-lightness($ist-color, 10%)
       //background-image: url("/images/gray_jean.png")
       +box-shadow(1px 1px 1px rgba(white, 1) inset, -1px -1px 5px rgba(black, 0.3) inset)
       padding: 1em
-    #details_Hamster
+    #details_1
       background-color: adjust-lightness($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
-    #details_Rodent
+    #details_2
+      background-color: adjust-lightness($ist-color, 10%)
+      //background-image: url("/images/gray_jean.png")
+      +box-shadow(1px 1px 1px rgba(white, 1) inset, -1px -1px 5px rgba(black, 0.3) inset)
+      padding: 1em
+    #details_3
+      background-color: adjust-lightness($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
+    #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)
diff --git a/views/details.haml b/views/details.haml
index 5663c1f..b69f1af 100644
--- a/views/details.haml
+++ b/views/details.haml
@@ -17,7 +17,7 @@
     %br
     %b="Names:"
     %p{:style=>"padding-left:0.5em;"}
-      = @names
+      = @names.join("; ")
     %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 39f6272..df03b85 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -12,7 +12,7 @@
       / each endpoint becomes a tab head ;
       - @prediction_models.each do |m|
         - count_m += 1
-        - m_title = m.title.split(" ").first
+        - m_title = m.title.split("_").last(2)[0]
         %li
           %a{:href => "#results_#{count_m}", :id => "link#{m_title}"}
             = m_title
@@ -90,9 +90,9 @@
                 / prevent conversion of nil
                 - c = p.data_entries[count][2] != nil ? p.data_entries[count][2] : '' 
                 - case c
-                - when /(0|false)/
+                - when /(0|false|inactive)/
                   - c = "non-carcinogen"
-                - when /(1|true)/
+                - when /(1|true|active)/
                   - c = "carcinogen"
                 - else
                   - c = Array.new
diff --git a/views/predict.haml b/views/predict.haml
index 5641f6a..6340def 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -68,26 +68,28 @@
       });
       
     #models
+      - @detail_count = 0
       // TODO order models by echa endpoint
       #endpoint
-        %b Acute toxicity to fish (lethality):
+      %b Acute toxicity to fish (lethality):
       - @models.each do |model|
-        - model_title = model.title.split(" ").first
-        - if model_title =~ /LC50/
+        - model_title = model.title.split("_").last(2)[0]
+        - if model_title =~ /LC50/i
+          - @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}]"}
-              = " EPA v4b Fathead Minnow Acute Toxicity "+model_title
-            %a{:href=>"#details", :id => "linkDetails#{model_title}", :title=>"#{model_title} details"}
+              = model.title
+            %a{:href=>"#details", :id => "linkDetails#{model_title}", :title=>"#{model_title} details", :style=>"font-size:small;"}
               [Details]
         
             :javascript
-              $("a#linkDetails#{model_title}").click(function () {
-                $("#details_#{model_title}").toggle();
+              $("a#linkDetails#{@detail_count}").click(function () {
+                $("#details_#{@detail_count}").toggle();
                 //document.location = document.location + "#" + "details";
               });
 
-          #details{:id => "#{model_title}", :style=> "display:none;"}
+          #details{:id => "#{@detail_count}", :style=> "display:none;"}
             %h3 Model Details:
             //%p= "Training Dataset:\t#{model[RDF::OT.trainingDataset]}"
             %p Algorithm: Lazar
@@ -104,22 +106,23 @@
       %br
       %b Carcinogenicity:
       - @models.each do |model|
-        - model_title = model.title.split(" ").first
+        - model_title = model.title.split("_").last(2)[0]
         - if model_title =~ /hamster|rodent/i
+          - @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}]"}
-              = " DSSTox Carcinogenic Potency DBS "+model_title
-            %a{:href=>"#details", :id => "linkDetails#{model_title}", :title=>"#{model_title} details"}
+              = model.title
+            %a{:href=>"#details", :id => "linkDetails#{@detail_count}", :title=>"#{model_title} details", :style=>"font-size:small;"}
               [Details]
 
             :javascript
-              $("a#linkDetails#{model_title}").click(function () {
-                $("#details_#{model_title}").toggle();
+              $("a#linkDetails#{@detail_count}").click(function () {
+                $("#details_#{@detail_count}").toggle();
                 //document.location = document.location + "#" + "details";
               });
 
-          #details{:id=>"#{model_title}", :style=> "display:none;"}
+          #details{:id=>"#{@detail_count}", :style=> "display:none;"}
             %h3 Model Details:
             //%p= "Training Dataset:\t#{model[RDF::OT.trainingDataset]}"
             %p Algorithm: Lazar
@@ -134,6 +137,40 @@
             %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
+          - @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
+            %a{:href=>"#details", :id => "linkDetails#{model_title}", :title=>"#{model_title} details", :style=>"font-size:small;"}
+              [Details]
+        
+            :javascript
+              $("a#linkDetails#{@detail_count}").click(function () {
+                $("#details_#{@detail_count}").toggle();
+                //document.location = document.location + "#" + "details";
+              });
+
+          #details{:id => "#{@detail_count}", :style=> "display:none;"}
+            %h3 Model Details:
+            //%p= "Training Dataset:\t#{model[RDF::OT.trainingDataset]}"
+            %p Algorithm: Lazar
+            %p Type: classification
+            %p Training compounds: integer
+            %p Descriptors: Fminer
+            //%p= "Training Dataset:\t#{model[RDF::OT.trainingDataset]}"
+            //%p= "Feature Dataset:\t#{model[RDF::OT.featureDataset]}"
+            %h3 Validation: 
+            %a{:href => "#"} 
+              Detailed report link
+            %p Number of predictions: integer
+            %p Correct predictions: %
+
 
       %br
 
diff --git a/views/prediction.haml b/views/prediction.haml
index 4002cbd..5de0564 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -14,7 +14,7 @@
 
       %tbody
         %tr
-          %td{:id=>"compound"}
+          %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"}
             %p
@@ -40,16 +40,16 @@
                 - database_hit = 1
               - c = p.data_entries[0][0] != nil ? p.data_entries[0][0] : ''
               - case c
-              - when /(0|false)/
+              - when /(0|false|inactive)/
                 - c = "non-carcinogen"
-              - when /(1|true)/
+              - 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
+              %td{:style=>"valign:top;"}
                 %b{:class => "title"}
-                  = @prediction_models[count].title.split(" ").first
+                  = @prediction_models[count].title.gsub("_", " ")
                 - @model_uri = @prediction_models[count].uri
                 %p
                 / model type (classification|regression)
@@ -101,7 +101,7 @@
                         Predictions with a high confidence can be expected to be more reliable than predictions 
                         with low confidence.
                         Confidence values may take any value between 0 and 1.
-                        For most models confidence > 0.025 is a sensible (hard) cutoff to distiguish between 
+                        For most models confidence > 0.025 is a sensible (hard) cutoff to distinguish between 
                         reliable and unreliable predictions.
                   %p
                   /TODO add tooltip for significant ftagments and descriptors
@@ -150,15 +150,6 @@
                   %b Measured activity:
                   = p.data_entries[0][2]
                   %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}" });
-                      });
                     
                   - count+=1
 
diff --git a/views/significant_fragments.haml b/views/significant_fragments.haml
index 7d342d0..46cca5f 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:1px solid;"}
+          %th{:style=>"border:2px solid #C0C0C0;"}
             Predominantly in compounds with activity "non-carcinogen"
-          %th{:style=>"border:1px solid;"}
+          %th{:style=>"border:2px solid #C0C0C0;"}
             p value
           - @significant_fragments.each do |fragments|
             / fragments == [1||2, smarts, pValue]
@@ -28,9 +28,9 @@
           %td
             %br
         %tr
-          %th{:style=>"border:1px solid;"}
+          %th{:style=>"border:2px solid #C0C0C0;"}
             Predominantly in compounds with activity "carcinogen"   
-          %th{:style=>"border:1px solid;"}
+          %th{:style=>"border:2px solid #C0C0C0;"}
             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:1px solid;"}
+          %th{:style=>"border:2px solid #C0C0C0;"}
             Descriptor
-          %th{:style=>"border:1px solid;"}
+          %th{:style=>"border:2px solid #C0C0C0;"}
             value
           - @significant_fragments.each do |fragments|
             %tr