html representation of lazar predictions moved from model service to toxcreate

8 files changed, 265 insertions, 11 deletions

diff --git a/application.rb b/application.rb
index 9501b4c..2eca13d 100644
--- a/application.rb
+++ b/application.rb
@@ -66,7 +66,6 @@ get '/model/:id/:view/?' do
 				end
 		  else
 				return "unable to render model: id #{params[:id]}, view #{params[:view]}"
-		    #return "render error"
 		end
 	rescue
     return "unable to render model: id #{params[:id]}, view #{params[:view]}"
@@ -176,8 +175,9 @@ post '/predict/?' do # post chemical name to model
 		confidence = nil
 		title = nil
 		db_activities = []
-		LOGGER.debug "curl -X POST -d 'compound_uri=#{@compound.uri}' -H 'Accept:application/x-yaml' #{model.uri}"
+		#LOGGER.debug "curl -X POST -d 'compound_uri=#{@compound.uri}' -H 'Accept:application/x-yaml' #{model.uri}"
 		prediction = YAML.load(`curl -X POST -d 'compound_uri=#{@compound.uri}' -H 'Accept:application/x-yaml' #{model.uri}`)
+    #prediction = YAML.load(OpenTox::Model::Lazar.predict(params[:compound_uri],params[:model_uri]))
 		source = prediction.creator
 		if prediction.data[@compound.uri]
 			if source.to_s.match(/model/) # real prediction
@@ -185,9 +185,19 @@ post '/predict/?' do # post chemical name to model
 				LOGGER.debug prediction[File.join(@@config[:services]["opentox-model"],"lazar#classification")]
 				LOGGER.debug prediction[File.join(@@config[:services]["opentox-model"],"lazar#confidence")]
 				if !prediction[File.join(@@config[:services]["opentox-model"],"lazar#classification")].nil?
-					@predictions << {:title => model.name, :prediction => prediction[File.join(@@config[:services]["opentox-model"],"lazar#classification")], :confidence => prediction[File.join(@@config[:services]["opentox-model"],"lazar#confidence")]}
+					@predictions << {
+            :title => model.name,
+            :model_uri => model.uri,
+            :prediction => prediction[File.join(@@config[:services]["opentox-model"],"lazar#classification")],
+            :confidence => prediction[File.join(@@config[:services]["opentox-model"],"lazar#confidence")]
+            }
 				elsif !prediction[File.join(@@config[:services]["opentox-model"],"lazar#regression")].nil?
-					@predictions << {:title => model.name, :prediction => prediction[File.join(@@config[:services]["opentox-model"],"lazar#regression")], :confidence => prediction[File.join(@@config[:services]["opentox-model"],"lazar#confidence")]}
+					@predictions << {
+            :title => model.name,
+            :model_uri => model.uri,
+            :prediction => prediction[File.join(@@config[:services]["opentox-model"],"lazar#regression")],
+            :confidence => prediction[File.join(@@config[:services]["opentox-model"],"lazar#confidence")]
+            }
 				end
 			else # database value
 				prediction = prediction.data[@compound.uri].first.values
@@ -202,6 +212,36 @@ post '/predict/?' do # post chemical name to model
 	haml :prediction
 end
 
+post "/lazar/?" do
+  @page = 0
+  @page = params[:page].to_i if params[:page]
+  @highlight = params[:highlight]
+  @model_uri = params[:model_uri]
+  @prediction = YAML.load(OpenTox::Model::Lazar.predict(params[:compound_uri],params[:model_uri]))
+  @compound = OpenTox::Compound.new(:uri => params[:compound_uri])
+  @title = @prediction.title
+  if @prediction.data[@compound.uri]
+    if @prediction.creator.to_s.match(/model/) # real prediction
+      p = @prediction.data[@compound.uri].first.values.first
+      if !p[File.join(@@config[:services]["opentox-model"],"lazar#classification")].nil?
+        feature = File.join(@@config[:services]["opentox-model"],"lazar#classification")
+      elsif !p[File.join(@@config[:services]["opentox-model"],"lazar#regression")].nil?
+        feature = File.join(@@config[:services]["opentox-model"],"lazar#regression")
+      end
+      @activity = p[feature]
+      @confidence = p[File.join(@@config[:services]["opentox-model"],"lazar#confidence")]
+      @neighbors = p[File.join(@@config[:services]["opentox-model"],"lazar#neighbors")]#.sort{|a,b| b.last[:similarity] <=> a.last[:similarity]}
+      #@training_activities = p[File.join(@@config[:services]["opentox-model"],"lazar#activities")]
+      @features = p[File.join(@@config[:services]["opentox-model"],"lazar#features")]
+    else # database value
+      @measured_activities = @prediction.data[@compound.uri].first.values
+    end
+  else
+    @activity = "not available (no similar compounds in the training dataset)"
+  end
+  haml :lazar
+end
+
 delete '/?' do
   ToxCreateModel.auto_migrate!
 	response['Content-Type'] = 'text/plain'
diff --git a/views/fragment.haml b/views/fragment.haml
new file mode 100644
index 0000000..fa7495d
--- /dev/null
+++ b/views/fragment.haml
@@ -0,0 +1,9 @@
+%form{:name => "form", :action => url_for('/lazar'), :method => "post", :enctype => "multipart/form-data" }
+  %input{:type => :hidden, :name => :compound_uri, :value => compound_uri}
+  %input{:type => :hidden, :name => :model_uri, :value => model_uri}
+  %input{:type => :hidden, :name => :highlight, :value => smarts}
+  - if smarts.nil?
+    %input{ :type => "submit", :value => "Reset"}
+  - else
+    %input{ :type => "submit", :value => smarts}
+
diff --git a/views/layout.haml b/views/layout.haml
index 7935b33..61d1650 100755
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -10,11 +10,7 @@
 
   %body
     .logo= image_tag "/ToxCreate_rgb_72.png", :alt => 'ToxCreate', :align => "right"
-    -#.headline
-      .logo
-        .span1="Tox" 
-        .span2="Create"
-         
+
     .index
       %ul
         %li{:class => ("selected" if /\/create/ =~ request.path )}
@@ -27,7 +23,7 @@
           = link_to "Help", "/help"
 
     .content
-      - if `hostname`.match(/ot-test|ot-dev/)
+      - if `hostname`.match(/ot-test/)
         .notice 
           This service is for testing purposes only - once a week all models will be deleted. Please send bug reports and feature requests to our 
           %a{:href => 'http://github.com/helma/opentox-toxmodel/issues'} issue tracker.
diff --git a/views/lazar.haml b/views/lazar.haml
new file mode 100644
index 0000000..057b1cd
--- /dev/null
+++ b/views/lazar.haml
@@ -0,0 +1,163 @@
+.lazar-predictions
+  %table
+    %tr
+      %th= @title.gsub(/_lazar_.*$/,' ').capitalize
+      %th Prediction
+      %th 
+        %a{:href => "#", :id => "linkConfidence#{p.object_id}"} Confidence
+        :javascript
+          $("a#linkConfidence#{p.object_id}").click(function () {
+            $("dl#confidence").toggle();  
+          });
+      -#%th
+        Significant fragments
+        = haml :fragment, :locals => {:compound_uri => @compound.uri, :model_uri => @model_uri, :smarts => nil}, :layout => false
+      -#%th Additional data
+
+    %tr
+      %td
+        %img{:src => @compound.display_smarts_uri(@features[:activating].keys,@features[:deactivating].keys, params[:highlight]), :alt => @compound.smiles}
+        %td
+          - if @measured_activities
+            %br
+            - @measured_activities.each do |a|
+              - if activity(a) == 'active'
+                .active
+                  = activity(a)
+              - elsif activity(a) == 'inactive'
+                .inactive
+                  = activity(a)
+              - else
+                = a
+            %br
+              (
+              %a{:href => "#", :id => "linkTrainingData#{p.object_id}"} Training data
+              :javascript
+                $("a#linkTrainingData#{p.object_id}").click(function () {
+                  $("dl#training_data").toggle();  
+                });
+              )
+
+          - else
+            - if activity(@activity) == 'active'
+              .active
+                = activity(@activity)
+            - elsif activity(@activity) == 'inactive'
+              .inactive
+                = activity(@activity)
+            - elsif @activity.is_a?(Float)
+              .other
+                = sprintf('%.03g', @activity)
+            - else
+              .other
+                %em= @activity.to_s
+        %td= sprintf('%.03g', @confidence.to_f.abs) if @confidence
+        -#%td
+          %table
+            - unless @features[:activating].empty?
+              %tr
+                %th activating
+                %th p value
+              - if @features[:activating]
+                - @features[:activating].sort{|a,b| b.last <=> a.last }.each do |f|
+                  %tr
+                  - if @highlight == f[0]
+                    %td.selected= haml :fragment, :locals => {:compound_uri => @compound.uri, :model_uri => @model_uri, :smarts => f[0]}, :layout => false
+                    %td.selected= f[1]
+                  - else
+                    %td= haml :fragment, :locals => {:compound_uri => @compound.uri, :model_uri => @model_uri, :smarts => f[0]}, :layout => false
+                    %td= f[1]
+            - unless @features[:deactivating].empty?
+              %tr
+                %th deactivating
+                %th p value
+              - if @features[:deactivating]
+                - @features[:deactivating].sort{|a,b| b.last <=> a.last }.each do |f|
+                  %tr
+                  - if @highlight == f[0]
+                    %td.selected= haml :fragment, :locals => {:compound_uri => @compound.uri, :model_uri => @model_uri, :smarts => f[0]}, :layout => false
+                    %td.selected= f[1]
+                  - else
+                    %td= haml :fragment, :locals => {:compound_uri => @compound.uri, :model_uri => @model_uri, :smarts => f[0]}, :layout => false
+                    %td= f[1]
+        -#%td
+
+    %tr
+      %th
+        Neighbors 
+        = haml :prev, :locals => {:compound_uri => @compound.uri, :model_uri => @model_uri, :smarts => @highlight, :page => @page, :size => @neighbors.size}, :layout => false
+        = "(#{5*@page+1}-#{5*@page+5}/#{@neighbors.size})"
+        = haml :next, :locals => {:compound_uri => @compound.uri, :model_uri => @model_uri, :smarts => @highlight, :page => @page, :size => @neighbors.size}, :layout => false
+      %th Activity
+      %th Similarity (activity specific)
+      -#%th
+        Significant fragemnts
+        = haml :fragment, :locals => {:compound_uri => @compound.uri, :model_uri => @model_uri, :smarts => nil}, :layout => false
+      -#%th Additional data
+      -#%th Exclude
+    - first = 5*@page
+    - last = first+4
+    - @neighbors.sort{|a,b| b.last[:similarity] <=> a.last[:similarity]}[first..last].each do |uri,data|
+      - c = OpenTox::Compound.new(:uri => uri)
+      %tr
+        %td 
+          -#%br
+            %a{:href => c.display_smarts_uri(data[:features][:activating].collect{|f| f[:smarts]}, data[:features][:deactivating].collect{|f| f[:smarts]}, params[:highlight])} #{c.smiles}
+          %br
+            %img{:src => c.display_smarts_uri(data[:features][:activating].collect{|f| f[:smarts]}, data[:features][:deactivating].collect{|f| f[:smarts]}, params[:highlight]), :alt => c.smiles}
+        %td
+          - data[:activities].each do |act|
+            - if activity(act) == 'active'
+              .active
+                = activity(act)
+            - elsif activity(act) == 'inactive'
+              .inactive
+                = activity(act)
+            - elsif act.is_a?(Float)
+              .other
+                = sprintf('%.03g', act)
+            - else
+              .other
+                %em= act.to_s
+        %td
+          = sprintf('%.03g', data[:similarity])
+        -#%td
+          %table
+            - unless data[:features][:activating].empty?
+              %tr
+                %th activating
+                %th p value
+              - data[:features][:activating].sort{|a,b| b[:p_value] <=> a[:p_value] }.each do |f|
+                %tr
+                  - if @highlight == f[:smarts]
+                    %td.selected= haml :fragment, :locals => {:compound_uri => @compound.uri, :model_uri => @model_uri, :smarts => f[:smarts]}, :layout => false
+                    %td.selected= f[:p_value]
+                  - else
+                    %td= haml :fragment, :locals => {:compound_uri => @compound.uri, :model_uri => @model_uri, :smarts => f[:smarts]}, :layout => false
+                    %td= f[:p_value]
+            - unless data[:features][:deactivating].empty?
+              %tr
+                %th deactivating
+                %th p value
+              - data[:features][:deactivating].sort{|a,b| b[:p_value] <=> a[:p_value] }.each do |f|
+                %tr
+                  - if @highlight == f[:smarts]
+                    %td.selected= haml :fragment, :locals => {:compound_uri => @compound.uri, :model_uri => @model_uri, :smarts => f[:smarts]}, :layout => false
+                    %td.selected= f[:p_value]
+                  - else
+                    %td= haml :fragment, :locals => {:compound_uri => @compound.uri, :model_uri => @model_uri, :smarts => f[:smarts]}, :layout => false
+                    %td= f[:p_value]
+        -#%td 
+        -#%td 
+
+
+%dl#confidence{ :style => "display: none;" }
+  %dt Confidence:
+  %dd Indicates the applicability domain of a model. 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 &gt; 0.025 is a sensible (hard) cutoff to distiguish between reliable and unreliable predictions.
+
+
+%dl#training_data{ :style => "display: none;" }
+  %dt Training data:
+  %dd Experimental result(s) from the training dataset are displayed here. 
+
+
diff --git a/views/next.haml b/views/next.haml
new file mode 100644
index 0000000..b7a2b3a
--- /dev/null
+++ b/views/next.haml
@@ -0,0 +1,7 @@
+- unless 5*page.to_i+5 >= size
+  %form{:name => "form", :action => url_for('/lazar'), :method => "post", :enctype => "multipart/form-data" }
+    %input{:type => :hidden, :name => :compound_uri, :value => compound_uri}
+    %input{:type => :hidden, :name => :model_uri, :value => model_uri}
+    %input{:type => :hidden, :name => :highlight, :value => smarts}
+    %input{:type => :hidden, :name => :page, :value => page.to_i+1}
+    %input{ :type => "submit", :value => "&gt;&gt;"}
diff --git a/views/prediction.haml b/views/prediction.haml
index 1edb2e8..94d7987 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -6,7 +6,7 @@
       %th{:colspan => @predictions.size+1}
         = @identifier
     %tr
-      %th
+      %td
         %img{:src => @compound.image_uri, :alt => @compound.smiles}
       - @predictions.each do |p|
         %td
@@ -55,6 +55,11 @@
                     $("dl#confidence").toggle();  
                   });
                 )
+            %br
+              %form{:name => "form", :action => url_for('/lazar'), :method => "post", :enctype => "multipart/form-data" }
+                %input{:type => :hidden, :name => :compound_uri, :value => @compound.uri}
+                %input{:type => :hidden, :name => :model_uri, :value => p[:model_uri]}
+                %input{ :type => "submit", :value => "Details"}
 
 %dl#confidence{ :style => "display: none;" }
   %dt Confidence:
diff --git a/views/prev.haml b/views/prev.haml
new file mode 100644
index 0000000..9a00579
--- /dev/null
+++ b/views/prev.haml
@@ -0,0 +1,8 @@
+- unless page.to_i == 0
+  %form{:name => "form", :action => url_for('/lazar'), :method => "post", :enctype => "multipart/form-data" }
+    %input{:type => :hidden, :name => :compound_uri, :value => compound_uri}
+    %input{:type => :hidden, :name => :model_uri, :value => model_uri}
+    %input{:type => :hidden, :name => :highlight, :value => smarts}
+    %input{:type => :hidden, :name => :page, :value => page.to_i-1}
+    %input{ :type => "submit", :value => "&lt;&lt;"}
+
diff --git a/views/style.sass b/views/style.sass
index 1900517..ce579e3 100644
--- a/views/style.sass
+++ b/views/style.sass
@@ -138,6 +138,32 @@ body
         img
           padding: 0
           height: 100%
+    .lazar-predictions
+      clear: both
+      margin-top: 2%
+      table
+        border-spacing: 0
+        border-collapse: collapse
+        margin: 0
+        th
+          border: 1px solid
+          color: $body_color
+          background-color: $fg_color
+          //border: 1px solid
+          margin: 0.5em
+        td
+          border: 1px solid
+          background-color: $bg_color2
+          padding: 0.5em
+          table
+            font-size: x-small
+            td
+              border: none
+            td.selected
+              background-color: blue
+        //img
+          padding: 0
+          //height: 100%
   .model
     padding: 0em 1em
     background-color: $bg_color2