tasks as trees, prediction of database structures, improved error checking

6 files changed, 88 insertions, 60 deletions

diff --git a/application.rb b/application.rb
index ff9b964..a649b82 100644
--- a/application.rb
+++ b/application.rb
@@ -2,7 +2,6 @@
 	require lib
 end
 require 'rack-flash'
-#require 'benchmark'
 gem 'opentox-ruby-api-wrapper', '= 1.2.7'
 require 'opentox-ruby-api-wrapper'
 gem 'sinatra-static-assets'
@@ -11,6 +10,20 @@ require 'sinatra/static_assets'
 use Rack::Flash
 set :sessions, true
 
+helpers do
+	def activity(a)
+		case a.to_s
+		when "true"
+			act = "active"
+		when "false"
+			act = "inactive"
+		else
+			act = "not available"
+		end
+		act
+	end
+end
+
 get '/?' do
 	redirect url_for('/create')
 end
@@ -75,14 +88,15 @@ post '/predict/?' do # post chemical name to model
 		@compound = OpenTox::Compound.new(:name => params[:identifier])
 	rescue
 		flash[:notice] = "Could not find a structure for #{@identifier}. Please try again."
-		redirect '/predict'
+		redirect url_for('/predict')
 	end
 	@predictions = []
 	params[:selection].keys.each do |uri|
 		prediction = nil
 		confidence = nil
 		title = nil
-		prediction = RestClient.post uri, :compound_uri => @compound.uri, :accept => "application/x-yaml"
+		db_activities = []
+		prediction = RestClient.post uri, :compound_uri => @compound.uri#, :accept => "application/x-yaml"
 		model = Redland::Model.new Redland::MemoryStore.new
 		parser = Redland::Parser.new
 		parser.parse_string_into_model(model,prediction,'/')
@@ -93,18 +107,13 @@ post '/predict/?' do # post chemical name to model
 			feature_name = model.object(feature,DC['title']).to_s
 			prediction = model.object(v,OT['value']).to_s if feature_name.match(/classification/)
 			confidence = model.object(v,OT['value']).to_s if feature_name.match(/confidence/)
+			db_activities << model.object(v,OT['value']).to_s if feature_name.match(/#{title}/)
 		end
-		case prediction.to_s
-		when "true"
-			prediction = "active"
-		when "false"
-			prediction = "inactive"
-		else
-			prediction = "not available"
-		end
-		@predictions << {:title => title, :prediction => prediction, :confidence => confidence}
+		@predictions << {:title => title, :prediction => prediction, :confidence => confidence, :measured_activities => db_activities}
+		LOGGER.debug db_activities.to_yaml
 	end
 
+		LOGGER.debug @predictions.to_yaml
 	haml :prediction
 	#@predictions.to_yaml 
 end
diff --git a/config.ru b/config.ru
index efe0004..78b1144 100644
--- a/config.ru
+++ b/config.ru
@@ -1,5 +1,5 @@
 require 'rubygems'
 require 'opentox-ruby-api-wrapper'
-require 'tasks/config'
+require 'config/config_ru'
 set :app_file, __FILE__ # to get the view path right
 run Sinatra::Application
diff --git a/views/create.haml b/views/create.haml
index 9477210..5527d70 100644
--- a/views/create.haml
+++ b/views/create.haml
@@ -1,17 +1,15 @@
-.upload
+.input
   %form{ :action => url_for('/upload'), :method => "post", :enctype => "multipart/form-data" }
-    %ol
-      %li 
-        %label{:for => 'endpoint'}Enter endpoint name:
-        %input{:type => 'text', :name => 'endpoint', :id => 'endpoint'}
-      %li
-        %label{:for => 'file'}
-          Upload training data in CSV format:
-        %input{:type => 'file', :name => 'file', :id => 'file'}
-        (
-        = link_to "formatting instructions ", 'csv_format'
-        )
-      %li
-        %input{ :type => "submit", :value => "Create model"}
-        = link_to "Cancel", 'create'
+    %fieldset
+      %legend Upload training data and create a prediction model
+      %label{:for => 'endpoint'} 1. Enter endpoint name:
+      %input{:type => 'text', :name => 'endpoint', :id => 'endpoint'}
+      %br
+      %label{:for => 'file'} 2. Select training data in CSV format:
+      %input{:type => 'file', :name => 'file', :id => 'file'}
+      (
+      = link_to "formatting instructions ", 'csv_format'
+      )
+    %input{ :type => "submit", :value => "Create model"}
+    = link_to "Cancel", 'create'
 
diff --git a/views/predict.haml b/views/predict.haml
index 7c4b980..f6ed6a3 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -1,25 +1,20 @@
-.upload
+.input
   - unless @models.nil?
     %form{ :action => url_for('/predict'), :method => "post", :enctype => "multipart/form-data" }
-      %ol
-        %li
-          %label{:for => 'identifier'}Enter a compound identifier:
-          %input{:type => 'text', :name => 'identifier', :id => 'identifier'}
-          (Name, InChI, Smiles, CAS, ...)
-        %li
-          %label{:for => 'model'}Choose one or more prediction models:
-          %ul
-          - @models.each do |model|
-            - yaml = RestClient.get model, :accept => 'application/x-yaml'
-            - yaml = YAML.load yaml
-            %br
-              -# %input{:type => 'checkbox', :name => 'model_uri', :value => model}
-              -# %input{:type => 'checkbox', :name => "selection[#{model}]", :value => true}
-              %input{:type => 'checkbox', :name => "selection[#{model}]", :value => true, :id => 'model'}
-              = yaml[:endpoint].split(/#/).last
+      %fieldset
+        %legend Enter a compound identifier
+        %label{:for => 'identifier'} Name, InChI, Smiles, CAS, ...
+        %input{:type => 'text', :name => 'identifier', :id => 'identifier'}
+      %fieldset
+        %legend Choose one or more prediction models
+        - @models.each do |model|
+          - yaml = RestClient.get model, :accept => 'application/x-yaml'
+          - yaml = YAML.load yaml
+          %label{:for => model}
+            = yaml[:endpoint].split(/#/).last.gsub(/_/,' ')
+          %input{:type => 'checkbox', :name => "selection[#{model}]", :value => true, :id => model} 
+          %br
 
-        %li
-          %p
-            %input{ :type => "submit", :value => "Predict"}
-            = link_to 'Cancel', '/' 
+      %input{ :type => "submit", :value => "Predict"}
+      = link_to 'Cancel', '/' 
 
diff --git a/views/prediction.haml b/views/prediction.haml
index aa84fee..74e0956 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -9,8 +9,24 @@
       - @predictions.each do |p|
         %td
           %b
-            = p[:title] + ":"
-            = p[:prediction]
-          %br
-            Confidence:
-            = p[:confidence]
+            = p[:title].gsub(/_/,' ') + ":"
+          - if p[:measured_activities].size > 0
+            %br
+            - p[:measured_activities].each do |a|
+              - if activity(a) == 'active'
+                .active
+                  = activity(a)
+              - elsif activity(a) == 'inactive'
+                .inactive
+                  = activity(a)
+            %br (training data)
+          - else
+            - if activity(p[:prediction]) == 'active'
+              .active
+                = activity(p[:prediction])
+            - elsif activity(p[:prediction]) == 'inactive'
+              .inactive
+                = activity(p[:prediction])
+            - if p[:confidence]
+              %br
+                = "(confidence: #{sprintf('%.03f', p[:confidence].to_f.abs)})"
diff --git a/views/style.sass b/views/style.sass
index 4d29ddd..c509c3b 100644
--- a/views/style.sass
+++ b/views/style.sass
@@ -62,16 +62,20 @@ body
       padding: 1%
       border: 1px solid red
 
-    .upload
+    .input
       text-align: left
       form
-        li
-          clear: left
+        fieldset
+          border: 0
+        legend
+          font-weight: bold
+          color = !fg_color
         label
-          width: 20em
-          float: left
-          margin-right: 0.5em
+          width: 25em
           display: block
+          float: left
+        br
+          clear: both
 
     .predictions
       :text-align center
@@ -89,4 +93,10 @@ body
           :border 1px solid
           :padding 2%
 
+.active
+  color: red
+
+.inactive
+  color: green
+
   .footer