Initial import of lazar-webservice-gui

14 files changed, 560 insertions, 0 deletions

diff --git a/.gitignore b/.gitignore
new file mode 100644
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--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,2 @@
+tmp/*
+TODO
diff --git a/config.ru b/config.ru
new file mode 100644
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--- /dev/null
+++ b/config.ru
@@ -0,0 +1,5 @@
+require 'rubygems'
+require 'sinatra'
+require 'lazar.rb'
+
+run Sinatra::Application
diff --git a/lazar.rb b/lazar.rb
new file mode 100644
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--- /dev/null
+++ b/lazar.rb
@@ -0,0 +1,100 @@
+['rubygems', 'sinatra', 'rest_client', 'sinatra/url_for', 'haml', 'sass', 'crack/xml'].each do |lib|
+	require lib
+end
+
+LAZAR_URI = 'http://webservices.in-silico.ch/lazar/models/'
+#LAZAR_URI = 'http://localhost:3000/models/'
+COMPOUNDS_URI = 'http://webservices.in-silico.ch/compounds/'
+
+get '/' do 
+	@models = []
+	(RestClient.get LAZAR_URI).chomp.each_line do |uri|
+		puts uri
+		xml = RestClient.get uri
+		@models << Crack::XML.parse(xml)['model']
+		name = Crack::XML.parse(xml)['model']['name']
+	end
+	haml :index
+end
+
+get '/create' do
+	haml :create
+end
+
+get '/neighbors' do
+	#@lazar  = params[:lazar]
+	#haml :neighbors
+	"Sorry, display of neighbors is not (yet) implemented."
+end
+
+get '/:id' do # input form for predictions
+	begin
+		xml = RestClient.get "#{LAZAR_URI}#{params[:id]}"
+		@model = Crack::XML.parse(xml)['model']
+	 	YAML.load(RestClient.get "#{@model['validation']['details_uri']}") # check if model creation is finished
+		haml :show
+ 	rescue
+		redirect "/tmp/#{params[:id]}"
+ 	end
+end
+
+get '/validation/:id' do 
+	begin
+	 xml = RestClient.get "#{LAZAR_URI}#{params[:id]}"
+	 @model = Crack::XML.parse(xml)['model']
+	 @summary = YAML.load(RestClient.get "#{@model['validation']['summary_uri']}")
+	 haml :validation
+ 	rescue
+		redirect "/tmp/#{params[:id]}"
+ 	end
+end
+
+get '/delete/:id' do
+	xml = RestClient.get "#{LAZAR_URI}#{params[:id]}"
+	@model = Crack::XML.parse(xml)['model']
+	haml :delete
+end
+
+get '/tmp/:id' do
+	haml :tmp
+end
+
+post '/' do # create a new model
+	# create dataset
+	# validate lazar on the dataset
+	sanitized_name = params[:name].gsub(/\s+/,'_').gsub(/[^[:alnum:]]/, '')
+	uri = `curl -F name=#{sanitized_name} -F file=@#{params[:file][:tempfile].path} -F username=#{params[:username]} -F password=#{params[:password]} #{LAZAR_URI}`
+	id = uri.chomp.gsub(/^.*\/(\d+)$/,'\1')
+	redirect "/#{id}"
+end
+
+post '/:id' do # post chemical name to model
+	begin
+		smiles = RestClient.get "#{COMPOUNDS_URI}#{URI.encode(params[:name])}.smiles"
+	rescue
+		@message = "Can not retrieve Smiles from #{params[:name]}. Please try again."
+		redirect "/#{params[:id]}"
+	end
+	begin
+		xml = RestClient.get "#{LAZAR_URI}#{params[:id]}?smiles=#{URI.encode(smiles)}"
+		@lazar = Crack::XML.parse(xml)['lazar']
+		haml :prediction
+	rescue
+		"Prediction for #{params[:name]} (SMILES #{smiles}) failed." 
+	end
+end
+
+delete '/:id' do
+	begin
+		RestClient.delete "#{LAZAR_URI}#{params[:id]}", :username => params[:username], :password => params[:password]
+		redirect '/'
+	rescue
+		"Deletion of model with ID #{params[:id]} failed. Please check your username and password."
+	end
+end
+
+# SASS stylesheet
+get '/stylesheets/style.css' do
+  headers 'Content-Type' => 'text/css; charset=utf-8'
+  sass :style
+end
diff --git a/public/opentox-rgb-72.png b/public/opentox-rgb-72.png
new file mode 100644
index 0000000..ab53b01
--- /dev/null
+++ b/public/opentox-rgb-72.png
diff --git a/views/create.haml b/views/create.haml
new file mode 100644
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--- /dev/null
+++ b/views/create.haml
@@ -0,0 +1,30 @@
+&rarr; Create
+
+%h1
+  Create and validate a
+  %code lazar
+  model
+
+%form{ :action => '/', :method => "post", :enctype => "multipart/form-data" }
+  %table
+    %tr
+      %th Username:
+      %td
+        %input{:type => "text", :name => "username"}
+    %tr
+      %th Password:
+      %td
+        %input{:type => "text", :name => "password"}
+    %tr
+      %th Endpoint:
+      %td
+        %input{:type => "text", :name => "name"}
+    %tr
+      %th Training data:
+      %td
+        %input{:type => 'file', :name => 'file'}
+    %tr
+      %td
+        %input{ :type => "submit", :value => "Submit"}
+
+
diff --git a/views/delete.haml b/views/delete.haml
new file mode 100644
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--- /dev/null
+++ b/views/delete.haml
@@ -0,0 +1,22 @@
+%p
+  You are going to remove the
+  = @model['name']
+  model permanently!
+%p Enter your username/password if you are sure or cancel the operation.
+
+%form{ :action => "/#{params[:id]}", :method => "delete" }
+  %table
+    %tr
+      %th Username:
+      %td
+        %input{:type => "text", :name => "username"}
+    %tr
+      %th Password:
+      %td
+        %input{:type => "text", :name => "password"}
+
+    %tr
+      %td
+        %input{:type => "submit", :value => "Delete"}
+      %td
+        %a{:href => '/'} Cancel
diff --git a/views/index.haml b/views/index.haml
new file mode 100644
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--- /dev/null
+++ b/views/index.haml
@@ -0,0 +1,16 @@
+%h1
+  %code lazar
+  prediction models
+
+%a{ :href => '/create' } Create a model
+
+%ul
+  - @models.each do |model|
+    %li
+      %a{:href => "/#{model['id']}"}
+        = model['name'].capitalize.gsub(/_/,' ')
+      from 
+      = model['user']
+      (
+      %a{:href => "/validation/#{model['id']}"} Validation 
+      ) 
diff --git a/views/layout.haml b/views/layout.haml
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index 0000000..720c801
--- /dev/null
+++ b/views/layout.haml
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+!!!
+%html{:xmlns => "http://www.w3.org/1999/xhtml", "xml:lang" => "en", :lang => "en"}
+
+  %head
+    %meta{'http-equiv' => 'Content-Type', :content => 'text/html'}
+    %title Lazar
+    %link{:rel=>'stylesheet', :href=>'/stylesheets/style.css', :type => "text/css"}       
+
+  %body
+
+    %a{ :href => "/" } Home
+
+    = yield
+
+    %hr
+    &copy;
+    %a{:href => 'http://www.in-silico.ch'} in silico toxicology
+    2009, powered by
+    %a{:href => 'http://www.opentox.org'} OpenTox
+
diff --git a/views/neighbors.haml b/views/neighbors.haml
new file mode 100644
index 0000000..5bf5aba
--- /dev/null
+++ b/views/neighbors.haml
@@ -0,0 +1,34 @@
+&rarr;
+%a{ :href => "/#{params[:id]}" } Enter structure
+&rarr; Prediction
+
+%h1= @lazar['endpoint'].gsub(/\"|\'/,'')
+
+%table
+  %tr
+    %th Structure
+    %th Prediction
+    %th Measured activity
+  %tr
+    %td
+      %img{:src => "http://cactus.nci.nih.gov/chemical/structure/#{URI.encode(@lazar['smiles'])}/image", :alt => "#{@lazar['smiles']}"}
+    %td
+      %p= @lazar['prediction']
+      %p
+        (
+        = @lazar['confidence']
+        )
+    %td= @lazar['database_activity']
+  %tr
+    %td{:colspan => 4} Neighbors
+  %tr
+    %th Structure
+    %th Similarity
+    %th Measured activity
+
+  - @lazar['neighbors']['neighbor'].each do |neighbor|
+    %tr
+      %td
+        %img{:src => "http://cactus.nci.nih.gov/chemical/structure/#{URI.encode(neighbor['smiles'])}/image", :alt => "#{neighbor['smiles']}"}
+      %td= neighbor['similarity']
+      %td= neighbor['activity']
diff --git a/views/prediction.haml b/views/prediction.haml
new file mode 100644
index 0000000..5842dfc
--- /dev/null
+++ b/views/prediction.haml
@@ -0,0 +1,29 @@
+&rarr;
+%a{ :href => "/#{params[:id]}" } Enter structure
+&rarr; Prediction
+
+%h1
+  = @lazar['endpoint'].gsub(/\"|\'/,'').capitalize.gsub(/_/,' ')
+  of
+  = params[:name]
+
+.prediction
+  %table
+    %tr
+      %th Structure
+      %th
+        %p Prediction
+        %p (Confidence)
+      %th Measured activity
+    %tr
+      %td
+        %img{:src => "http://cactus.nci.nih.gov/chemical/structure/#{URI.encode(@lazar['smiles'])}/image", :alt => "#{@lazar['smiles']}"}
+      %td
+        %br= @lazar['prediction']
+        %br
+          (
+          = @lazar['confidence']
+          )
+      %td= @lazar['database_activity']
+
+%a{:href => "/neighbors", :lazar => @lazar } Show neighbors
diff --git a/views/show.haml b/views/show.haml
new file mode 100644
index 0000000..2660f5e
--- /dev/null
+++ b/views/show.haml
@@ -0,0 +1,17 @@
+&rarr; Enter structure
+
+%h1
+  = @model['name'].capitalize.gsub(/_/,' ')
+  prediction
+
+%a{ :href => "/validation/#{params[:id]}" } Validation results
+
+%a{:href => "/delete/#{params[:id]}"} Delete model
+
+%p= @message if @message
+
+%form{ :action => "/#{params[:id]}", :method => "post" }
+
+  %p Enter a chemical identifier (e.g. name, CAS number, Smiles, InChI, InChI key):
+  %input{:type => "text", :name => "name"}
+  %input{ :type => "submit", :value => "Predict"}
diff --git a/views/style.sass b/views/style.sass
new file mode 100644
index 0000000..2b9d7ce
--- /dev/null
+++ b/views/style.sass
@@ -0,0 +1,18 @@
+form
+  th
+    :text-align right
+
+.prediction
+  :text-align center
+  table
+    :border-spacing 0
+    :border-collapse collapse
+    :margin 0
+    :border 1px solid
+
+    th
+      :border 1px solid
+      :margin 2%
+    td
+      :border 1px solid
+      :margin 2%
diff --git a/views/tmp.haml b/views/tmp.haml
new file mode 100644
index 0000000..31589f2
--- /dev/null
+++ b/views/tmp.haml
@@ -0,0 +1,3 @@
+%p Model not (yet) available - it is likely that model creation and validation is still running. 
+%a{ :href => "/#{params[:id]}" } Reload this page
+to see if the process has finished.
diff --git a/views/validation.haml b/views/validation.haml
new file mode 100644
index 0000000..d1af379
--- /dev/null
+++ b/views/validation.haml
@@ -0,0 +1,264 @@
+= "-> "
+%a{ :href => "/validation/#{params[:id]}" } Validation
+
+%h1
+  = @model['name'].capitalize.gsub(/_/,' ')
+  validation
+
+Created on 
+= @model['created_at']
+by
+= @model['user']
+(
+%a{ :href => @model['validation']['details_uri'] } Prediction details
+)
+
+%h3 Predictions weighted by confidence index
+%p
+  %em Best indication of the overall performance
+
+%table
+  %tr
+    %th
+      True positive predictions
+    %td
+      tp
+    %td
+      = sprintf("%0.2f",@summary[:weighted][:tp].to_f)
+  %tr
+    %th
+      True negative predictions
+    %td
+      tn
+    %td
+      = sprintf("%0.2f",@summary[:weighted][:tn].to_f)
+  %tr
+    %th
+      False positive predictions
+    %td
+      fp
+    %td
+      = sprintf("%0.2f",@summary[:weighted][:fp].to_f)
+  %tr
+    %th
+      False negative predictions
+    %td
+      fn
+    %td
+      = sprintf("%0.2f",@summary[:weighted][:fn].to_f)
+  %tr
+    %th
+      Sensitivity (true positive rate)
+    %td
+      tp/(tp+fn)
+    %td
+      = (100*@summary[:weighted][:tp].to_f/(@summary[:weighted][:tp].to_f+@summary[:weighted][:fn].to_f)).round/100.00
+  %tr
+    %th
+      Specificity (true negative rate)
+    %td
+      tn/(tn+fp)
+    %td
+      = (100*@summary[:weighted][:tn].to_f/(@summary[:weighted][:tn].to_f+@summary[:weighted][:fp].to_f).to_f).round/100.00
+  %tr
+    %th
+      Positive predictivity
+    %td
+      tp/(tp+fp)
+    %td
+      = (100*@summary[:weighted][:tp].to_f/(@summary[:weighted][:tp].to_f+@summary[:weighted][:fp].to_f).to_f).round/100.00
+  %tr
+    %th
+      Negative predictivity
+    %td
+      tn/(tn+fn)
+    %td
+      = (100*@summary[:weighted][:tn].to_f/(@summary[:weighted][:tn].to_f+@summary[:weighted][:fn].to_f).to_f).round/100.00
+  %tr
+    %th
+      False positive rate
+    %td
+      fp/(tp+fn)
+    %td
+      = (100*@summary[:weighted][:fp].to_f/(@summary[:weighted][:tp].to_f+@summary[:weighted][:fn].to_f).to_f).round/100.00
+  %tr
+    %th
+      False negative rate
+    %td
+      fn/(tn+fp)
+    %td
+      = (100*@summary[:weighted][:fn].to_f/(@summary[:weighted][:tn].to_f+@summary[:weighted][:fp].to_f).to_f).round/100.00
+  %tr
+    %th
+      Accuracy (concordance)
+    %td
+      (tp+tn)/(tp+fp+tn+fn)
+    %th
+      = (100*(@summary[:weighted][:tp].to_f+@summary[:weighted][:tn].to_f)/(@summary[:weighted][:tp].to_f+@summary[:weighted][:tn].to_f+@summary[:weighted][:fn].to_f+@summary[:weighted][:fp].to_f).to_f).round/100.00
+
+
+%h3 Predictions within the applicability domain
+%p
+  %em Hard cutoff at confidence > 0.025
+
+%table
+  %tr
+    %th
+      True positive predictions
+    %td
+      tp
+    %td
+      = @summary[:within_ad][:tp].to_i
+  %tr
+    %th
+      True negative predictions
+    %td
+      tn
+    %td
+      = @summary[:within_ad][:tn].to_i
+  %tr
+    %th
+      False positive predictions
+    %td
+      fp
+    %td
+      = @summary[:within_ad][:fp].to_i
+  %tr
+    %th
+      False negative predictions
+    %td
+      fn
+    %td
+      = @summary[:within_ad][:fn].to_i
+  %tr
+    %th
+      Sensitivity (true positive rate)
+    %td
+      tp/(tp+fn)
+    %td
+      = (100*@summary[:within_ad][:tp].to_i/(@summary[:within_ad][:tp].to_i+@summary[:within_ad][:fn].to_i).to_f).round/100.00
+  %tr
+    %th
+      Specificity (true negative rate)
+    %td
+      tn/(tn+fp)
+    %td
+      = (100*@summary[:within_ad][:tn].to_i/(@summary[:within_ad][:tn].to_i+@summary[:within_ad][:fp].to_i).to_f).round/100.00
+  %tr
+    %th
+      Positive predictivity
+    %td
+      tp/(tp+fp)
+    %td
+      = (100*@summary[:within_ad][:tp].to_i/(@summary[:within_ad][:tp].to_i+@summary[:within_ad][:fp].to_i).to_f).round/100.00
+  %tr
+    %th
+      Negative predictivity
+    %td
+      tn/(tn+fn)
+    %td
+      = (100*@summary[:within_ad][:tn].to_i/(@summary[:within_ad][:tn].to_i+@summary[:within_ad][:fn].to_i).to_f).round/100.00
+  %tr
+    %th
+      False positive rate
+    %td
+      fp/(tp+fn)
+    %td
+      = (100*@summary[:within_ad][:fp].to_i/(@summary[:within_ad][:tp].to_i+@summary[:within_ad][:fn].to_i).to_f).round/100.00
+  %tr
+    %th
+      False negative rate
+    %td
+      fn/(tn+fp)
+    %td
+      = (100*@summary[:within_ad][:fn].to_i/(@summary[:within_ad][:tn].to_i+@summary[:within_ad][:fp].to_i).to_f).round/100.00
+  %tr
+    %th
+      Accuracy (concordance)
+    %td
+      (tp+tn)/(tp+fp+tn+fn)
+    %th
+      = (100*(@summary[:within_ad][:tp].to_i+@summary[:within_ad][:tn].to_i)/(@summary[:within_ad][:tp].to_i+@summary[:within_ad][:tn].to_i+@summary[:within_ad][:fn].to_i+@summary[:within_ad][:fp].to_i).to_f).round/100.00
+
+%h3 All predictions
+%p
+  %em Poor indication of the overall performance. Depends predominatly on the fraction of compounds within the applicability domain.
+
+%table
+  %tr
+    %th
+      True positive predictions
+    %td
+      tp
+    %td
+      = @summary[:all][:tp].to_i
+  %tr
+    %th
+      True negative predictions
+    %td
+      tn
+    %td
+      = @summary[:all][:tn].to_i
+  %tr
+    %th
+      False positive predictions
+    %td
+      fp
+    %td
+      = @summary[:all][:fp].to_i
+  %tr
+    %th
+      False negative predictions
+    %td
+      fn
+    %td
+      = @summary[:all][:fn].to_i
+  %tr
+    %th
+      Sensitivity (true positive rate)
+    %td
+      tp/(tp+fn)
+    %td
+      = (100*@summary[:all][:tp].to_i/(@summary[:all][:tp].to_i+@summary[:all][:fn].to_i).to_f).round/100.00
+  %tr
+    %th
+      Specificity (true negative rate)
+    %td
+      tn/(tn+fp)
+    %td
+      = (100*@summary[:all][:tn].to_i/(@summary[:all][:tn].to_i+@summary[:all][:fp].to_i).to_f).round/100.00
+  %tr
+    %th
+      Positive predictivity
+    %td
+      tp/(tp+fp)
+    %td
+      = (100*@summary[:all][:tp].to_i/(@summary[:all][:tp].to_i+@summary[:all][:fp].to_i).to_f).round/100.00
+  %tr
+    %th
+      Negative predictivity
+    %td
+      tn/(tn+fn)
+    %td
+      = (100*@summary[:all][:tn].to_i/(@summary[:all][:tn].to_i+@summary[:all][:fn].to_i).to_f).round/100.00
+  %tr
+    %th
+      False positive rate
+    %td
+      fp/(tp+fn)
+    %td
+      = (100*@summary[:all][:fp].to_i/(@summary[:all][:tp].to_i+@summary[:all][:fn].to_i).to_f).round/100.00
+  %tr
+    %th
+      False negative rate
+    %td
+      fn/(tn+fp)
+    %td
+      = (100*@summary[:all][:fn].to_i/(@summary[:all][:tn].to_i+@summary[:all][:fp].to_i).to_f).round/100.00
+  %tr
+    %th
+      Accuracy (concordance)
+    %td
+      (tp+tn)/(tp+fp+tn+fn)
+    %th
+      = (100*(@summary[:all][:tp].to_i+@summary[:all][:tn].to_i)/(@summary[:all][:tp].to_i+@summary[:all][:tn].to_i+@summary[:all][:fn].to_i+@summary[:all][:fp].to_i).to_f).round/100.00