error handling compound names;smiles validation

1 files changed, 72 insertions, 39 deletions

diff --git a/application.rb b/application.rb
index 69cf031..54b2d10 100644
--- a/application.rb
+++ b/application.rb
@@ -8,10 +8,6 @@ require File.join(File.dirname(__FILE__),'helper.rb')
 require File.join(ENV["HOME"],".opentox","config","lazar-gui.rb")
 
 helpers do
-  def compound_uri(uri)
-    $logger.debug "\ncompound_uri: #{uri}\n"
-    @compound_uri = OpenTox::Compound.new uri
-  end
 end
 
 get '/?' do
@@ -20,50 +16,87 @@ end
 
 get '/predict/?' do
   @models = OpenTox::Model.all $model[:uri]
-
   haml :predict
 end
 
-post '/predict/?' do
-  # transfered input
-  @identifier = params[:identifier]
-  # get compound from SMILES
-  @compound = OpenTox::Compound.from_smiles $compound[:uri], @identifier.to_s
-  # init
-  @@prediction_models = []
-  @@predictions = []
-  # init lazar algorithm
-  lazar = OpenTox::Algorithm.new File.join($algorithm[:uri],"lazar")
-  # gather models from service and compare if selected
-  params[:selection].each do |model|
-    @mselected = model[0]
-    @mall = OpenTox::Model.all $model[:uri]
-    @mall.each do |m|
-      m.get
-      @@prediction_models << m if m.title =~ /#{@mselected}/
-    end
-    $logger.debug "@prediction_models: #{@@prediction_models.inspect}"
-  end
+get '/jme_help/?' do
+  File.read(File.join('views','jme_help.html'))
+end
 
-  # predict with selected models
-  # results in prediction variable
-  # store prediction in array for better handling
-  @@prediction_models.each do |m| 
-    @prediction_uri = m.run :compound_uri => "#{@compound.uri}"
-    prediction = OpenTox::Dataset.new @prediction_uri
-    pa = []
-    pa << prediction
-    @@predictions << pa
+# best way to get individual compound uri for details
+get '/prediction/:neighbour/details/?' do
+  @compound_uri = OpenTox::Compound.new params[:neighbour]
+  @smiles = @compound_uri.smiles
+  task = OpenTox::Task.create($task[:uri], @subjectid, RDF::DC.description => "look for names.") do
+    names = @compound_uri.names
   end
-
-  haml :prediction
+  sleep 1
+  task.get
+  case task[RDF::OT.hasStatus]
+  when "Error"
+    @names = "There are no names for this compound available."
+  when "Completed"
+    @names = @compound_uri.names
+  end
+  @inchi = @compound_uri.inchi.gsub("InChI=", "InChI: ")
+  haml :details, :layout => false
 end
 
+post '/predict/?' do
+  # validate identifier input
+  task = OpenTox::Task.create($task[:uri], @subjectid, RDF::DC.description => "#{params[:identifier] ? params[:identifier] : "no valid SMILES string."}: Validate SMILES string.") do
+    # transfered input
+    @identifier = params[:identifier]
+    # get compound from SMILES
+    @compound = OpenTox::Compound.from_smiles $compound[:uri], @identifier.to_s
+    # validate SMILES by converting to INCHI
+    inchi = @compound.inchi
+  end
+  # necessary to wait for task
+  sleep 1
+  task.get
+  $logger.debug "task uri: #{task.uri}"
+  $logger.debug "task status: #{task[RDF::OT.hasStatus]}"
+  # case task fails return message smiles invalid  
+  # case task completed go ahead
+  case task[RDF::OT.hasStatus]
+  when "Error"
+    @error_report = "Not a valid SMILES string."
+    haml :error
+  when "Completed"
+    @identifier = params[:identifier]
+    @compound = OpenTox::Compound.from_smiles $compound[:uri], @identifier.to_s
+    # init
+    @@prediction_models = []
+    @@predictions = []
+    # init lazar algorithm
+    lazar = OpenTox::Algorithm.new File.join($algorithm[:uri],"lazar")
+    # gather models from service and compare if selected
+    params[:selection].each do |model|
+      @mselected = model[0]
+      @mall = OpenTox::Model.all $model[:uri]
+      @mall.each do |m|
+        m.get
+        @@prediction_models << m if m.title =~ /#{@mselected}/
+      end
+      $logger.debug "@prediction_models: #{@@prediction_models.inspect}"
+    end
 
-get '/prediction/:neighbour/details/?' do
-  @compound_uri = OpenTox::Compound.new params[:neighbour]
+    # predict with selected models
+    # results in prediction variable
+    # store prediction in array for better handling
+    @@prediction_models.each do |m| 
+      @prediction_uri = m.run :compound_uri => "#{@compound.uri}"
+      prediction = OpenTox::Dataset.new @prediction_uri
+      pa = []
+      pa << prediction
+      @@predictions << pa
+    end
+    
+    haml :prediction
+  end
+  
   
-  haml :details, :layout => false
 end
 
 get '/stylesheets/:name.css' do