several major changes in code, several minor changes in style; prepared for OT meeting

1 files changed, 124 insertions, 22 deletions

diff --git a/application.rb b/application.rb
index 925c208..5cd5093 100644
--- a/application.rb
+++ b/application.rb
@@ -8,10 +8,11 @@ require_relative 'helper.rb'
 require File.join(ENV["HOME"],".opentox","config","lazar-gui.rb") # until added to ot-tools
 
 helpers do
-  # fetch models from uri-list
+  # get prediction models from text file, ignore validation models
+  # model uris must be manually added
   @@models = []
-  uris = `curl -Lk -X GET -H accept:text/uri-list #{$model[:uri]} `.chomp.split("\n")
-  uris.each{|u| m = OpenTox::Model::Lazar.find u; @@models << m}
+  CSV.foreach("./prediction_models.csv"){|uri| m = OpenTox::Model::Lazar.find uri[0]; @@models << m}
+  #$logger.debug "model uris from csv file:\t#{@@models}\n"
 end
 
 get '/?' do
@@ -27,36 +28,126 @@ get '/jme_help/?' do
   File.read(File.join('views','jme_help.html'))
 end
 
-# best way to get individual compound uri for details
+# get individual compound details
 get '/prediction/:neighbor/details/?' do
-  @compound_uri = OpenTox::Compound.new params[:neighbor]
-  @smiles = @compound_uri.smiles
+  @compound = OpenTox::Compound.new params[:neighbor]
+  @smiles = @compound.smiles
+
   task = OpenTox::Task.run("look for names.") do
-    names = @compound_uri.names
+    names = @compound.names
   end
   task.wait
+
   case task[RDF::OT.hasStatus]
   when "Error"
     @names = "No names for this compound available."
   when "Completed"
-    @names = @compound_uri.names.join(",")
+    @names = @compound.names
   end
-  @inchi = @compound_uri.inchi.gsub("InChI=", "")
+  @inchi = @compound.inchi.gsub("InChI=", "")
+
   haml :details, :layout => false
 end
 
+# fingerprints for compound in predictions
+get '/prediction/:model_uri/:type/:compound_uri/fingerprints/?' do
+  @type = params[:type]
+  model = OpenTox::Model::Lazar.find params[:model_uri]
+  feature_dataset = OpenTox::Dataset.find model[RDF::OT.featureDataset]
+  @compound = OpenTox::Compound.new params[:compound_uri]
+
+  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]
+    #$logger.debug "fingerprints:\t#{fingerprints}\n"
+
+    # collect fingerprints with value 1
+    @fingerprint_values = []
+    fingerprints.each{|smarts, value| @fingerprint_values << [smarts, value] if value > 0}
+    
+    # collect all features from feature_dataset
+    @features = feature_dataset.features.collect{|f| f }
+    
+    # search for each fingerprint in all features and collect feature values(smarts, pValue, effect)
+    @significant_fragments = []
+    @fingerprint_values.each{ |fi, v| @features.each{ |f| @significant_fragments << [f[RDF::OT.effect].to_i, f[RDF::OT.smarts], f[RDF::OT.pValue]] if fi == f[RDF::OT.smarts] } }
+  else #regression
+    @significant_fragments = []
+  end
+
+  haml :significant_fragments, :layout => false
+end
+
+get '/prediction/:model_uri/:type/:neighbor/significant_fragments/?' do
+  @type = params[:type]
+  #$logger.debug "sf type:\t#{@type}"
+  @compound = OpenTox::Compound.new params[:neighbor]
+  #$logger.debug "neighbor compound uri:\t#{@compound.uri}\n"
+  
+  model = OpenTox::Model::Lazar.find params[:model_uri]
+  #$logger.debug "model for significant fragments:\t#{model.uri}"
+  
+  feature_dataset = OpenTox::Dataset.find model[RDF::OT.featureDataset]
+  $logger.debug "fd :\t#{feature_dataset.uri}"
+  
+  # load all compounds
+  feature_dataset.compounds
+  
+  # load all features
+  @features = []
+  feature_dataset.features.each{|f| @features << f}
+  #$logger.debug "all features in fd:\t#{@features}\n"
+  
+  # find all features and values for a neighbor compound
+  @significant_fragments = []
+  # check type first
+  if @type =~ /classification/i
+    @feat = []
+    # get compound index in feature dataset
+    c_idx = feature_dataset.compound_indices @compound.uri
+    #$logger.debug "compound idx:\t#{c_idx}\n"
+
+    # collect feature uris with value
+    @features.each{|f| @feat << [feature_dataset.data_entry_value(c_idx[0], f.uri), f.uri]}
+    #$logger.debug "collected features:\t#{@feat}\n"
+
+    # pass feature uris if value > 0
+    @feat.each do |f|
+      if f[0] > 0
+        f = OpenTox::Feature.find f[1]
+        @significant_fragments << [f[RDF::OT.effect].to_i, f[RDF::OT.smarts], f[RDF::OT.pValue].to_f.round(3)]
+      end
+    end
+  else # regression
+    # find a value in feature dataset by compound and feature
+    @values = []
+    @features.each{|f| @values << feature_dataset.values(@compound, f)}
+    #$logger.debug "values in fd:\t#{@values}"
+    
+    count = 0
+    @features.each{|f| @significant_fragments << [f.description, @values[count]]; count +=1}
+  end  
+  #$logger.debug "significant fragments:\t#{@significant_fragments}\n"
+  
+  haml :significant_fragments, :layout => false
+end
+
 post '/predict/?' do
   # validate identifier input
   task = OpenTox::Task.run("Validate SMILES string.") do
     # transfered input
     @identifier = params[:identifier]
+
     # get compound from SMILES
     @compound = OpenTox::Compound.from_smiles @identifier.to_s
+
     # validate SMILES by converting to INCHI
     inchi = @compound.inchi
   end
+
   # necessary to wait for task
   task.wait
+
   # case task fails return message smiles invalid  
   # case task completed go ahead
   case task[RDF::OT.hasStatus]
@@ -66,30 +157,41 @@ post '/predict/?' do
   when "Completed"
     @identifier = params[:identifier]
     @compound = OpenTox::Compound.from_smiles @identifier.to_s
-    # init
-    @@prediction_models = []
-    @@predictions = []
+    # init arrays
+    @prediction_models = []
+    @predictions = []
     # init lazar algorithm
     lazar = OpenTox::Algorithm::Fminer.new File.join($algorithm[:uri],"lazar")
-    # gather models from service and compare if selected
-    #TODO compare selected by uri
+    
+    # get selected models
+    #TODO compare if model is selected by uri not title
     params[:selection].each do |model|
-      @mselected = model[0]
-      @mall = @@models
-      @mall.each do |m|
-        @@prediction_models << m if m.title =~ /#{@mselected}/
+      # selected model = model[0]
+      # compare selected with all models
+      @@models.each do |m|
+        @prediction_models << m if m.title =~ /#{model[0]}/
       end
     end
 
     # predict with selected models
-    # results in prediction variable
-    # store prediction in array for better handling
-    @@prediction_models.each do |m|
+    # one prediction in 'pa' array = OpenTox::Dataset
+    # all collected predictions in '@predictions' array
+    # init model_type array
+    @model_type = []
+    @prediction_models.each do |m|
+      # define type (classification|regression)
+      m.type.join =~ /classification/i ? (@model_type << "classification") : (@model_type << "regression")
+      
+      #TODO each prediction get a task; load predictions page if first task finished and load results individually
+
+      # predict against compound
       @prediction_uri = m.run :compound_uri => "#{@compound.uri}"
+      $logger.debug "prediction dataset:\t#{@prediction_uri}\n"
+      
       prediction = OpenTox::Dataset.new @prediction_uri
       pa = []
       pa << prediction
-      @@predictions << pa
+      @predictions << pa
     end
     
     haml :prediction