Passes tests in opentox-test

1 files changed, 6 insertions, 62 deletions

diff --git a/application.rb b/application.rb
index 18ba435..4f125d8 100644
--- a/application.rb
+++ b/application.rb
@@ -1,66 +1,10 @@
 require 'rubygems'
-require 'sinatra'
-require 'libfminer/fminer'
+require 'libfminer/fminer' # has to be included before openbabel, otherwise we have strange SWIG overloading problems
 require 'opentox-ruby-api-wrapper'
 
-ENV['FMINER_SMARTS'] = 'true'
-ENV['FMINER_PVALUES'] = 'true'
-@@fminer = Fminer::Fminer.new
+require 'smarts.rb'
+require 'similarity.rb'
+require 'fminer.rb'
+require 'lazar.rb'
 
-post '/?' do
-
-	dataset = OpenTox::Dataset.find :uri => params[:dataset_uri]
-	id = 1
-	compound_list = []
-	dataset.compounds.each do |c|
-		activities = dataset.features(c)
-		smiles = c.smiles
-		activities.each do |feature|
-			activity = feature.value('classification')
-			case activity.to_s
-			when 'true'
-				compound_list[id] = c.uri
-				@@fminer.AddCompound(smiles,id)
-				@@fminer.AddActivity(true, id)
-			when 'false'
-				compound_list[id] = c.inchi
-				@@fminer.AddCompound(smiles,id)
-				@@fminer.AddActivity(false, id)
-			end
-		end
-		id += 1
-	end
-
-	@@fminer.SetConsoleOut(false)
-	features = []
-	# run @@fminer
-	(0 .. @@fminer.GetNoRootNodes()-1).each do |j|
-		result = @@fminer.MineRoot(j)
-	 (0 .. result.size-1).each do |i|
-		 features << YAML.load(result[i])[0]
-		end
-	end
-
-	@@fminer.Reset
-
-	smarts_features = {}
-	features.each do |f|
-		smarts = f[0]
-		p = f[1]
-		ids = f[2] + f[3]
-		if f[2].size > f[3].size
-			effect = 'activating'
-		else
-			effect = 'deactivating'
-		end
-		ids.each do |id|
-			smarts_features[compound_list[id]] = [] unless smarts_features[compound_list[id]]
-			smarts_features[compound_list[id]] << OpenTox::Feature.new(:name => smarts, :values => {:p_value => p, :effect => effect}).uri
-		end
-	end
-
-	feature_dataset = OpenTox::Dataset.create :name => dataset.name + "_BBRC_representatives"
-	feature_dataset.add(smarts_features)
-	feature_dataset.uri
-
-end
+set :default_content, :yaml