dumpfiles implemented

1 files changed, 33 insertions, 22 deletions

diff --git a/fminer.rb b/fminer.rb
index 93644c4..87ea4a4 100644
--- a/fminer.rb
+++ b/fminer.rb
@@ -5,47 +5,58 @@ require 'validate-owl.rb'
 
 class FminerTest < Test::Unit::TestCase
 
+  def setup
+    @dump_dir = FileUtils.mkdir_p File.join(File.dirname(__FILE__),"dump",File.basename(__FILE__,".rb"))
+    FileUtils.mkdir_p File.join(File.dirname(__FILE__),"reference",File.basename(__FILE__,".rb"))
+  end
+
+  def cleanup # executed only when assertions succeed (teardown is called even when assertions fail)
+    FileUtils.cp @dumpfile, @dumpfile.sub(/dump/,"reference")
+    FileUtils.rm @dumpfile
+    @dataset.delete(@@subjectid)
+  end
+
+  def dump(method)
+    @dataset = OpenTox::Dataset.find @dataset_uri, @@subjectid
+    @dumpfile = File.join(@dump_dir,method.to_s)+".yaml"
+    File.open(@dumpfile,"w+"){|f| f.puts @dataset.to_yaml}
+  end
+
   def test_bbrc
     feature = @@classification_training_dataset.features.keys.first
-    dataset_uri = OpenTox::Algorithm::Fminer::BBRC.new.run({:dataset_uri => @@classification_training_dataset.uri, :prediction_feature => feature, :subjectid => @@subjectid}).to_s
-    d =OpenTox::Dataset.new dataset_uri, @@subjectid
-    d.load_features(@@subjectid)
-    assert_equal 52, d.features.size
-    d.delete(@@subjectid)
+    @dataset_uri = OpenTox::Algorithm::Fminer::BBRC.new.run({:dataset_uri => @@classification_training_dataset.uri, :prediction_feature => feature, :subjectid => @@subjectid}).to_s
+    dump __method__
+    assert_equal 52, @dataset.features.size
+    cleanup
   end
 
   def test_regression_bbrc
     feature = File.join @@regression_training_dataset.uri,"feature/LC50_mmol" 
-    dataset_uri = OpenTox::Algorithm::Fminer::BBRC.new.run({:dataset_uri => @@regression_training_dataset.uri, :prediction_feature => feature, :subjectid => @@subjectid, :feature_type=>"paths"}).to_s
-    d =OpenTox::Dataset.new dataset_uri, @@subjectid
-    d.load_features(@@subjectid)
-    #assert_equal 185, d.features.size
-    assert_equal 219, d.features.size
-    d.delete(@@subjectid)
+    @dataset_uri = OpenTox::Algorithm::Fminer::BBRC.new.run({:dataset_uri => @@regression_training_dataset.uri, :prediction_feature => feature, :subjectid => @@subjectid, :feature_type=>"paths"}).to_s
+    dump __method__
+    assert_equal 219, @dataset.features.size
+    cleanup
   end
 
   def test_last
     feature = @@classification_training_dataset.features.keys.first
-    dataset_uri = OpenTox::Algorithm::Fminer::LAST.new.run({:dataset_uri => @@classification_training_dataset.uri, :prediction_feature => feature, :subjectid => @@subjectid}).to_s
-    d =OpenTox::Dataset.new dataset_uri, @@subjectid
-    d.load_features(@@subjectid)
-    assert_equal 23, d.features.size
-    d.delete(@@subjectid)
+    @dataset_uri = OpenTox::Algorithm::Fminer::LAST.new.run({:dataset_uri => @@classification_training_dataset.uri, :prediction_feature => feature, :subjectid => @@subjectid}).to_s
+    dump __method__
+    assert_equal 23, @dataset.features.size
+    cleanup
   end
 
   def test_bbrc_rest_parameters
     feature = @@classification_training_dataset.features.keys.first
-    #call = "curl -X POST #{File.join CONFIG[:services]["opentox-algorithm"],"fminer","bbrc"} -d \"dataset_uri=#{CGI.escape @@classification_training_dataset.uri}\" -d \"prediction_feature=#{CGI.escape feature}\" -d \"backbone=true\" -d \"min_frequency=2\""
-    dataset_uri = OpenTox::RestClientWrapper.post(File.join(CONFIG[:services]["opentox-algorithm"],"fminer","bbrc"),{
+    @dataset_uri = OpenTox::RestClientWrapper.post(File.join(CONFIG[:services]["opentox-algorithm"],"fminer","bbrc"),{
       "dataset_uri" => @@classification_training_dataset.uri,
       "prediction_feature" => feature,
       "backbone" => true,
       "min_frequency" => 2,
        :subjectid => @@subjectid })
-    d =OpenTox::Dataset.new dataset_uri, @@subjectid
-    d.load_features(@@subjectid)
-    assert_equal 52, d.features.size
-
+    dump __method__
+    assert_equal 52, @dataset.features.size
+    cleanup
   end
 
 # Deactivated by AM because of efficiency problems (does not return)