error handling fixed

5 files changed, 36 insertions, 13 deletions

diff --git a/Rakefile b/Rakefile
index d260989..9d6afff 100644
--- a/Rakefile
+++ b/Rakefile
@@ -1,13 +1,27 @@
 require 'rubygems'
 require 'opentox-ruby'
 
-if File.exists? "auth.rb"
-  require "auth"
-else
+=begin
+=end
+class Exception
+
+  def message
+    unless errorCause == nil
+      errorCause.to_yaml
+    else
+      self.to_s
+    end
+  end
+
+end
+
+#if File.exists? "auth.rb"
+  #require "auth"
+#else
   #exit "Please create an authenticatio
     TEST_USER = "guest"
     TEST_PW   = "guest"
-end
+#end
 
 task ARGV[0] do
   puts "Environment: #{ENV["RACK_ENV"]}"
@@ -27,7 +41,8 @@ task :teardown do
   OpenTox::Authorization.logout(@@subjectid)
 end
 
-[:all, :feature, :dataset, :fminer, :lazar, :authorization].each do |t|
+[:all, :feature, :dataset, :fminer, :lazar, :authorization, :validation].each do |t|
+#[:all, :feature, :dataset, :fminer, :lazar, :authorization].each do |t|
   task :teardown => t
   task t => :setup 
 end
diff --git a/all.rb b/all.rb
index 8712794..8c5babd 100644
--- a/all.rb
+++ b/all.rb
@@ -1,6 +1,7 @@
 require 'rubygems'
 require 'test/unit'
 require 'opentox-ruby'
+require './authorization.rb'
 require './compound.rb'
 require './feature.rb'
 require './dataset.rb'
@@ -9,3 +10,4 @@ require './task.rb'
 require './algorithm.rb'
 require './fminer.rb'
 require './lazar.rb'
+#require './validation.rb'
diff --git a/dataset.rb b/dataset.rb
index d15baf7..a243b00 100644
--- a/dataset.rb
+++ b/dataset.rb
@@ -5,6 +5,8 @@ require 'validate-owl'
 
 class DatasetTest < Test::Unit::TestCase
 
+=begin
+=end
   def setup
     @datasets = {
       @@classification_training_dataset.uri => {
@@ -26,7 +28,6 @@ class DatasetTest < Test::Unit::TestCase
     #@new_dataset.delete
   end
 
-=begin
   def test_save_external
 
     @dataset = OpenTox::Dataset.find "http://apps.ideaconsult.net:8080/ambit2/dataset/2698", @@subjectid
@@ -37,13 +38,13 @@ class DatasetTest < Test::Unit::TestCase
     #@dataset.load_csv(File.open("data/hamster_carcinogenicity.csv").read)
     #@dataset.save
   end
-=end
 
   def test_create
     dataset = OpenTox::Dataset.create(CONFIG[:services]["opentox-dataset"], @@subjectid)
     dataset.save(@@subjectid)
     assert_kind_of URI::HTTP, URI.parse(dataset.uri)
-    dataset.delete(@@subjectid)
+    puts `curl #{dataset.uri}`
+    #dataset.delete(@@subjectid)
   end
 
   def test_all
@@ -65,14 +66,14 @@ class DatasetTest < Test::Unit::TestCase
   end
 
   def test_rest_csv
-    uri = OpenTox::RestClientWrapper.post(CONFIG[:services]["opentox-dataset"],{:accept => "text/uri-list"}, {:file => File.new("data/hamster_carcinogenicity.csv"), :subjectid => @@subjectid}).to_s.chomp
+    uri = OpenTox::RestClientWrapper.post(CONFIG[:services]["opentox-dataset"], {:file => File.new("data/hamster_carcinogenicity.csv")} ,{:accept => "text/uri-list", :subjectid => @@subjectid}).to_s.chomp
     @dataset = OpenTox::Dataset.new uri, @@subjectid
     @dataset.load_all(@@subjectid)
     hamster_carc?
   end
 
   def test_multicolumn_csv
-    uri = OpenTox::RestClientWrapper.post(CONFIG[:services]["opentox-dataset"],{:accept => "text/uri-list"}, {:file => File.new("data/multicolumn.csv"), :subjectid => @@subjectid}).to_s.chomp
+    uri = OpenTox::RestClientWrapper.post(CONFIG[:services]["opentox-dataset"], {:file => File.new("data/multicolumn.csv")},{:accept => "text/uri-list", :subjectid => @@subjectid}).to_s.chomp
     @dataset = OpenTox::Dataset.new uri, @@subjectid
     @dataset.load_all(@@subjectid)
     assert_equal 5, @dataset.features.size
diff --git a/lazar.rb b/lazar.rb
index a1ab6db..c2f10ce 100644
--- a/lazar.rb
+++ b/lazar.rb
@@ -17,7 +17,12 @@ class LazarTest < Test::Unit::TestCase
     lazar = OpenTox::Model::Lazar.find model_uri, @@subjectid
     assert_equal lazar.features.size, 222
     compound = OpenTox::Compound.from_smiles("c1ccccc1NN")
+    #puts lazar.uri
+    #puts compound.inspect
+    #puts "prediction"
+    #puts prediction.value(compound).inspect
     prediction_uri = lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid)
+    #puts prediction_uri
     prediction = OpenTox::LazarPrediction.find(prediction_uri, @@subjectid)
     assert_equal prediction.value(compound).round_to(4), 0.149518871336721.round_to(4)
     assert_equal prediction.confidence(compound).round_to(4), 0.615246530364447.round_to(4)
@@ -62,8 +67,8 @@ class LazarTest < Test::Unit::TestCase
     assert_equal prediction.value(compound), false
     prediction.delete(@@subjectid)
     lazar.delete(@@subjectid)
+  end
 =begin
 =end
-  end
 
 end
diff --git a/model.rb b/model.rb
index 098ed5f..f63d6e2 100644
--- a/model.rb
+++ b/model.rb
@@ -7,7 +7,7 @@ class ModelTest < Test::Unit::TestCase
 
   def setup
     @models = [
-      OpenTox::Model.all.last,
+      OpenTox::Model.find_all.last,
       #"http://apps.ideaconsult.net:8080/ambit2/algorithm/J48",
     ]
   end
@@ -37,6 +37,6 @@ class ModelTest < Test::Unit::TestCase
     end
   end
 
-end
 =end
+end