Merge branch 'development' of github.com:opentox/test into development

9 files changed, 403 insertions, 154 deletions

diff --git a/5x_cv/5x_crossvalidation.rb b/5x_cv/5x_crossvalidation.rb
new file mode 100644
index 0000000..bdde2dc
--- /dev/null
+++ b/5x_cv/5x_crossvalidation.rb
@@ -0,0 +1,58 @@
+# Do a five times 10-fold crossvalidation
+# # Author: Andreas Maunz, David Vorgrimmler
+# # @params: CSV-File, Method (LAST, BBRC), Minimum Frequency
+
+require 'rubygems'
+require 'opentox-ruby'
+require 'lib/cv_am.rb'
+
+subjectid = nil
+
+if ARGV.size != 1
+  puts
+  puts "Error! Arguments: <algorithm_params> in the form p1=v1;p2=v2;...;pn=vn"
+  exit 1
+end
+
+# Arguments for lib/cv.rb: file_or_dataset_uri feature_generation min_frequency min_chisq_significance backbone stratified random_seed prediction_algorithm local_svm_kernel nr_hits conf_stdev
+position_mapper={
+  "dataset_uri" => 0, 
+  "feature_generation_uri" => 1,
+  "min_frequency" => 2,
+  "min_chisq_significance" => 3,
+  "backbone" => 4,
+  "stratified" => 5,
+  "random_seed" => 6,
+  "prediction_algorithm" => 7,
+  "local_svm_kernel" => 8,
+  "nr_hits" => 9,
+  "conf_stdev" => 10
+}
+
+param_str=$ARGV[0]
+puts param_str
+params = Array.new(position_mapper.size,"")
+param_str.split(";").each { |param|
+  k,v = param.split("=")
+  params[position_mapper[k]] = v
+}
+params[5]="false" # stratified 
+
+exception_config = YAML.load_file("exceptions_config.yaml")
+if ! exception_config[params[0]].nil?
+  exception_config[params[0]].each { |k,v|
+    puts "Setting exception: #{k} => #{v}"
+    params[position_mapper[k]] = v
+  }
+end
+
+for i in 1..5
+  begin
+    puts
+    puts "Round #{i.to_s}."
+    params[6]=i # random seed
+    cv(params)
+  rescue Exception => e
+    puts "Error in 5xCV: #{e.message}: #{e.backtrace}"
+  end
+end
diff --git a/5x_cv/comparealgs_dv.sh b/5x_cv/comparealgs_dv.sh
new file mode 100755
index 0000000..1b7a7b4
--- /dev/null
+++ b/5x_cv/comparealgs_dv.sh
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+if [ $# -ne 4 ]; then
+  echo "\"validation_uri1,validation_uri2,...\" \"identifier1,identifier2,...\" \"significance [0.95-0.6]\" \"attributes: weighted_r_square,weighted_root_mean_squared_error,weighted_mean_absolute_error,r_square,root_mean_squared_error,sample_correlation_coefficient\""
+  exit 1
+fi
+
+uris="$1"
+iden="$2"
+signi="$3" #default 0.9; 0.95 - 0.6
+attri="$4" #weighted_r_square,weighted_root_mean_squared_error,weighted_mean_absolute_error,r_square,root_mean_squared_error,sample_correlation_coefficient
+host="toxcreate3.in-silico.ch:8080"
+
+curl -X POST -d "validation_uris=$uris" -d "identifier=$iden" -d "ttest_significance=$signi" -d "ttest_attributes=$attri" http://$host/validation/report/algorithm_comparison
diff --git a/5x_cv/dataset_config b/5x_cv/dataset_config
new file mode 100644
index 0000000..a52649c
--- /dev/null
+++ b/5x_cv/dataset_config
@@ -0,0 +1,13 @@
+#EPA v4b Fathead Minnow Acute Toxicity LC50_mmol
+http://toxcreate3.in-silico.ch:8080/dataset/2133
+#CPDBAS_v5d_20Nov2008_rat_TD50
+#http://toxcreate3.in-silico.ch:8080/dataset/1408
+#CPDBAS_v5d_20Nov2008_mouse_TD50
+#http://toxcreate3.in-silico.ch:8080/dataset/1384
+#MultiCellCall: DSSTox Carcinogenic Potency DBS MultiCellCall_no_duplicates.csv
+#http://toxcreate3.in-silico.ch:8080/dataset/130
+#Bloodbarr: bloodbarr_no_duplicate.csv
+#http://toxcreate3.in-silico.ch:8080/dataset/271
+#Salmonella Mutagenicity: DSSTox Carcinogenic Potency DBS Mutagenicity_no_duplicates.csv
+#http://toxcreate3.in-silico.ch:8080/dataset/233
+
diff --git a/5x_cv/exceptions_config.yaml b/5x_cv/exceptions_config.yaml
new file mode 100644
index 0000000..7124c62
--- /dev/null
+++ b/5x_cv/exceptions_config.yaml
@@ -0,0 +1,6 @@
+http://toxcreate3.in-silico.ch:8080/dataset/271:
+  min_frequency: 12
+http://x61s.fdm.uni-freiburg.de/dataset/3546:
+  min_frequency: 8
+http://x61s.fdm.uni-freiburg.de/dataset/3543:
+  min_frequency: 6
diff --git a/5x_cv/factors_config b/5x_cv/factors_config
new file mode 100644
index 0000000..72dbb5f
--- /dev/null
+++ b/5x_cv/factors_config
@@ -0,0 +1 @@
+feature_generation_uri=http://toxcreate3.in-silico.ch:8080/algorithm/fminer/bbrc
diff --git a/5x_cv/lib/cv_am.rb b/5x_cv/lib/cv_am.rb
new file mode 100644
index 0000000..965cd5b
--- /dev/null
+++ b/5x_cv/lib/cv_am.rb
@@ -0,0 +1,161 @@
+# Do a 10-fold crossvalidation with mutiple datasets
+# Author: Andreas Maunz, David Vorgrimmler
+# @params: CSV-File, Method (LAST, BBRC), Minimum Frequency
+
+def cv (args)
+
+  subjectid = nil#OpenTox::Authorization.authenticate(guest,guest) 
+
+  if args.size != 11 
+    puts
+    puts "Error! Arguments: file_or_dataset_uri feature_generation min_frequency min_chisq_significance backbone stratified random_seed prediction_algorithm local_svm_kernel nr_hits conf_stdev"
+    exit 1
+  end
+
+  reg=/^(http|https):\/\/[a-z0-9]+([\-\.]{1}[a-z0-9]+)*\.[a-z]{2,5}(:[0-9]{1,5})?(\/.*)?$/ix
+
+  file=args[0]
+  
+
+ # dataset_is_uri=false
+ # if reg.match(file)? true : false
+ #   #file.include? "http"
+ #   puts "Uri is valid"
+    dataset_is_uri=true
+#    files = [ file ]
+ # elsif ! File.exists? file
+ #   puts "File #{file} missing"
+ #   exit 1
+ # end
+
+#  if args[1].to_s != "last" && args[1].to_s != "bbrc"
+  if !(args[1].to_s.include? "/algorithm/fminer/bbrc") && !(args[1].to_s.include? "/algorithm/fminer/last")
+    puts "feature_generation_uri must contain '/algorithm/fminer/last' or '/algorithm/fminer/bbrc'"
+#    puts "feature_generation must be 'last' or 'bbrc'"
+    exit 1
+  end
+
+  if ! args[2] == ""
+    if args[2].to_i < 2  
+      puts "min_frequency must be at least 2 or \"\""
+      exit 1
+    end
+  end
+
+  if ! args[3] == ""
+    if ! (args[3].to_f <= 1.0 && args[3].to_f >= 0.0)  
+      puts "min_chisq_significance must be between 0 and 1 or \"\""
+      exit 1
+    end
+  end
+
+  if ! args[4] == ""
+    if args[4].to_s != "true" && args[4].to_s != "false"
+      puts "backbone must be 'true' or 'false'."
+      exit 1
+    end
+  end
+
+
+  if args[5].to_s != "true" && args[5].to_s != "false"
+    puts "stratified must be 'true' or 'false'"
+    exit 1
+  end
+
+  if ! args[6] == ""
+    if ! (args[6].to_i <= 1)  
+      puts "random_seed must be a natural number or \"\""
+      exit 1
+    end
+  end
+
+  if ! args[7] == ""
+    if ! (args[7] == "local_svm_classification")  
+      puts "lazar_prediction_method must be \"local_svm_classification\""
+      exit 1
+    end
+  end
+
+  if ! args[8] == ""
+    if ! (args[8] == "weighted_tanimoto" || args[8] == "propositionalized")  
+      puts "local_svm_kernel must be \"weighted_tanimoto\" or \"propositionalized\""
+      exit 1
+    end
+  end
+
+  if ! args[9] == ""
+    if ! (args[9] == "true")  
+      puts "nr_hits must be \"true\""
+      exit 1
+    end
+  end
+
+  if ! args[10] == ""
+    if ! (args[10] == "true")  
+      puts "conf_stdev must be \"true\""
+      exit 1
+    end
+  end
+
+
+
+  #if !dataset_is_uri 
+  #  # Upload a dataset
+  #  training_dataset = OpenTox::Dataset.create_from_csv_file(file, subjectid)
+  #  prediction_feature = training_dataset.features.keys[0]
+  #  training_dataset_uri=training_dataset.uri
+  #  puts prediction_feature
+  #else
+    training_dataset_uri=file
+    puts training_dataset_uri
+    prediction_feature = OpenTox::Dataset.find(training_dataset_uri).features.keys.first
+    puts prediction_feature
+ # end
+  puts training_dataset_uri
+
+
+  # Crossvalidation
+  # @param [Hash] params (required:algorithm_uri,dataset_uri,prediction_feature, optional:algorithm_params,num_folds(10),random_seed(1),stratified(false))
+  alg_params = "feature_generation_uri=#{args[1]}";
+  alg_params = alg_params << ";min_frequency=#{args[2]}" unless args[2]==""
+  alg_params = alg_params << ";min_chisq_significance=#{args[3]}" unless args[3]==""
+  alg_params = alg_params << ";backbone=#{args[4]}" unless args[4]==""   
+  alg_params = alg_params << ";prediction_algorithm=#{args[7]}" unless args[7]==""   
+  alg_params = alg_params << ";local_svm_kernel=#{args[8]}" unless args[8]==""   
+  alg_params = alg_params << ";nr_hits=#{args[9]}" unless args[9]==""
+  alg_params = alg_params << ";conf_stdev=#{args[10]}" unless args[10]==""
+
+  stratified_param = args[5]
+  random_seed_param = args[6]
+
+  cv_args = {:dataset_uri => training_dataset_uri, :prediction_feature => prediction_feature, :algorithm_uri => args[1].split('fminer')[0] + "lazar", :algorithm_params => alg_params, :stratified => stratified_param }
+  cv_args[:random_seed] = random_seed_param unless random_seed_param == ""
+  puts file
+  puts cv_args.to_yaml
+  puts
+  begin
+    lazar_single_args = {}
+    lazar_single_args[:feature_generation_uri] = "#{args[1]}";
+    lazar_single_args[:min_frequency] = args[2] unless args[2]==""
+    lazar_single_args[:min_chisq_significance] = args[3] unless args[3]==""
+    lazar_single_args[:backbone] = args[4] unless args[4]==""   
+    lazar_single_args[:prediction_algorithm] = args[7] unless args[7]==""   
+    lazar_single_args[:local_svm_kernel] = args[8] unless args[8]==""   
+    lazar_single_args[:nr_hits] = args[9] unless args[9]==""
+    lazar_single_args[:conf_stdev] = args[10] unless args[10]==""
+    #m = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => training_dataset_uri, :subjectid => subjectid}.merge lazar_single_args ).to_s
+    #puts m
+    cv = OpenTox::Crossvalidation.create(cv_args).uri
+    puts cv
+    cvr = OpenTox::CrossvalidationReport.create( cv , subjectid).uri
+    puts cvr
+    #qmrfr = OpenTox::QMRFReport.create(m).uri
+    #puts qmrfr 
+    #cv_stat = OpenTox::Validation.from_cv_statistics( cv, subjectid )
+    #puts cv_stat.metadata.to_yaml
+    #[ cv_stat, training_dataset_uri ]
+  rescue Exception => e
+    puts "cv failed: #{e.message} #{e.backtrace}"
+  end
+
+end
diff --git a/5x_cv/wrapper5cv.sh b/5x_cv/wrapper5cv.sh
new file mode 100755
index 0000000..2155635
--- /dev/null
+++ b/5x_cv/wrapper5cv.sh
@@ -0,0 +1,38 @@
+#!/bin/bash
+# Wrapper Skript for CV
+# Set Factors, Datasets, Exceptions in the respective config_files
+# AM, 2011
+
+if [ $# -lt 2 ]; then
+  echo "Usage: $0 factors datasets"
+  exit
+fi
+
+# Configure basics
+source $HOME/.bash_aliases
+otconfig
+THIS_DATE=`date +%Y%m%d_%H_`
+FACTORS="$1"
+DATASETS="$2"
+
+# Don't start when running
+while ps x | grep 5x | grep -v grep >/dev/null 2>&1; do sleep 3; done
+
+LOGFILE="$THIS_DATE""$USER""_wrapper5cv.log"
+rm "$LOGFILE" >/dev/null 2>&1
+
+cat $DATASETS | while read dataset_uri; do
+  if ! [[ "$dataset_uri" =~ "#" ]]; then # allow comments
+    cat $FACTORS | while read factor; do
+      if ! [[ "$factor" =~ "#" ]]; then # allow comments
+        echo "${THIS_DATE}: $factor" >> $LOGFILE>&1
+        factor="$factor;dataset_uri=$dataset_uri"
+        echo "ruby 5x_crossvalidation.rb $factor" >> $LOGFILE 2>&1
+        ruby 5x_crossvalidation.rb $factor >> $LOGFILE 2>&1
+      fi
+    done
+  else
+   echo >> $LOGFILE 2>&1
+   echo $dataset_uri >> $LOGFILE 2>&1
+  fi
+done
diff --git a/lazar.rb b/lazar.rb
index a46e2f2..6aa8239 100644
--- a/lazar.rb
+++ b/lazar.rb
@@ -65,8 +65,8 @@ class LazarTest < Test::Unit::TestCase
   def test_create_regression_model
     create_model :dataset_uri => @@regression_training_dataset.uri
     predict_compound OpenTox::Compound.from_smiles("c1ccccc1NN")
-    assert_equal 1.09.round_to(2), @predictions.first.value(@compounds.first).round_to(2)
-    assert_equal 0.453.round_to(3), @predictions.first.confidence(@compounds.first).round_to(3)
+    assert_in_delta @predictions.first.value(@compounds.first), 0.517, 0.1
+    assert_equal 0.61.round_to(3), @predictions.first.confidence(@compounds.first).round_to(3)
     assert_equal 253, @predictions.first.neighbors(@compounds.first).size
     cleanup
   end
@@ -74,7 +74,7 @@ class LazarTest < Test::Unit::TestCase
   def test_create_regression_prop_model
     create_model :dataset_uri => @@regression_training_dataset.uri, :local_svm_kernel => "propositionalized"
     predict_compound  OpenTox::Compound.from_smiles("c1ccccc1NN")
-    assert_equal 0.453.round_to(3), @predictions.first.confidence(@compounds.first).round_to(3)
+    assert_equal 0.61.round_to(3), @predictions.first.confidence(@compounds.first).round_to(3)
     assert_equal 253, @predictions.first.neighbors(@compounds.first).size
     assert_equal 131, @model.features.size
     cleanup
@@ -91,7 +91,7 @@ class LazarTest < Test::Unit::TestCase
     # assertions
     # single prediction
     assert_equal "false", @predictions[0].value(@compounds[0])
-    assert_equal 0.2938.round_to(4), @predictions[0].confidence(@compounds[0]).round_to(4)
+    assert_equal 0.3383.round_to(4), @predictions[0].confidence(@compounds[0]).round_to(4)
     assert_equal 16, @predictions[0].neighbors(@compounds[0]).size
     # dataset activity
     assert !@predictions[1].measured_activities(@compounds[1]).empty?
@@ -103,7 +103,7 @@ class LazarTest < Test::Unit::TestCase
     assert_equal "true", @predictions[2].measured_activities(c).first.to_s
     c = OpenTox::Compound.from_smiles("c1ccccc1NN")
     assert_equal "false", @predictions[2].value(c)
-    assert_equal 0.2938.round_to(4) , @predictions[2].confidence(c).round_to(4)
+    assert_equal 0.3383.round_to(4) , @predictions[2].confidence(c).round_to(4)
     # model
     assert_equal 41, @model.features.size
     cleanup
@@ -116,7 +116,7 @@ class LazarTest < Test::Unit::TestCase
     predict_dataset OpenTox::Dataset.create_from_csv_file("data/multicolumn.csv", @@subjectid)
 
     assert_equal "false", @predictions[0].value(@compounds[0])
-    assert_equal 0.3952.round_to(4), @predictions[0].confidence(@compounds[0]).round_to(4)
+    assert_equal 0.5587.round_to(4), @predictions[0].confidence(@compounds[0]).round_to(4)
     assert_equal 16, @predictions[0].neighbors(@compounds[0]).size
 
     c = OpenTox::Compound.from_smiles("c1ccccc1NN")
@@ -135,7 +135,7 @@ class LazarTest < Test::Unit::TestCase
    
    assert_equal "false", @predictions[0].value(@compounds[0])
    #assert_equal 0.2938.round_to(4), @predictions[0].confidence(@compounds[0]).round_to(4)
-   assert_equal 0.3952.round_to(4), @predictions[0].confidence(@compounds[0]).round_to(4)
+   assert_equal 0.5587.round_to(4), @predictions[0].confidence(@compounds[0]).round_to(4)
    assert_equal 16, @predictions[0].neighbors(@compounds[0]).size
 
    c = OpenTox::Compound.from_smiles("c1ccccc1NN")
@@ -146,33 +146,33 @@ class LazarTest < Test::Unit::TestCase
    cleanup
  end
 
- def test_regression_mlr_prop_model
-    create_model :dataset_uri => @@regression_training_dataset.uri, :prediction_algorithm => "local_mlr_prop"
-    predict_compound  OpenTox::Compound.from_smiles("c1ccccc1NN")
-    assert_equal 0.453, @predictions.first.confidence(@compounds.first).round_to(3)
-    assert_equal 0.265, @predictions.first.value(@compounds.first).round_to(3)
-    assert_equal 253, @predictions.first.neighbors(@compounds.first).size
-    assert_equal 131, @model.features.size
- end
-
- def test_regression_mlr_prop_conf_stdev
-    create_model :dataset_uri => @@regression_training_dataset.uri, :prediction_algorithm => "local_mlr_prop", :conf_stdev => "true"
-    predict_compound  OpenTox::Compound.from_smiles("c1ccccc1NN")
-    assert_equal 0.154, @predictions.first.confidence(@compounds.first).round_to(3)
-    assert_equal 0.265, @predictions.first.value(@compounds.first).round_to(3)
-    assert_equal 253, @predictions.first.neighbors(@compounds.first).size
-    assert_equal 131, @model.features.size
- end
-
-
- def test_regression_mlr_prop_weighted_model
-    create_model :dataset_uri => @@regression_training_dataset.uri, :prediction_algorithm => "local_mlr_prop", :nr_hits => "true"
-    predict_compound  OpenTox::Compound.from_smiles("c1ccccc1NN")
-    assert_equal 0.453, @predictions.first.confidence(@compounds.first).round_to(3)
-    assert_equal 0.265, @predictions.first.value(@compounds.first).round_to(3)
-    assert_equal 253, @predictions.first.neighbors(@compounds.first).size
-    assert_equal 131, @model.features.size
- end
+# def test_regression_mlr_prop_model
+#    create_model :dataset_uri => @@regression_training_dataset.uri, :prediction_algorithm => "local_mlr_prop"
+#    predict_compound  OpenTox::Compound.from_smiles("c1ccccc1NN")
+#    assert_equal 0.453, @predictions.first.confidence(@compounds.first).round_to(3)
+#    assert_equal 0.265, @predictions.first.value(@compounds.first).round_to(3)
+#    assert_equal 253, @predictions.first.neighbors(@compounds.first).size
+#    assert_equal 131, @model.features.size
+# end
+#
+# def test_regression_mlr_prop_conf_stdev
+#    create_model :dataset_uri => @@regression_training_dataset.uri, :prediction_algorithm => "local_mlr_prop", :conf_stdev => "true"
+#    predict_compound  OpenTox::Compound.from_smiles("c1ccccc1NN")
+#    assert_equal 0.154, @predictions.first.confidence(@compounds.first).round_to(3)
+#    assert_equal 0.265, @predictions.first.value(@compounds.first).round_to(3)
+#    assert_equal 253, @predictions.first.neighbors(@compounds.first).size
+#    assert_equal 131, @model.features.size
+# end
+#
+#
+# def test_regression_mlr_prop_weighted_model
+#    create_model :dataset_uri => @@regression_training_dataset.uri, :prediction_algorithm => "local_mlr_prop", :nr_hits => "true"
+#    predict_compound  OpenTox::Compound.from_smiles("c1ccccc1NN")
+#    assert_equal 0.453, @predictions.first.confidence(@compounds.first).round_to(3)
+#    assert_equal 0.265, @predictions.first.value(@compounds.first).round_to(3)
+#    assert_equal 253, @predictions.first.neighbors(@compounds.first).size
+#    assert_equal 131, @model.features.size
+# end
 
   def test_conf_stdev
    params = {:sims => [0.6,0.72,0.8], :acts => [1,1,1], :neighbors => [1,1,1], :conf_stdev => true} # stdev = 0
diff --git a/toxcreate.rb b/toxcreate.rb
index 9b40e0e..14e61c4 100644
--- a/toxcreate.rb
+++ b/toxcreate.rb
@@ -4,12 +4,14 @@ require 'opentox-ruby'
 require 'test/unit'
 require 'akephalos'
 require 'capybara/dsl'
+gem 'capybara-envjs'
+require 'capybara/envjs' # gem install capybara-envjs
+# requires firefox 3.6 for akephalos and selenium !!!
 Capybara.default_driver = :akephalos # use this without visual inspection
 #Capybara.default_driver = :selenium # use this for visual inspection
 Capybara.run_server = false
 Capybara.default_wait_time = 1000
-#Capybara.javascript_driver = :selenium
-
+Capybara.javascript_driver = :envjs
 
 class ToxCreateTest < Test::Unit::TestCase
   include Capybara
@@ -18,37 +20,38 @@ class ToxCreateTest < Test::Unit::TestCase
     @user = "guest"
     @password = "guest"
   end
-
-  def teardown
-  end
-
-=begin
+=begin # works only with AA enabled  
   def test_01_login
     visit File.join(CONFIG[:services]["opentox-toxcreate"], "login")
-    click_button "Login"
-    puts "Login without credentials"
-    assert  page.has_content?("Please enter username and password.")
+    assert page.has_content?('User: guest')
     fill_in('Username', :with => @user)
     fill_in('Password', :with => @password + "nonsense")
-    click_button "Login"
-    puts "Login with wrong password"
-    assert page.has_content?('Login failed. Please try again.') 
-    fill_in('Username', :with => "anonymous")
-    fill_in('Password', :with => "anonymous")
-    click_button "Login"
-    assert page.has_content?("Welcome anonymous!")
+    click_button('Login')
+    assert page.has_content? "Login failed. Please try again."
+    fill_in('Username', :with => @user)
+    fill_in('Password', :with => @password)
+    click_button('Login')
+    assert page.has_content? "Welcome #{@user}!"
     visit File.join(CONFIG[:services]["opentox-toxcreate"], "login")
-    click_button "Login as guest"
-    puts "Login as user guest"    
-    assert page.has_content?("Welcome guest!")
+    assert page.has_content?('User: guest')
+    fill_in('Username', :with => @user)
+    fill_in('Password', :with => @password + "nonsense")
+    click_button('Login')
+    assert page.has_content? "Login failed. Please try again."
+    click_button('Login as guest')
+    assert page.has_content? "Welcome #{@user}!"
   end
-
+=end
   def test_02_toxcreate # works only with akephalos
+    # create a model and check status is complete
     Capybara.current_driver = :akephalos 
-    #login(@browser, @user, @password)
-    visit CONFIG[:services]["opentox-toxcreate"]
+    visit File.join(CONFIG[:services]["opentox-toxcreate"], "create")
     assert page.has_content?('Upload training data')
-    attach_file('file', "./data/hamster_carcinogenicity.mini.csv")
+    attach_file('file', "./data/hamster_carcinogenicity.csv")
+    assert page.has_button?('endpoint_list_button')
+    click_on "Select endpoint"
+    choose('EcotoxicEffects')
+    choose('Acute_toxicity_to_fish_lethality')
     click_on "Create model"
     assert first("h2").has_content? "hamster_carcinogenicity"
     time = 0
@@ -57,119 +60,84 @@ class ToxCreateTest < Test::Unit::TestCase
       time +=5
     end
     assert first(".model_status").has_content?("Completed")
+    sleep 5
   end
-=end
+
   def test_03_predict
+  # predict with the model from test_02
     Capybara.register_driver :akephalos do |app|
       Capybara::Driver::Akephalos.new(app, :validate_scripts => false)
+    visit File.join(CONFIG[:services]["opentox-toxcreate"], "predict")
+    fill_in 'identifier', :with => 'NNc1ccccc1'
+    find(:xpath, '//form/fieldset[2]/input[contains(@name, "select")]').click
+    click_button("Predict")
+    click_button("Details")
+    page.has_content? "false"
+    page.has_content? "0.294"   
+    page.has_content? "0.875"
+    page.has_content? "next"
     end
-    session = Capybara::Session.new(:akephalos)
-    session.visit CONFIG[:services]["opentox-toxcreate"]
-    session.click_on "Predict"
-    session.fill_in "or enter a Smiles string", :with => "NNc1ccccc1"
-    session.check "hamster carcinogenicity"
-    session.click_button "Predict"
-    assert session.has_content?("Not enough similar compounds in training dataset")
-    session.click_on "Confidence"
-    assert session.has_content?("Indicates the applicability domain of a model")
-    session.click_button "Details"
-
-    #assert page.has_content? "false"
-    #assert page.has_content? "0.294"   
-    #assert page.has_content? "0.875"
-  end
-=begin
-  def test_04_inspect_policies 
-    Capybara.current_driver = :selenium
-    visit CONFIG[:services]["opentox-toxcreate"]
-    click_on "Inspect"
-    assert first('h2').has_content? 'hamster_carcinogenicity'
-    click_on "edit"
-    click_on "manage policy"    
-    within(:xpath, '//form[contains(@id, "form_policy_group_member_")]') do
-      find(:xpath, './/input[5]').click
-      click_on "update"
-    end
-    sleep 5
-  end
-  
-  def test_05_inspect_policies
-    Capybara.current_driver = :selenium
-    visit CONFIG[:services]["opentox-toxcreate"]
-    click_on "Inspect"
-    assert first('h2').has_content? 'hamster_carcinogenicity'
-    click_on "edit"
-    click_on "manage policy"
-  
-    within(:xpath, '//form[contains(@id, "form_policy_group_member_")]') do 
-      find(:xpath, './/input[4]').click
-      click_on "update"
-    end
-    sleep 5
-  end
-  
-  def test_06_inspect_policies
-    Capybara.current_driver = :selenium
-    visit CONFIG[:services]["opentox-toxcreate"]
-    click_on "Inspect"
-    assert first('h2').has_content? 'hamster_carcinogenicity'
-    click_on "edit"
-    click_on "manage policy"  
-    within(:xpath, '//form[contains(@id, "form_development")]') do 
-      find(:xpath, './/input[4]').click     
-      click_on "add" 
-    end
-    sleep 5
   end
-  
-  def test_07_inspect_policies
-    Capybara.current_driver = :selenium
-    visit CONFIG[:services]["opentox-toxcreate"]
-    click_on "Inspect"
-    assert first('h2').has_content? 'hamster_carcinogenicity'
-    click_on "edit"
-    click_on "manage policy" 
-    within(:xpath, '//form[contains(@id, "form_policy_group_development_")]') do 
-      find(:xpath, './/input[3]').click
-      click_on "update"
-    end
+
+  def test_04_delete_model
+  # delete the model from test_02
+    visit File.join(CONFIG[:services]["opentox-toxcreate"], "models")
+    assert (first(".model_status").has_content?("Completed") or first(".model_status").has_content?("Error"))
+    click_on "delete"
+    page.evaluate_script('window.confirm = function() { return true; }')
     sleep 5
-    page.evaluate_script('window.confirm = function() { return true; }')   
-    click_on "delete"   
   end
-  
 =begin
-  def test_08_multi_cell_call
+  def test_09_multi_cell_call
     #login(@browser, @user, @password)
-    Capybara.current_driver = :akephalos 
-    visit CONFIG[:services]["opentox-toxcreate"]
+    #Capybara.current_driver = :akephalos 
+    visit File.join(CONFIG[:services]["opentox-toxcreate"], "create")
     assert page.has_content?('Upload training data')
     attach_file('file', "./data/multi_cell_call.csv")
     click_on "Create model"
   end
 
-  def test_09_kazius
-    Capybara.current_driver = :akephalos 
+  def test_10_kazius
+    #Capybara.current_driver = :akephalos 
     #login(@browser, @user, @password)
-    visit CONFIG[:services]["opentox-toxcreate"]
+    visit File.join(CONFIG[:services]["opentox-toxcreate"], "create")
     assert page.has_content?('Upload training data')
     attach_file('file', "./data/kazius.csv")
     # wait until validation is completed
     # check results (links, reports, results)
     puts @browser.url
   end
-
-  def test_10_parallel_models
-    #login(@browser, @user, @password)
-    10.times do
-      visit CONFIG[:services]["opentox-toxcreate"]
+ 
+  def test_11_parallel_models
+    5.times do
+      visit File.join(CONFIG[:services]["opentox-toxcreate"], "create")
       assert page.has_content?('Upload training data')
-      attach_file('file', "./data/multi_cell_call.csv")
+      attach_file('file', "./data/hamster_carcinogenicity.csv")
       click_on "Create model"
     end
+    while (first(".model_status").has_no_content?("Completed") and first(".model_status").has_no_content?("Error")) do
+      sleep 1
+    end
+    assert first(".model_status").has_content?("Completed")
+  end
+ 
+  def test_12_delete_parallel_models  
+    5.times do
+      visit File.join(CONFIG[:services]["opentox-toxcreate"], "models")
+      click_on "delete"
+      page.evaluate_script('window.confirm = function() { return true; }')
+      #sleep 5
+    end
+    sleep 5
+    visit File.join(CONFIG[:services]["opentox-toxcreate"], "models")
+    while page.has_no_content? "There are currently no models" do
+      sleep 1
+    end
+    assert page.has_content? "There are currently no models"
   end
+=begin
   # raises capybara errors, but gui works from browser
-  def test_11_toxcreate_sdf # works only with akephalos
+  def test_12_toxcreate_sdf # works only with akephalos
     Capybara.current_driver = :akephalos 
     #login(@browser, @user, @password)
     visit CONFIG[:services]["opentox-toxcreate"]
@@ -186,14 +154,4 @@ class ToxCreateTest < Test::Unit::TestCase
   end
 =end
 
-
-=begin
-def login(browser, user, password)
-  browser.goto File.join(CONFIG[:services]["opentox-toxcreate"], "login")
-  browser.text_field(:id, "username").set(user)
-  browser.text_field(:id, "password").set(password)
-  browser.button(:value, "Login").click
-end
-
-=end
 end