diff options
| -rw-r--r-- | algorithm.rb | 3 | ||||
| -rw-r--r-- | authorization.rb | 11 | ||||
| -rw-r--r-- | dataset.rb | 22 | ||||
| -rw-r--r-- | feature.rb | 2 | ||||
| -rw-r--r-- | lazar.rb | 16 | ||||
| -rw-r--r-- | validate-owl.rb | 6 |
6 files changed, 37 insertions, 23 deletions
diff --git a/algorithm.rb b/algorithm.rb index 055f0a2..94f3b5c 100644 --- a/algorithm.rb +++ b/algorithm.rb @@ -6,6 +6,7 @@ require "./validate-owl.rb" class AlgorithmTest < Test::Unit::TestCase def setup + @@subjectid = OpenTox::Authorization.authenticate(TEST_USER,TEST_PW) @algorithms = [ File.join(CONFIG[:services]["opentox-algorithm"],"fminer","bbrc"), File.join(CONFIG[:services]["opentox-algorithm"],"fminer","last"), @@ -20,7 +21,7 @@ class AlgorithmTest < Test::Unit::TestCase def test_metadata @algorithms.each do |algorithm| puts algorithm - validate_owl(algorithm) + validate_owl(algorithm, @@subjectid) end end diff --git a/authorization.rb b/authorization.rb index 0d3508b..3772638 100644 --- a/authorization.rb +++ b/authorization.rb @@ -85,7 +85,16 @@ class TestOpenToxAuthorizationLDAP < Test::Unit::TestCase logout(tok_anonymous) end - + def test_03_check_different_uris + res = OpenTox::Authorization.send_policy(TEST_URI, @@subjectid) + assert OpenTox::Authorization.uri_has_policy(TEST_URI, @@subjectid) + assert OpenTox::Authorization.authorize(TEST_URI, "GET", @@subjectid), "GET request" + policies = OpenTox::Authorization.list_uri_policies(TEST_URI, @@subjectid) + policies.each do |policy| + assert OpenTox::Authorization.delete_policy(policy, @@subjectid) + end + + end end @@ -47,7 +47,7 @@ class DatasetTest < Test::Unit::TestCase end def test_all - datasets = OpenTox::Dataset.all + datasets = OpenTox::Dataset.all(CONFIG[:services]["opentox-dataset"], @@subjectid) assert_kind_of Array, datasets end @@ -67,14 +67,14 @@ class DatasetTest < Test::Unit::TestCase 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 @dataset = OpenTox::Dataset.new uri - @dataset.load_all + @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 @dataset = OpenTox::Dataset.new uri - @dataset.load_all + @dataset.load_all(@@subjectid) assert_equal 5, @dataset.features.size assert_equal 4, @dataset.compounds.size @@ -96,7 +96,7 @@ class DatasetTest < Test::Unit::TestCase def test_load_metadata @datasets.each do |uri,data| - @dataset = OpenTox::Dataset.find(uri) + @dataset = OpenTox::Dataset.find(uri, @@subjectid) assert @dataset.metadata.size != 0 end end @@ -104,7 +104,7 @@ class DatasetTest < Test::Unit::TestCase def test_load_compounds @datasets.each do |uri,data| @dataset = OpenTox::Dataset.new(uri) - @dataset.load_compounds + @dataset.load_compounds(@@subjectid) assert_equal @dataset.compounds.size,data[:nr_compounds] end end @@ -120,7 +120,7 @@ class DatasetTest < Test::Unit::TestCase def test_load_all @datasets.each do |uri,data| @dataset = OpenTox::Dataset.new(uri) - @dataset.load_all + @dataset.load_all(@@subjectid) validate data end end @@ -128,7 +128,7 @@ class DatasetTest < Test::Unit::TestCase def test_yaml @datasets.each do |uri,data| @dataset = OpenTox::Dataset.new(uri) - @dataset.load_all + @dataset.load_all(@@subjectid) #@dataset = YAML.load @dataset.to_yaml validate data end @@ -137,7 +137,7 @@ class DatasetTest < Test::Unit::TestCase def test_csv @datasets.each do |uri,data| @dataset = OpenTox::Dataset.new(uri) - @dataset.load_all + @dataset.load_all(@@subjectid) csv = @dataset.to_csv.split("\n") assert_equal csv.size, data[:nr_compounds]+1 assert_equal csv.first.split(", ").size, data[:nr_dataset_features]+1 @@ -147,7 +147,7 @@ class DatasetTest < Test::Unit::TestCase def test_excel @datasets.each do |uri,data| @dataset = OpenTox::Dataset.new(uri) - @dataset.load_all + @dataset.load_all(@@subjectid) book = @dataset.to_spreadsheet assert_kind_of Spreadsheet::Workbook, book #File.open("#{@dataset.id}.xls","w+"){|f| book.write f.path} @@ -157,7 +157,7 @@ class DatasetTest < Test::Unit::TestCase def test_ntriples @datasets.each do |uri,data| @dataset = OpenTox::Dataset.new(uri) - @dataset.load_all + @dataset.load_all(@@subjectid) assert_kind_of String, @dataset.to_ntriples end end @@ -165,7 +165,7 @@ class DatasetTest < Test::Unit::TestCase def test_owl @datasets.each do |uri,data| @dataset = OpenTox::Dataset.new(uri) - @dataset.load_all + @dataset.load_all(@@subjectid) assert_kind_of String, @dataset.to_rdfxml end end @@ -25,7 +25,7 @@ class FeatureTest < Test::Unit::TestCase def test_owl #@features.each do |uri| - validate_owl @features.first + validate_owl @features.first, @@subjectid # Ambit does not validate #end end @@ -14,11 +14,11 @@ class LazarTest < Test::Unit::TestCase =end def test_create_regression_model model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => @@regression_training_dataset.uri, :subjectid => @@subjectid}).to_s - lazar = OpenTox::Model::Lazar.find model_uri + lazar = OpenTox::Model::Lazar.find model_uri, @@subjectid assert_equal lazar.features.size, 222 compound = OpenTox::Compound.from_smiles("c1ccccc1NN") prediction_uri = lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid) - prediction = OpenTox::LazarPrediction.find(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) assert_equal prediction.neighbors(compound).size, 81 @@ -29,12 +29,12 @@ class LazarTest < Test::Unit::TestCase def test_default_classification_model # create model model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => @@classification_training_dataset.uri, :subjectid => @@subjectid}).to_s - lazar = OpenTox::Model::Lazar.find model_uri + lazar = OpenTox::Model::Lazar.find model_uri, @@subjectid assert_equal lazar.features.size, 41 # single prediction compound = OpenTox::Compound.from_smiles("c1ccccc1NN") prediction_uri = lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid) - prediction = OpenTox::LazarPrediction.find(prediction_uri) + prediction = OpenTox::LazarPrediction.find(prediction_uri, @@subjectid) assert_equal prediction.value(compound), false assert_equal prediction.confidence(compound).round_to(4), 0.25857114104619.round_to(4) assert_equal prediction.neighbors(compound).size, 15 @@ -42,7 +42,7 @@ class LazarTest < Test::Unit::TestCase # dataset activity compound = OpenTox::Compound.from_smiles("CNN") prediction_uri = lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid) - prediction = OpenTox::LazarPrediction.find prediction_uri + prediction = OpenTox::LazarPrediction.find prediction_uri, @@subjectid assert !prediction.measured_activities(compound).empty? puts prediction.measured_activities(compound).first.inspect assert_equal prediction.measured_activities(compound).first, true @@ -50,9 +50,13 @@ class LazarTest < Test::Unit::TestCase prediction.delete(@@subjectid) # dataset prediction test_dataset = OpenTox::Dataset.create_from_csv_file("data/multicolumn.csv", @@subjectid) - prediction = OpenTox::LazarPrediction.find lazar.run(:dataset_uri => test_dataset.uri, :subjectid => @@subjectid) + prediction = OpenTox::LazarPrediction.find lazar.run(:dataset_uri => test_dataset.uri, :subjectid => @@subjectid), @@subjectid assert_equal prediction.compounds.size, 4 compound = OpenTox::Compound.new prediction.compounds.first + puts "compound" + puts compound.inspect + puts "prediction" + puts prediction.value(compound).inspect assert_equal prediction.value(compound), false prediction.delete(@@subjectid) lazar.delete(@@subjectid) diff --git a/validate-owl.rb b/validate-owl.rb index 569813f..736531b 100644 --- a/validate-owl.rb +++ b/validate-owl.rb @@ -1,9 +1,9 @@ #require 'nokogiri' -def validate_owl(uri) +def validate_owl(uri, subjectid=nil) if validator_available? - owl = OpenTox::RestClientWrapper.get(uri,:accept => "application/rdf+xml") - html = OpenTox::RestClientWrapper.post("http://www.mygrid.org.uk/OWL/Validator",{:rdf => owl, :level => "DL"}) + owl = OpenTox::RestClientWrapper.get(uri,{:accept => "application/rdf+xml",:subjectid => subjectid}) + html = OpenTox::RestClientWrapper.post("http://www.mygrid.org.uk/OWL/Validator",{:rdf => owl, :level => "DL",:subjectid => subjectid}) assert_match(/YES/,html) else puts "http://www.mygrid.org.uk/OWL/Validator offline" |