Initial sketch of unit tests, cucumber tests are obsolete

1 files changed, 201 insertions, 0 deletions

diff --git a/dataset.rb b/dataset.rb
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+++ b/dataset.rb
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+require 'rubygems'
+require 'opentox-ruby-api-wrapper'
+require 'test/unit'
+require 'validate-owl'
+
+class DatasetTest < Test::Unit::TestCase
+
+  def setup
+    #@new_dataset = OpenTox::Dataset.from_csv(File.open("data/hamster_carcinogenicity.csv").read)
+    #@new_dataset.add_metadata( OT.hasSource => "data/hamster_carcinogenicity.csv", DC.creator => "opentox-test", DC.title => "Hamster Carcinogenicity" )
+    #@new_dataset.save
+    @datasets = {
+      #@new_dataset.uri => {
+      "http://localhost/dataset/1" => {
+        :nr_compounds => 85,
+        :nr_features => 1,
+        :nr_dataset_features => 1,
+        :nr_data_entries => 85
+      },
+      "http://apps.ideaconsult.net:8080/ambit2/dataset/2698" => {
+        :nr_compounds => 3,
+        :nr_features => 8,
+        :nr_dataset_features => 37,
+        :nr_data_entries => 3
+      }
+    }
+  end
+
+  def teardown
+    #@new_dataset.delete
+  end
+
+=begin
+=end
+  def test_save_external
+
+    @dataset = OpenTox::Dataset.find "http://apps.ideaconsult.net:8080/ambit2/dataset/2698"
+    #File.open("test.rdf","w+"){|f| f.puts @dataset.to_rdfxml}
+    @dataset.uri = "http://apps.ideaconsult.net:8080/ambit2/dataset" 
+    uri = @dataset.save
+    puts uri
+    #@dataset.load_csv(File.open("data/hamster_carcinogenicity.csv").read)
+    #@dataset.save
+  end
+
+  def test_create
+    dataset = OpenTox::Dataset.create
+    dataset.save
+    puts dataset.uri
+    assert_kind_of URI::HTTP, URI.parse(dataset.uri)
+    #dataset.delete
+  end
+
+  def test_all
+    datasets = OpenTox::Dataset.all
+    assert_kind_of Array, datasets
+  end
+
+  def test_owl
+    validate_owl  "http://localhost/dataset/1" 
+    # ambit datasets do ot validate
+    #@datasets.keys.each {|d| validate_owl d }
+  end
+
+  def test_from_yaml
+    # TODO: fix uri
+    @dataset = OpenTox::Dataset.new
+    @dataset.load_yaml(File.open("data/hamster_carcinogenicity.yaml").read)
+    hamster_carc?
+  end
+
+  def test_rest_csv
+    uri = OpenTox::RestClientWrapper.post('http://localhost/dataset',{:accept => "text/uri-list"}, {:file => File.new("data/hamster_carcinogenicity.csv")}).to_s.chomp
+    @dataset = OpenTox::Dataset.new uri
+    @dataset.load_all
+    hamster_carc?
+    #puts @dataset.to_yaml
+    #@dataset.delete
+  end
+
+  def test_multicolumn_csv
+    uri = OpenTox::RestClientWrapper.post('http://localhost/dataset',{:accept => "text/uri-list"}, {:file => File.new("data/multicolumn.csv")}).to_s.chomp
+    puts uri
+    @dataset = OpenTox::Dataset.new uri
+    @dataset.load_all
+    #puts @dataset.to_yaml
+    assert_equal 5, @dataset.features.size
+    assert_equal 4, @dataset.compounds.size
+    @dataset.delete
+  end
+
+  def test_from_csv
+    @dataset = OpenTox::Dataset.new
+    @dataset.load_csv(File.open("data/hamster_carcinogenicity.csv").read)
+    hamster_carc?
+  end
+
+  def test_from_excel
+    @dataset = OpenTox::Dataset.new
+    @dataset.load_spreadsheet(Excel.new("data/hamster_carcinogenicity.xls"))
+    hamster_carc?
+    #@dataset.delete
+  end
+
+  def test_load_metadata
+    @datasets.each do |uri,data|
+      @dataset = OpenTox::Dataset.find(uri)
+      #puts @dataset.inspect
+      assert_not_nil @dataset.metadata[DC.title]
+    end
+  end
+
+  def test_load_compounds
+    @datasets.each do |uri,data|
+      @dataset = OpenTox::Dataset.new(uri)
+      @dataset.load_compounds
+      assert_equal @dataset.compounds.size,data[:nr_compounds]
+    end
+  end
+
+  def test_load_features
+    @datasets.each do |uri,data|
+      @dataset = OpenTox::Dataset.new(uri)
+      @dataset.load_features
+      #puts @dataset.features.to_yaml
+      assert_equal @dataset.features.keys.size,data[:nr_dataset_features]
+    end
+  end
+
+  def test_load_all
+    @datasets.each do |uri,data|
+      @dataset = OpenTox::Dataset.new(uri)
+      @dataset.load_all
+      validate data
+    end
+  end
+
+  def test_yaml
+    @datasets.each do |uri,data|
+      @dataset = OpenTox::Dataset.new(uri)
+      @dataset.load_all
+      @dataset = YAML.load @dataset.to_yaml
+      validate data
+    end
+  end
+
+  def test_csv
+    @datasets.each do |uri,data|
+      @dataset = OpenTox::Dataset.new(uri)
+      @dataset.load_all
+      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
+    end
+  end
+
+  def test_excel
+    @datasets.each do |uri,data|
+      @dataset = OpenTox::Dataset.new(uri)
+      @dataset.load_all
+      book =  @dataset.to_spreadsheet
+      assert_kind_of Spreadsheet::Workbook, book
+      #File.open("#{@dataset.id}.xls","w+"){|f| book.write f.path}
+    end
+  end
+
+  def test_ntriples
+    @datasets.each do |uri,data|
+      @dataset = OpenTox::Dataset.new(uri)
+      @dataset.load_all
+      #puts @dataset.to_ntriples
+      assert_kind_of String, @dataset.to_ntriples
+    end
+  end
+
+  def test_owl
+    @datasets.each do |uri,data|
+      @dataset = OpenTox::Dataset.new(uri)
+      @dataset.load_all
+      #puts @dataset.to_rdfxml
+      assert_kind_of String, @dataset.to_rdfxml
+    end
+  end
+=begin
+=end
+  def validate(data)
+    #puts @dataset.yaml
+    assert_kind_of OpenTox::Dataset, @dataset
+    assert_equal @dataset.data_entries.size, data[:nr_data_entries]
+    assert_equal @dataset.compounds.size, data[:nr_compounds]
+    assert_equal @dataset.features.size, data[:nr_dataset_features]
+    assert_equal @dataset.uri, @dataset.metadata[XSD.anyURI]
+  end
+
+  def hamster_carc?
+    assert_kind_of OpenTox::Dataset, @dataset
+    assert_equal 85, @dataset.data_entries.size
+    assert_equal 85, @dataset.compounds.size
+    assert_equal @dataset.uri, @dataset.metadata[XSD.anyURI]
+  end
+end