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require 'rubygems'
require 'opentox-ruby'
require 'test/unit'
require 'validate-owl'
class DatasetTest < Test::Unit::TestCase
=begin
=end
def setup
@datasets = {
@@classification_training_dataset.uri => {
: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
def test_save_external
@dataset = OpenTox::Dataset.find "http://apps.ideaconsult.net:8080/ambit2/dataset/2698", @@subjectid
#File.open("test.rdf","w+"){|f| f.puts @dataset.to_rdfxml}
@dataset.uri = "http://apps.ideaconsult.net:8080/ambit2/dataset"
uri = @dataset.save(@@subjectid)
puts uri
#@dataset.load_csv(File.open("data/hamster_carcinogenicity.csv").read)
#@dataset.save
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)
puts `curl #{dataset.uri}`
#dataset.delete(@@subjectid)
end
def test_all
datasets = OpenTox::Dataset.all(CONFIG[:services]["opentox-dataset"], @@subjectid)
assert_kind_of Array, datasets
end
def test_owl
validate_owl @@classification_training_dataset.uri
validate_owl @@regression_training_dataset.uri
# ambit datasets do ot validate
#@datasets.keys.each {|d| validate_owl d }
end
def test_from_yaml
@dataset = OpenTox::Dataset.new nil, @@subjectid
@dataset.load_yaml(File.open("data/hamster_carcinogenicity.yaml").read)
hamster_carc?
end
def test_rest_csv
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"], {: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
assert_equal 4, @dataset.compounds.size
end
def test_from_csv
@dataset = OpenTox::Dataset.new(nil, @@subjectid)
@dataset.load_csv(File.open("data/hamster_carcinogenicity.csv").read, @@subjectid)
hamster_carc?
@dataset.delete(@@subjectid)
end
def test_from_excel
@dataset = OpenTox::Dataset.new(nil, @@subjectid)
@dataset.load_spreadsheet(Excel.new("data/hamster_carcinogenicity.xls"), @@subjectid)
hamster_carc?
@dataset.delete(@@subjectid)
end
def test_load_metadata
@datasets.each do |uri,data|
@dataset = OpenTox::Dataset.find(uri, @@subjectid)
assert @dataset.metadata.size != 0
end
end
def test_load_compounds
@datasets.each do |uri,data|
@dataset = OpenTox::Dataset.new(uri, @@subjectid)
@dataset.load_compounds(@@subjectid)
assert_equal @dataset.compounds.size,data[:nr_compounds]
end
end
def test_load_features
@datasets.each do |uri,data|
@dataset = OpenTox::Dataset.new(uri, @@subjectid)
@dataset.load_features(@@subjectid)
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, @@subjectid)
@dataset.load_all(@@subjectid)
validate data
end
end
def test_yaml
@datasets.each do |uri,data|
@dataset = OpenTox::Dataset.new(uri, @@subjectid)
@dataset.load_all(@@subjectid)
#@dataset = YAML.load @dataset.to_yaml
validate data
end
end
def test_csv
@datasets.each do |uri,data|
@dataset = OpenTox::Dataset.new(uri, @@subjectid)
@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
end
end
def test_excel
@datasets.each do |uri,data|
@dataset = OpenTox::Dataset.new(uri, @@subjectid)
@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}
end
end
def test_ntriples
@datasets.each do |uri,data|
@dataset = OpenTox::Dataset.new(uri, @@subjectid)
@dataset.load_all(@@subjectid)
assert_kind_of String, @dataset.to_ntriples
end
end
def test_owl
@datasets.each do |uri,data|
@dataset = OpenTox::Dataset.new(uri, @@subjectid)
@dataset.load_all(@@subjectid)
assert_kind_of String, @dataset.to_rdfxml
end
end
=begin
=end
def validate(data)
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
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