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require 'rubygems'
require 'opentox-ruby'
require 'test/unit'
require 'validate-owl'
class DatasetTest < Test::Unit::TestCase
def setup
@datasets = {
@@regression_training_dataset.uri => nil,
@@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 => 36,
: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(@@subjectid)
#@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)
#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
@dataset.load_yaml(File.open("data/hamster_carcinogenicity.yaml").read)
hamster_carc?
end
def test_sdf_with_multiple_features
uri = OpenTox::RestClientWrapper.post(CONFIG[:services]["opentox-dataset"], File.read("data/CPDBAS_v5c_1547_29Apr2008part.sdf") ,{:accept => "text/uri-list",:content_type => "chemical/x-mdl-sdfile", :subjectid => @@subjectid}).to_s.chomp
assert_kind_of URI::HTTP, URI.parse(uri)
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 = OpenTox::Dataset.new uri
@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 = OpenTox::Dataset.new uri
@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
@dataset.load_csv(File.open("data/hamster_carcinogenicity.csv").read, @@subjectid)
#puts @dataset.to_yaml
hamster_carc?
@dataset.delete(@@subjectid)
end
def test_from_excel
@dataset = OpenTox::Dataset.new
@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)
@dataset.load_compounds @@subjectid
assert_equal @dataset.compounds.size,data[:nr_compounds] if data
end
end
def test_load_features
@datasets.each do |uri,data|
@dataset = OpenTox::Dataset.new(uri)
@dataset.load_features @@subjectid
assert_equal @dataset.features.keys.size,data[:nr_dataset_features] if data
end
end
def test_load_all
@datasets.each do |uri,data|
@dataset = OpenTox::Dataset.new(uri)
@dataset.load_all @@subjectid
validate data
end
end
def test_yaml
@datasets.each do |uri,data|
@dataset = OpenTox::Dataset.new(uri)
@dataset.load_all @@subjectid
#@dataset = YAML.load @dataset.to_yaml
validate data
end
end
def test_sdf
@datasets.each do |uri,data|
@dataset = OpenTox::Dataset.new(uri)
@dataset.load_all @@subjectid
sdf = @dataset.to_sdf
size = sdf.lines.to_a.select{|i| i == "$$$$\n"}.size
assert_equal size, data[:nr_compounds] if data
end
end
def test_csv
@datasets.each do |uri,data|
@dataset = OpenTox::Dataset.new(uri)
@dataset.load_all @@subjectid
csv = @dataset.to_csv.split("\n")
assert_equal csv.size, data[:nr_compounds]+1 if data
assert_equal csv.first.split(", ").size, data[:nr_dataset_features]+1 if data
end
end
def test_excel
@datasets.each do |uri,data|
@dataset = OpenTox::Dataset.new(uri)
@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)
@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)
@dataset.load_all @@subjectid
assert_kind_of String, @dataset.to_rdfxml
end
end
def test_rdf_conversion
@datasets.each do |uri,data|
#puts "dataset "+uri.to_s
@dataset = OpenTox::Dataset.new(uri)
@dataset.load_all @@subjectid
#puts @dataset.features.keys.size.to_s+" # features"
#puts "download to rdf"
f = Tempfile.new("ot-rdf")
f.puts @dataset.to_rdfxml
f.close
#puts "upload as rdf"
d = OpenTox::Dataset.create(CONFIG[:services]["opentox-dataset"], @@subjectid)
d.load_rdfxml_file(f)
f.delete
d.save(@@subjectid)
assert d.uri.uri?
#puts "compare"
dataset_equal(@dataset,d)
#puts "download new dataset as yaml"
d2 = OpenTox::Dataset.new(d.uri)
d2.load_all @@subjectid
#puts "compare again"
dataset_equal(@dataset,d2)
end
end
=begin
=end
def dataset_equal(d,d2)
assert d.compounds.sort==d2.compounds.sort,
d.compounds.sort.to_yaml+"\n!=\n"+d2.compounds.sort.to_yaml
assert d.features.keys.size==d2.features.keys.size,
d.features.keys.to_yaml+"\n!=\n"+d2.features.keys.to_yaml
assert d.features.keys.sort==d2.features.keys.sort,
d.features.keys.sort.to_yaml+"\n!=\n"+d2.features.keys.sort.to_yaml
d.compounds.each do |c|
d.features.keys.each do |f|
assert_array_about_equal d.data_entries[c][f],d2.data_entries[c][f]
end
end
end
def assert_array_about_equal(a,a2)
if (a!=nil || a2!=nil)
raise "no arrays #{a.class} #{a2.class}" unless a.is_a?(Array) and a2.is_a?(Array)
assert a.size==a2.size
a.sort!
a2.sort!
a.size.times do |i|
if (a[i].is_a?(Float) and a2[i].is_a?(Float))
assert (a[i]-a2[i]).abs<0.0000001,"#{a[i]}(#{a[i].class}) != #{a2[i]}(#{a2[i].class})"
else
assert a[i]==a2[i],"#{a[i]}(#{a[i].class}) != #{a2[i]}(#{a2[i].class})"
end
end
end
end
def validate(data)
assert_kind_of OpenTox::Dataset, @dataset
assert_equal @dataset.data_entries.size, data[:nr_data_entries] if data
assert_equal @dataset.compounds.size, data[:nr_compounds] if data
assert_equal @dataset.features.size, data[:nr_dataset_features] if data
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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