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require 'application'
require 'test/unit'
require 'rack/test'
set :environment, :test
@@redis.flush_db
class DatasetsTest < Test::Unit::TestCase
include Rack::Test::Methods
def app
Sinatra::Application
end
def test_index
get '/'
assert last_response.ok?
end
def test_create_dataset
post '/', :name => "Test dataset"
assert last_response.ok?
uri = last_response.body.chomp
assert_equal "http://example.org/Test_dataset", uri
get uri
assert last_response.ok?
delete "/Test_dataset"
assert last_response.ok?
get "/Test_dataset"
assert !last_response.ok?
end
def test_create_dataset_and_insert_data
name = "Test dataset"
compounds = {
'[O-][N+](=O)C/C=C\C(=O)Cc1cc(C#N)ccc1' => 'true',
'F[B-](F)(F)F.[Na+]' => 'false',
'N#[N+]C1=CC=CC=C1.F[B-](F)(F)F' => 'false'
}
post '/', :name => name
assert last_response.ok?
uri = last_response.body.chomp
get uri
assert last_response.ok?
assert last_response.body.include?("Test_dataset")
compounds.each do |smiles,activity|
compound_uri = OpenTox::Compound.new(:smiles => smiles).uri
feature_uri = OpenTox::Feature.new(:name => name, :values => {:classification => activity}).uri
put uri, :compound_uri => compound_uri, :feature_uri => feature_uri
assert last_response.ok?
get uri + '/compounds'
assert last_response.ok?
assert last_response.body.include?(compound_uri)
get uri + '/features'
assert last_response.ok?
assert last_response.body.include?(activity)
assert last_response.body.include?(feature_uri)
get uri + '/compound/' + compound_uri + '/features'
assert last_response.ok?
assert last_response.body.include?(activity)
assert_equal feature_uri, last_response.body
end
get uri + '/compounds'
#puts last_response.body
delete uri
assert last_response.ok?
get "/Test_dataset"
assert !last_response.ok?
end
def test_create_dataset_from_csv
smiles = 'CC(=O)Nc1scc(n1)c1ccc(o1)[N+](=O)[O-]'
compound_uri = OpenTox::Compound.new(:smiles => smiles).uri
post '/', :name => "Hamster Carcinogenicity", :file => Rack::Test::UploadedFile.new(File.join(File.dirname(__FILE__), "hamster_carcinogenicity.csv"))
uri = last_response.body
get uri
assert last_response.ok?
get uri + '/compounds'
assert last_response.ok?
assert last_response.body.include?(compound_uri)
get uri + '/features'
assert last_response.ok?
assert last_response.body.include?("Hamster%20Carcinogenicity/classification/true")
assert last_response.body.include?("Hamster%20Carcinogenicity/classification/false")
get uri + '/compound/' + compound_uri + '/features'
assert last_response.ok?
assert last_response.body.include?("Hamster%20Carcinogenicity/classification/true")
delete uri
assert last_response.ok?
get uri
assert !last_response.ok?
end
=begin
def test_create_large_dataset_from_csv
post '/', :name => "Salmonella Mutagenicity", :file => Rack::Test::UploadedFile.new(File.join(File.dirname(__FILE__), "kazius.csv"))
uri = last_response.body
get uri
assert last_response.ok?
end
=end
def test_tanimoto_similarity
#@feature_set = OpenTox::Algorithms::Fminer.new :dataset_uri => @dataset
name = "Similarity test dataset"
data = {
'[O-][N+](=O)C/C=C\C(=O)Cc1cc(C#N)ccc1' =>
{
'A' => 1.0,
'B' => 0.9,
'C' => 0.8,
'D' => 0.7,
'E' => 0.5
},
'F[B-](F)(F)F.[Na+]' =>
{
'F' => 0.9,
'B' => 0.9,
'C' => 0.8,
'D' => 0.7,
'E' => 0.5
},
'N#[N+]C1=CC=CC=C1.F[B-](F)(F)F' =>
{
'A' => 1.0,
'B' => 0.9,
'F' => 0.9,
}
}
post '/', :name => name
assert last_response.ok?
uri = last_response.body
get uri
assert last_response.ok?
data.each do |smiles,features|
compound_uri = OpenTox::Compound.new(:smiles => smiles).uri
features.each do |k,v|
feature_uri = OpenTox::Feature.new(:name => k, :values => {:p_value => v}).uri
put uri, :compound_uri => compound_uri, :feature_uri => feature_uri
assert last_response.ok?
end
end
data.each do |smiles,features|
compound_uri = OpenTox::Compound.new(:smiles => smiles).uri
data.each do |s,f|
unless s == smiles
neighbor_uri = OpenTox::Compound.new(:smiles => s).uri
get uri + "/tanimoto/compound/#{compound_uri}/compound/#{neighbor_uri}"
assert last_response.ok?
sim = last_response.body
features_a = data[smiles].keys
features_b = data[s].keys
union = features_a | features_b
intersect = features_a & features_b
mysim = intersect.size.to_f/union.size.to_f
assert_equal sim, mysim.to_s
puts "tanimoto::#{smiles}::#{s}::#{last_response.body}"
get uri + "/weighted_tanimoto/compound/#{compound_uri}/compound/#{neighbor_uri}"
assert last_response.ok?
puts "weighted_tanimoto::#{smiles}::#{s}::#{last_response.body}"
end
end
end
end
=begin
def test_unauthorized_create
post '/', :name => "Test dataset"
assert !last_response.ok?
end
=end
end
|
