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require 'application'
require 'test/unit'
require 'rack/test'
require 'ruby-prof'
set :environment, :test
@@redis.flush_db
class DatasetsTest < Test::Unit::TestCase
include Rack::Test::Methods
#include RubyProf::Test
def app
Sinatra::Application
end
def test_index
get '/datasets'
assert last_response.ok?
end
def test_create_dataset
post '/datasets', :name => "Test dataset"
assert last_response.ok?
uri = last_response.body
assert_equal "http://example.org/dataset/Test%20dataset", uri
get uri
assert last_response.ok?
get uri + '/name'
puts last_response.body
assert last_response.ok?
assert_equal "Test dataset", last_response.body
delete uri
assert last_response.ok?
get uri
assert !last_response.ok?
end
def test_create_dataset_from_csv
smiles = 'CC(=O)Nc1scc(n1)c1ccc(o1)[N+](=O)[O-]'
compound = OpenTox::Compound.new(:smiles => smiles)
post '/datasets', :name => "Hamster Carcinogenicity"
uri = last_response.body
assert last_response.ok?
post uri + '/import', :file => Rack::Test::UploadedFile.new(File.join(File.dirname(__FILE__), "hamster_carcinogenicity.csv"), "text/csv"), :compound_format => "smiles"
get uri
assert last_response.ok?
get uri + '/compounds'
assert last_response.ok?
assert last_response.body.include?(compound.inchi)
get File.join(uri , 'compound', compound.inchi)
assert last_response.ok?
assert last_response.body.include?("Hamster%20Carcinogenicity/classification/true")
get File.join(uri , 'features')
puts last_response.body.to_yaml
delete uri
assert last_response.ok?
get uri
assert !last_response.ok?
end
=begin
def test_create_large_dataset_from_csv
post '/datasets', :name => "Salmonella Mutagenicity"
uri = last_response.body
post uri + '/import', :file => Rack::Test::UploadedFile.new(File.join(File.dirname(__FILE__), "kazius.csv"), "text/csv"), :compound_format => "smiles"
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 = {
'c1ccccc1' =>
#'[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
},
'CCCNN' =>
#'F[B-](F)(F)F.[Na+]' =>
{
'F' => 0.9,
'B' => 0.9,
'C' => 0.8,
'D' => 0.7,
'E' => 0.5
},
'C1CO1' =>
#'N#[N+]C1=CC=CC=C1.F[B-](F)(F)F' =>
{
'A' => 1.0,
'B' => 0.9,
'F' => 0.9,
}
}
post '/datasets', :name => name
assert last_response.ok?
uri = last_response.body
get uri
assert last_response.ok?
name = URI.encode(name)
feature_data = {}
data.each do |smiles,features|
compound = OpenTox::Compound.new(:smiles => smiles).uri
feature_data[compound] = []
features.each do |k,v|
feature= OpenTox::Feature.new(:name => k, :values => {:p_value => v}).uri
feature_data[compound] << feature
end
end
post uri , :features => feature_data.to_yaml
assert last_response.ok?
data.each do |smiles,features|
compound= OpenTox::Compound.new(:smiles => smiles).inchi
data.each do |s,f|
unless s == smiles
neighbor= OpenTox::Compound.new(:smiles => s).inchi
get "/dataset/#{name}/compounds"
assert last_response.ok?
get "/dataset/#{name}/compound/#{compound}"
assert last_response.ok?
get "/algorithm/tanimoto/dataset/#{name}/compound/#{compound}/dataset/#{name}/compound/#{neighbor}"
puts last_response.body
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 "/algorithm/weighted_tanimoto/dataset/#{name}/compound/#{compound}/dataset/#{name}/compound/#{neighbor}"
assert last_response.ok?
puts "weighted_tanimoto::#{smiles}::#{s}::#{last_response.body}"
end
end
end
end
end
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