diff options
Diffstat (limited to 'test/test.rb')
| -rw-r--r-- | test/test.rb | 115 |
1 files changed, 99 insertions, 16 deletions
diff --git a/test/test.rb b/test/test.rb index 5c4b2e7..b1bae83 100644 --- a/test/test.rb +++ b/test/test.rb @@ -32,28 +32,39 @@ class DatasetsTest < Test::Unit::TestCase def test_create_dataset_and_insert_data name = "Test dataset" - smiles = '[O-][N+](=O)C/C=C\C(=O)Cc1cc(C#N)ccc1' - compound_uri = OpenTox::Compound.new(:smiles => smiles).uri - feature_uri = OpenTox::Feature.new(:name => name, :values => {:classification => "true"}).uri + 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") - put uri, :compound_uri => compound_uri, :feature_uri => feature_uri - assert last_response.ok? + + 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' - assert last_response.ok? - assert_equal compound_uri, last_response.body - get uri + '/features' - assert last_response.ok? - assert last_response.body.include?("true") - assert_equal feature_uri, last_response.body - get uri + '/' + compound_uri + '/features' - assert last_response.ok? - assert last_response.body.include?("true") - assert_equal feature_uri, last_response.body + #puts last_response.body delete uri assert last_response.ok? get "/Test_dataset" @@ -70,7 +81,11 @@ class DatasetsTest < Test::Unit::TestCase get uri + '/compounds' assert last_response.ok? assert last_response.body.include?(compound_uri) - get uri + '/' + compound_uri + '/features' + 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 @@ -86,7 +101,75 @@ class DatasetsTest < Test::Unit::TestCase 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? |