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authorChristoph Helma <helma@in-silico.ch>2017-01-12 17:57:03 +0100
committerChristoph Helma <helma@in-silico.ch>2017-01-12 17:57:03 +0100
commitd7504cc422bbaeee3546589d87e7baeb4e977c0b (patch)
treef5c06159d0a529f263ea25f6354f89825fc41410 /test
parent85553b339acf3f9285a1c03b2fff342d9ddb9b6b (diff)
source uris for core and coating
Diffstat (limited to 'test')
-rw-r--r--test/feature.rb4
-rw-r--r--test/model-nanoparticle.rb7
-rw-r--r--test/nanomaterial-model-validation.rb5
-rw-r--r--test/validation-regression.rb5
4 files changed, 13 insertions, 8 deletions
diff --git a/test/feature.rb b/test/feature.rb
index 533ac0f..40edb9f 100644
--- a/test/feature.rb
+++ b/test/feature.rb
@@ -55,7 +55,7 @@ class FeatureTest < MiniTest::Test
end
def test_physchem_description
- assert_equal 355, PhysChem.descriptors.size
+ assert_equal 346, PhysChem.descriptors.size
assert_equal 15, PhysChem.openbabel_descriptors.size
assert_equal 295, PhysChem.cdk_descriptors.size
assert_equal 45, PhysChem.joelib_descriptors.size
@@ -63,7 +63,7 @@ class FeatureTest < MiniTest::Test
end
def test_physchem
- assert_equal 355, PhysChem.descriptors.size
+ assert_equal 346, PhysChem.descriptors.size
c = Compound.from_smiles "CC(=O)CC(C)C"
logP = PhysChem.find_or_create_by :name => "Openbabel.logP"
assert_equal 1.6215, logP.calculate(c)
diff --git a/test/model-nanoparticle.rb b/test/model-nanoparticle.rb
index 8dc6830..67bbfdd 100644
--- a/test/model-nanoparticle.rb
+++ b/test/model-nanoparticle.rb
@@ -8,6 +8,13 @@ class NanoparticleModelTest < MiniTest::Test
@prediction_feature = @training_dataset.features.select{|f| f["name"] == 'log2(Net cell association)'}.first
end
+ def test_core_coating_source_uris
+ @training_dataset.nanoparticles.each do |np|
+ refute_nil np.core.source
+ np.coating.each{|c| refute_nil c.source}
+ end
+ end
+
def test_nanoparticle_model
assert true, @prediction_feature.measured
model = Model::Lazar.create training_dataset: @training_dataset, prediction_feature: @prediction_feature
diff --git a/test/nanomaterial-model-validation.rb b/test/nanomaterial-model-validation.rb
index b91c389..9eaa17d 100644
--- a/test/nanomaterial-model-validation.rb
+++ b/test/nanomaterial-model-validation.rb
@@ -8,7 +8,7 @@ class NanomaterialValidationModelTest < MiniTest::Test
end
def test_default_nanomaterial_validation_model
- validation_model = Model::NanoValidation.create
+ validation_model = Model::Validation.from_enanomapper
[:endpoint,:species,:source].each do |p|
refute_empty validation_model[p]
end
@@ -39,7 +39,7 @@ class NanomaterialValidationModelTest < MiniTest::Test
:prediction => { :method => "OpenTox::Algorithm::Regression.weighted_average" },
:feature_selection => nil
}
- validation_model = Model::NanoValidation.create algorithms: algorithms
+ validation_model = Model::Validation.from_enanomapper algorithms: algorithms
assert validation_model.regression?
refute validation_model.classification?
validation_model.crossvalidations.each do |cv|
@@ -50,6 +50,5 @@ class NanomaterialValidationModelTest < MiniTest::Test
assert_includes nanoparticle.dataset_ids, @training_dataset.id
prediction = validation_model.predict nanoparticle
refute_nil prediction[:value]
- assert_includes prediction[:prediction_interval][0]..prediction[:prediction_interval][1], prediction[:measurements].median, "This assertion assures that measured values are within the prediction interval. It may fail in 5% of the predictions."
end
end
diff --git a/test/validation-regression.rb b/test/validation-regression.rb
index 7630521..01ed644 100644
--- a/test/validation-regression.rb
+++ b/test/validation-regression.rb
@@ -83,10 +83,9 @@ class ValidationRegressionTest < MiniTest::Test
model = Model::Lazar.create training_dataset: dataset
repeated_cv = RepeatedCrossValidation.create model
repeated_cv.crossvalidations.each do |cv|
- #assert cv.r_squared > 0.34, "R^2 (#{cv.r_squared}) should be larger than 0.034"
- #assert_operator cv.accuracy, :>, 0.7, "model accuracy < 0.7, this may happen by chance due to an unfavorable training/test set split"
+ assert cv.r_squared > 0.34, "R^2 (#{cv.r_squared}) should be larger than 0.034"
+ assert_operator cv.accuracy, :>, 0.7, "model accuracy < 0.7, this may happen by chance due to an unfavorable training/test set split"
end
- File.open("tmp.png","w+"){|f| f.puts repeated_cv.correlation_plot}
end
end