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-rw-r--r--test/nanoparticles.rb95
1 files changed, 38 insertions, 57 deletions
diff --git a/test/nanoparticles.rb b/test/nanoparticles.rb
index 6d91103..2082ec4 100644
--- a/test/nanoparticles.rb
+++ b/test/nanoparticles.rb
@@ -4,66 +4,12 @@ require_relative "setup.rb"
class NanoparticleTest < MiniTest::Test
def setup
+ Import::Enanomapper.import File.join(File.dirname(__FILE__),"data","enm")
#`mongorestore --db=development #{File.join(File.dirname(__FILE__),"..","dump","production")}`
end
- def test_mirror
- Import::Enanomapper.mirror File.join(File.dirname(__FILE__),"..","data")
- end
-
- def test_import
- Import::Enanomapper.import File.join(File.dirname(__FILE__),"..","data")
-# skip
-# dataset_ids = Import::Enanomapper.import
-# assert_operator Nanoparticle.count , :>, 570, "Only #{Nanoparticle.count} nanoparticles imported"
-# assert_operator dataset_ids.size, :>, 8, "Only #{dataset_ids.size} bundles imported"
-# assert dataset_ids.collect{|d| Dataset.find(d).name}.include? ("NanoWiki")
-# assert dataset_ids.collect{|d| Dataset.find(d).name}.include? ("Protein Corona Fingerprinting Predicts the Cellular Interaction of Gold and Silver Nanoparticles")
-# p dataset_ids.collect{|d| {d => Dataset.find(d).name}}
-# dataset_ids.collect do |d|
-# d = Dataset.find(d)
- #p d.name
- #puts d.to_csv
-# end
- end
-
- def test_summaries
- skip
- features = Feature.all.to_a
- #p features.collect do |f|
- #f if f.category == "TOX"
- #end.to_a.flatten.size
- toxcounts = {}
- pccounts = {}
- Nanoparticle.all.each do |np|
- np.toxicities.each do |t,v|
- toxcounts[t] ||= 0
- toxcounts[t] += 1#v.uniq.size
- end
- np.physchem_descriptors.each do |t,v|
- pccounts[t] ||= 0
- pccounts[t] += 1#v.uniq.size
- end
- end
- #puts counts.keys.collect{|i| Feature.find(i)}.to_yaml
- #pccounts.each{|e,n| p Feature.find(e),n if n > 100}
- #p toxcounts.collect{|e,n| Feature.find(e).name if n > 1}.uniq
- toxcounts.each{|e,n| p Feature.find(e),n if n > 100}
- end
-
-
- def test_import_ld
- skip
- dataset_ids = Import::Enanomapper.import_ld
- end
-
- def test_export
- Dataset.all.each do |d|
- puts d.to_csv
- end
- end
-
def test_create_model_with_feature_selection
+ skip
training_dataset = Dataset.find_or_create_by(:name => "Protein Corona Fingerprinting Predicts the Cellular Interaction of Gold and Silver Nanoparticles")
feature = Feature.find_or_create_by(name: "7.99 Toxicity (other) ICP-AES", category: "TOX", unit: "mL/ug(Mg)")
model = Model::LazarRegression.create(feature, training_dataset, {:prediction_algorithm => "OpenTox::Algorithm::Regression.local_physchem_regression", :neighbor_algorithm => "nanoparticle_neighbors"})
@@ -80,7 +26,6 @@ class NanoparticleTest < MiniTest::Test
feature = Feature.find_or_create_by(name: "7.99 Toxicity (other) ICP-AES", category: "TOX", unit: "mL/ug(Mg)")
model = Model::LazarRegression.create(feature, training_dataset, {:prediction_algorithm => "OpenTox::Algorithm::Regression.local_physchem_regression", :neighbor_algorithm => "nanoparticle_neighbors"})
nanoparticle = training_dataset.nanoparticles[-34]
- #p nanoparticle.neighbors
prediction = model.predict nanoparticle
p prediction
#p prediction
@@ -97,4 +42,40 @@ class NanoparticleTest < MiniTest::Test
p cv
end
+ def test_export
+ skip
+ Dataset.all.each do |d|
+ puts d.to_csv
+ end
+ end
+
+ def test_summaries
+ skip
+ features = Feature.all.to_a
+ #p features.collect do |f|
+ #f if f.category == "TOX"
+ #end.to_a.flatten.size
+ toxcounts = {}
+ pccounts = {}
+ Nanoparticle.all.each do |np|
+ np.toxicities.each do |t,v|
+ toxcounts[t] ||= 0
+ toxcounts[t] += 1#v.uniq.size
+ end
+ np.physchem_descriptors.each do |t,v|
+ pccounts[t] ||= 0
+ pccounts[t] += 1#v.uniq.size
+ end
+ end
+ #puts counts.keys.collect{|i| Feature.find(i)}.to_yaml
+ #pccounts.each{|e,n| p Feature.find(e),n if n > 100}
+ #p toxcounts.collect{|e,n| Feature.find(e).name if n > 1}.uniq
+ toxcounts.each{|e,n| p Feature.find(e),n if n > 100}
+ end
+
+
+ def test_import_ld
+ skip
+ dataset_ids = Import::Enanomapper.import_ld
+ end
end