From 611bac891177f8d9185d45486dd574b6ef4d1912 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Mon, 9 May 2016 15:11:46 +0200
Subject: nanoparticle models fixed

---
 test/nanoparticles.rb | 95 +++++++++++++++++++++------------------------------
 1 file changed, 38 insertions(+), 57 deletions(-)

(limited to 'test/nanoparticles.rb')

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
-- 
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