added file to test automatic build

1 files changed, 104 insertions, 0 deletions

diff --git a/create_test_prediction_models.rb b/create_test_prediction_models.rb
new file mode 100644
index 0000000..4fc2412
--- /dev/null
+++ b/create_test_prediction_models.rb
@@ -0,0 +1,104 @@
+ENV["LAZAR_ENV"] = "production"
+require_relative '../lazar/lib/lazar'
+#require 'lazar'
+include OpenTox
+$mongo.database.drop
+$gridfs = $mongo.database.fs # recreate GridFS indexes
+
+@models = OpenTox::Model::Validation.all
+
+def delete_models type
+  case type
+  when "classification"
+    models = @models.delete_if{|m| !m.classification?}
+  when "regression"
+    models = @models.delete_if{|m| !m.regression?}
+  else
+    puts "Unknown model type #{type}"
+    exit
+  end
+  models.each do |m|
+    m.training_dataset.delete
+    m.crossvalidations.each{|cv| cv.delete}
+    m.model.delete
+    m.delete
+  end unless models.empty?
+end
+
+puts CENTRAL_MONGO_IP.blank? ? "Use local mongodb on port: 127.0.0.1" : "Use central mongodb on port: #{CENTRAL_MONGO_IP}"
+
+#=begin
+# classification models
+#delete_models "classification"
+Dir["classification/*csv"].each do |file|
+  if file.match(/hamster/i)
+    puts "### #{file} ###\n"
+    Model::Validation.from_csv_file file
+  end
+  puts "### done: #{file} ###\n"
+end
+#=end
+
+=begin
+# regression models
+#delete_models "regression"
+Dir["regression/*log10.csv"].each do |file|
+  unless file.match(/fathead/)#until dublicates not cleared
+    puts "### #{file} ###\n"
+    Model::Validation.from_csv_file file
+  end
+  puts "### done: #{file} ###\n"
+end
+=end
+
+## nano-lazar
+=begin
+
+# creates 3 models: one with physchem, one with proteomics, one with fingerprints
+feature_categories = ["fingerprint", "P-CHEM", "Proteomics"]
+
+feature_categories.each do |category|
+  if category == "fingerprint"
+		algorithms = {
+			:descriptors => { :method => "fingerprint", :type => "MP2D", },
+			:feature_selection => nil,
+			:similarity => {
+				:method => "Algorithm::Similarity.tanimoto",
+				:min => 0.1
+			}
+		}
+		
+		OpenTox::Model::Validation.from_enanomapper algorithms: algorithms
+	else
+		algorithms = {
+			:descriptors => {
+				:method => "properties",
+				:categories => (category.is_a?(Array) ? [category].flatten : [category]),
+			},
+			:similarity => {
+				:method => "Algorithm::Similarity.weighted_cosine",
+				:min => 0.5
+			},
+			:prediction => {
+				:method => "Algorithm::Caret.rf",
+			},
+			:feature_selection => {
+				:method => "Algorithm::FeatureSelection.correlation_filter",
+			},
+		}
+
+		OpenTox::Model::Validation.from_enanomapper algorithms: algorithms
+	end
+end
+=end
+
+# remove existing local dump
+`rm -r dump/#{ENV["LAZAR_ENV"]}`
+# store local dump but git ignored
+`mongodump -h #{CENTRAL_MONGO_IP.blank? ? "127.0.0.1" : CENTRAL_MONGO_IP} -d #{ENV["LAZAR_ENV"]}`
+
+# build reports and users dump
+eval File.read('./lazar_validation_reports.rb')
+
+# restore
+#`mongorestore --host #{(CENTRAL_MONGO_IP.blank? ? "127.0.0.1" : CENTRAL_MONGO_IP)}`