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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
`if [ -d dump/#{ENV["LAZAR_ENV"]} ]; then rm -Rf dump/#{ENV["LAZAR_ENV"]}; fi`
# 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)}`
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