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namespace :renew do
desc "renews the triple store backend in case of damage or disfunction."
task :backend do
#TODO finish
require_relative '../setup.rb'
STDOUT.puts "Remind this command does not enable data save of a destroyed backend!"
STDOUT.puts "do you really want to proceed (y/n)"
answer = STDIN.gets.strip
case answer
when "y"
puts "delete"
when "n"
puts "exit"
else
puts "exit"
end
end
end
namespace :service_uri do
desc "Rewriting service uris for prediction models and components"
task :rewrite do
#TODO fix sed
STDOUT.puts "Please enter models directory name.\n#{`ls -d */`}\n"
input = STDIN.gets.strip
dir = File.join(File.dirname(File.expand_path __FILE__), input)
if File.directory?(dir)
STDOUT.puts "Directory found."
else
STDOUT.puts "Directory not found."
end
# change working directory
Dir.chdir dir
original = IO.readlines("logfile.txt")[1].gsub(/\/model\/[0-9a-f]{8}-([0-9a-f]{4}-){3}[0-9a-f]{12}$/, "")
STDOUT.puts "Service url is: #{original}\nPlease enter new service path:"
new = STDIN.gets.strip
if new != ""# and new.uri?
puts "processing with '#{new}'"
#cmd for rewriting service url
`sed -i 's,#{original},#{new},g' *.nt`
`sed -i 's,#{original},#{new},g' *.txt`
else
STDOUT.puts "Original service url is #{}.\nPlease enter new service url:"
end
end #task
end #namespace
namespace :save do
desc "Save models used to predict compounds"
task :prediction_models do
require_relative '../setup.rb'
d = Time.new
date = d.strftime("%d-%m-%Y_%H-%M-%S")
dir = File.join File.dirname(File.expand_path __FILE__), "models_save_#{date}"
puts "Created dir 'models_save_#{date}'."
`mkdir #{dir}`
File.new("#{dir}/logfile.txt", "w")
File.new("#{dir}/details.txt", "w")
models = `curl -Lk -X GET -H accept:text/plain #{$model[:uri]}`.chomp.split("\n")
model_uris = models.collect{|m| m.split(" ").first.gsub(/\<|\>/, "")}
puts "#{model_uris.size} models found." unless model_uris.size == 0
puts "-----------------------------"
puts "service uri is: #{$model[:uri]}"
model_uris.each_with_index do |model_uri, idx|
# get model by uri
model = OpenTox::Model::Lazar.find "#{model_uri}"
puts "model details:\n#{model.metadata}\n"
if model.type.include?(RDF::OT.PredictionModel)
# store model as nt file
`curl -Lk -X GET -H accept:text/plain #{model_uri} -o #{dir}/model_#{idx}.nt`.chomp
puts "model #{idx}:\t#{model.title} stored."
# write to logfile
File.open("#{dir}/logfile.txt", 'a'){|f| f.write("model_#{idx}\n#{model_uri}\n\n")}
# write details
File.open("#{dir}/details.txt", 'a'){|f| f.write("ID:\tmodel_#{idx}\ntitle:\t#{model.title}\nuri:\t#{model_uri}\n---\n")}
# get models features
model_features = []
model_features << model[RDF::OT.dependentVariables]
model_features << model[RDF::OT.predictedVariables]
puts "#{model_features.flatten.size} features for model #{idx} found."
model_features.flatten!.each_with_index do |uri, i|
`curl -Lk -X GET -H accept:text/plain #{uri} -o #{dir}/feature_#{i}_model#{idx}.nt`.chomp
# write to logfile
File.open("#{dir}/logfile.txt", 'a'){|f| f.write("feature_#{i}_model#{idx}\n#{uri}\n\n")}
puts "model feature #{i} stored."
end
puts " | | "
# get all datasets and single dataset features
puts "collect datasets."
[model[RDF::OT.trainingDataset], model[RDF::OT.featureDataset]].each_with_index do |dataset_uri, index|
if index == 0
which = "trainingDataset"
else
which = "featureDataset"
end
# get dataset
dataset = OpenTox::Dataset.find "#{dataset_uri}"
# store dataset
puts "#{which}: #{dataset_uri}"
`curl -Lk -X GET -H accept:text/plain #{dataset_uri} -o #{dir}/#{which}_model_#{idx}.nt`.chomp
puts "#{which} of model #{idx} stored."
# write to logfile
File.open("#{dir}/logfile.txt", 'a'){|f| f.write("#{which}_model_#{idx}\n#{dataset_uri}\n\n")}
features =[]
feature_uris =[]
dataset.features.each{|f| features << f}
features.each{|f| feature_uris << f.uri}
# store each feature as file
feature_uris.each_with_index do |uri, i|
`curl -Lk -X GET -H accept:text/plain #{uri} -o #{dir}/feature_#{i}_#{which}_model_#{idx}.nt`.chomp
puts "feature #{i} of #{which} stored."
# write to logfile
File.open("#{dir}/logfile.txt", 'a'){|f| f.write("feature_#{i}_#{which}_model_#{idx}\n#{uri}\n\n")}
end
end
else
puts "ignore #{model.title}, is no prediction model."
end
puts "#######################################"
end
puts "------------------------------\n"
puts "all prediction models from #{$model[:uri]} locally stored !"
puts "------------------------------\n"
puts "Execute 'rake models:rewrite' to set a new service uri inside the saved models and components."
end # task
end # namespace
namespace :prediction_models do
desc "Imports local models to service backend."
task :import do
require_relative "../setup.rb"
require File.join "../../../opentox-server/lib/4store.rb"
pair = {}
#files = Dir["models_save/*.nt"]
STDOUT.puts "Please enter models directory name.\n#{`ls -d */`}\n"
input = STDIN.gets.strip
dir = File.join(File.dirname(File.expand_path __FILE__), input)
if File.directory?(dir)
STDOUT.puts "Directory found."
else
STDOUT.puts "Directory not found."
end
files = Dir["#{input}/*.nt"]
# change working directory
Dir.chdir dir
uris = File.read(File.join "logfile.txt")
uris.split("\n\n").each do |u|
pair["#{u.split.first}"] = u.split.last
end
files.each do |file|
file = file.split("/").last
f = file.split("/").last.gsub(".nt", "")
puts "file:\t#{file}\ntarget:\t#{pair[f]}\n"
OpenTox::Backend::FourStore.put pair[f].to_s, File.read(file), "text/plain"
puts "imported."
end
end #task
end #namespace
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