ontohub/lib/hets.rb

	hets.rb revision a837d007b255d7a6cca7994e1e555aba95ce41cc
require 'date'

module Hets
  class HetsError < Exception; end
  class HetsDeploymentError < Exception; end
  class HetsNotFoundError < HetsError; end
  class HetsVersionOutdatedError < HetsError; end
  class HetsConfigDateFormatError < HetsError; end
  class HetsVersionDateFormatError < HetsError; end

  EXTENSIONS = %w(casl clf clif dg dol het hol hs kif owl rdf spcf thy)

  class Config
    attr_reader :path, :library_path

    def initialize
      yaml = YAML.load_file(File.join(Rails.root, 'config', 'hets.yml'))

      @path = first_which_exists yaml['hets_path']

      raise HetsNotFoundError, 'Could not find hets' unless @path

      unless is_compatible? yaml['hets_version_minimum_date']
        raise HetsVersionOutdatedError, 'The installed version of Hets is too old'
      end

      # Set hets environment variables for when the wrapper script is not used.
      yaml.each_pair do |key, value|
        if key != 'hets_path' and value.is_a? Array
          ENV[key.upcase] = first_which_exists value
        end
      end

      @library_path = first_which_exists yaml['hets_lib']

      raise HetsDeploymentError, 'Hets library not found.' unless @library_path
    end

  private

    # Checks Hets installation compatibility by its version date
    #
    # * *Args* :
    # * - +minimum_date+ -> Minimum working hets version date
    # * *Returns* :
    # * - true if hets version minimum date prior or equal to actual hets version date
    # * - false otherwise
    def is_compatible?(minimum_date)
      # Read Hets version minimum date
      raise HetsConfigDateFormatError, 'Could not read hets version minimum date in YAML' unless minimum_date

      # Read Hets version date
      version = `#{@path} -V`
      version_date = begin
        Date.parse version.split.last
      rescue ArgumentError
        nil
      end

      raise HetsVersionDateFormatError, 'Could not read hets version date in output of `hets -V`' unless version_date

      # Return true if minimum date is prior or equal to version date
      return minimum_date <= version_date
    end

    def first_which_exists(paths)
      paths.map { |path| File.expand_path path }.each do |path|
        return path if File.exists? path
      end

      nil
    end
  end

  # Runs hets with input_file and returns XML output file path.
  def self.parse(input_file, output_path = '')
    @@config ||= Config.new

    output_path = "-O \"#{output_path}\"" unless output_path.blank?

    command = "#{@@config.path} -o xml --full-signatures -v2 #{output_path} '#{input_file}' 2>&1"

    Rails.logger.debug command

    # Executes command with low priority
    output = `nice #{command}`

    # Exclude usage message if exit status equals 2
    if $?.exitstatus == 2 and output.include? 'Usage:'
      output = output.split("Usage:").first
    end

    output = output.split("\n").last
    Rails.logger.debug output

    # Raise error if exit status different from 0
    if $?.exitstatus != 0 or output.starts_with? '*** Error'
      raise HetsError.new(output)
    end

    return output.split(': ').last
  end

  # Traverses a directory for ontologies with supported extensions recursively,
  # yielding their path.
  def self.find_ontologies(dir)
    EXTENSIONS.each do |extension|
      Dir.glob("#{dir}/**/*.#{extension}").each { |path| yield path }
    end
  end

  # Traverses a directory recursively, importing ontology file with supported
  # extension.
  #
  # @param user [User] the user that imports the ontology files
  # @param dir  [String] the path to the ontology library
  #
  def self.import_ontologies(user, dir)
    find_ontologies(dir) { |path| import_ontology(user, path) }
  end

  # Imports an ontology in demand of a user.
  #
  # @param user [User] the user that imports the ontology file
  # @param file_path [String] the path to the ontology file
  # @param extension [String] the extension of the ontology file
  #
  def self.import_ontology(user, path)
    puts path

    o = Ontology.new
    # TODO Use custom ontology iris detached from the local file system
    o.iri = "file://#{path}"
    o.name = File.basename(path, ".#{extension}")
    begin
      o.save!
    rescue
      puts "ERROR: " + o.name + " <" + o.iri + ">"
      return
    end

    ov = OntologyVersion.new
    ov.user = user
    ov.raw_file = File.open path
    ov.ontology = ontology
    ov.save!

    ov.async :parse
  end

end