Class: Inferno::Terminology::Tasks::RunUMLSJar

Inherits:
Object
  • Object
show all
Includes:
TempDir
Defined in:
lib/inferno/terminology/tasks/run_umls_jar.rb

Overview

More information on batch running UMLS www.nlm.nih.gov/research/umls/implementation_resources/community/mmsys/BatchMetaMorphoSys.html

Constant Summary collapse

VERSIONED_PROPS = 
{
  '2019' => 'inferno_2019.prop',
  '2020' => 'inferno_2020.prop',
  '2021' => 'inferno_2021.prop',
  '2022' => 'inferno_2022.prop',
  '2023' => 'inferno_2023.prop',
  '2024' => 'inferno_2024.prop'
}.freeze

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from TempDir

#pipe_files, #umls_dir, #umls_subset_dir, #umls_zip_path, #versioned_temp_dir

Constructor Details

#initialize(version:) ⇒ RunUMLSJar

Returns a new instance of RunUMLSJar.



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# File 'lib/inferno/terminology/tasks/run_umls_jar.rb', line 22

def initialize(version:)
  @version = version
end

Instance Attribute Details

#version ⇒ Object (readonly)

Returns the value of attribute version.



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# File 'lib/inferno/terminology/tasks/run_umls_jar.rb', line 20

def version
  @version
end

Instance Method Details

#platform ⇒ Object 



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# File 'lib/inferno/terminology/tasks/run_umls_jar.rb', line 66

def platform
  if !(/cygwin|mswin|mingw|bccwin|wince|emx/ =~ RUBY_PLATFORM).nil?
    'windows64'
  elsif !(/darwin/ =~ RUBY_PLATFORM).nil?
    'macos'
  else
    'linux'
  end
end

#run ⇒ Object 



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# File 'lib/inferno/terminology/tasks/run_umls_jar.rb', line 26

def run
  Inferno.logger.info "#{platform} system detected"
  config_file = File.join(Dir.pwd, 'resources', VERSIONED_PROPS[version])
  output_dir = File.join(Dir.pwd, versioned_temp_dir, 'umls_subset')
  FileUtils.mkdir(output_dir)

  Inferno.logger.info "Using #{config_file}"
  Dir.chdir(Dir[File.join(Dir.pwd, versioned_temp_dir, '/umls/20*')][0]) do
    Inferno.logger.info Dir.pwd
    Dir['lib/*.jar'].each do |jar|
      File.chmod(0o555, jar)
    end
    Dir["jre/#{platform}/bin/*"].each do |file|
      File.chmod(0o555, file)
    end

    Inferno.logger.info 'Running MetamorphoSys (this may take a while)...'
    output = system("./jre/#{platform}/bin/java " \
                    '-Djava.awt.headless=true ' \
                    '-cp .:lib/jpf-boot.jar ' \
                    '-Djpf.boot.config=./etc/subset.boot.properties ' \
                    '-Dlog4j.configuration=./etc/log4j.properties ' \
                    '-Dinput.uri=. ' \
                    "-Doutput.uri=#{output_dir} " \
                    "-Dmmsys.config.uri=#{config_file} " \
                    '-Xms300M -Xmx8G ' \
                    'org.java.plugin.boot.Boot')
    unless output
      Inferno.logger.info 'MetamorphoSys run failed'
      # The cwd at this point is 2 directories above where umls_subset
      # is, so we have to navigate up to it
      umls_subset_directory = File.join(Dir.pwd, '..', '..', 'umls_subset')
      FileUtils.remove_dir(umls_subset_directory) if File.directory?(umls_subset_directory)
      exit 1
    end
  end

  Inferno.logger.info 'done'
end