Class: Inferno::Terminology::Tasks::UnzipUMLS

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

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:) ⇒ UnzipUMLS

Returns a new instance of UnzipUMLS.



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# File 'lib/inferno/terminology/tasks/unzip_umls.rb', line 12

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/unzip_umls.rb', line 10

def version
  @version
end

Instance Method Details

#run ⇒ Object 



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# File 'lib/inferno/terminology/tasks/unzip_umls.rb', line 16

def run
  # https://stackoverflow.com/questions/19754883/how-to-unzip-a-zip-file-containing-folders-and-files-in-rails-while-keeping-the
  Zip::File.open(umls_zip_path) do |zip_file|
    # Handle entries one by one
    zip_file.each do |entry|
      # Extract to file/directory/symlink
      Inferno.logger.info "Extracting #{entry.name}"
      f_path = File.join(umls_dir, entry.name)
      FileUtils.mkdir_p(File.dirname(f_path))
      zip_file.extract(entry, f_path) unless File.exist?(f_path)
    end
  end

  wildcard_path = "#{umls_dir}/20*"
  Zip::File.open(File.expand_path("#{Dir[wildcard_path][0]}/mmsys.zip")) do |zip_file|
    zip_file.each do |entry|
      Inferno.logger.info "Extracting #{entry.name}"
      f_path = File.join((Dir[wildcard_path][0]).to_s, entry.name)
      FileUtils.mkdir_p(File.dirname(f_path))
      zip_file.extract(entry, f_path) unless File.exist?(f_path)
    end
  end
end