Module: BioInterchange

Defined in:

lib/biointerchange/core.rb,
lib/biointerchange/so.rb,
lib/biointerchange/sio.rb,
lib/biointerchange/cdao.rb,
lib/biointerchange/gfvo.rb,
lib/biointerchange/sofa.rb,
lib/biointerchange/faldo.rb,
lib/biointerchange/model.rb,
lib/biointerchange/goxref.rb,
lib/biointerchange/reader.rb,
lib/biointerchange/writer.rb,
lib/biointerchange/registry.rb,
lib/biointerchange/life_science_registry.rb

Overview

BioInterchange converts non-RDF data formats into RDF.

Convert TSV, XML, GFF3, GVF and other files into RDF triples using BioInterchange’s command-line tool, its web-services or make use of it as a gem in your own Ruby implementation.

Defined Under Namespace

Modules: Exceptions, Genomics, Phylogenetics, TextMining Classes: CDAO, FALDO, GFVO, GOXRef, LifeScienceRegistry, Model, Reader, Registry, SIO, SO, SOFA, Writer

Constant Summary

@@evaluation =

If true, then RDF::Graph’s & co will be used. Should only be applied for performance comparisons between the “standard” Ruby gem implementation and BioInterchange’s optimized RDF handling.

false

@@format =

BioInterchange can output RDF in two formats: Turtle (default) and N-Triples. The two corresponding Ruby constants for these two output formats are:

Turtle:    `:turtle`
N-Triples: `:ntriples`

:turtle

@@default_uri_prefix =

Default URI prefix that is used when RDFizing data:

''

@@default_batch_size =

If input/rdf options permit batching, but no batchsize has been provided by the user, then use this default batch size.

100

Class Method Summary

• .cli ⇒ Object
• .evaluation ⇒ Object
• .format ⇒ Object
• .get_parameters(map, parameters) ⇒ Object

  Returns the values of several named parameters.

• .make_safe_label(label) ⇒ Object

  Returns a “safe” version of a label that can be used as a Ruby method name.

Class Method Details

.cli ⇒ Object

# File 'lib/biointerchange/core.rb', line 140

def self.cli
  begin
    opts = [
      ["--help", "-h", Getopt::BOOLEAN],
      ["--debug", "-d", Getopt::BOOLEAN],                     # set debug mode => print stack traces
      ["--batchsize", "-b", Getopt::OPTIONAL],                # batchsize for readers/writers that support +postpone?+
      ["--ntriples", "-n", Getopt::BOOLEAN],                  # produce N-Triples instead of Turtle
      ["--evaluation", "-z", Getopt::BOOLEAN],                # use RDF gem implementation for mem/speed comparison
      ["--uri", "-u", Getopt::OPTIONAL],                      # URI prefix to use when serializing RDF
      ["--input", "-i", Getopt::REQUIRED],                    # input file format
      ["--rdf", "-r", Getopt::REQUIRED],                      # output file format
      ["--file", "-f", Getopt::OPTIONAL],                     # file to read, will read from STDIN if not supplied
      ["--out", "-o", Getopt::OPTIONAL],                      # output file, will out to STDOUT if not supplied
      ["--version", "-v", Getopt::BOOLEAN]                    # output the version number of the gem and exit
    ]
    reader_writer_pairs = Registry.reader_writer_pairs
    reader_writer_pairs.each_index { |reader_writer_pair_index|
      reader_id, writer_id = reader_writer_pairs[reader_writer_pair_index]
      Registry.options_help(reader_id).each { |option_description|
        option, description = option_description
        opts |= [ [ "--annotate_#{option.sub(/\s.*$/, '')}", Getopt::OPTIONAL ] ]
      }
    }
    opt = Getopt::Long.getopts(*opts)
    
    if opt['help'] or not (opt['input'] and opt['rdf'] or opt['version']) then
      puts "Usage: ruby #{$0} -i <format> -r <format> [options]"
      puts ''
      puts 'Supported input formats (--input <format>/-i <format>):'
      Registry.reader_descriptions.each_pair { |reader_id, description|
        puts "  #{reader_id}#{' ' * (34 - reader_id.length)} : #{description}"
      }
      puts ''
      puts 'Supported output formats (--rdf <format>/-r <format>)'
      Registry.writer_descriptions.each_pair { |writer_id, description|
        puts "  #{writer_id}#{' ' * (34 - writer_id.length)} : #{description}"
      }
      puts ''
      puts 'I/O options:'
      puts '  -f <file> / --file <file>          : file to read; STDIN used if not supplied'
      puts '  -o <file> / --out <file>           : output file; STDOUT used if not supplied'
      puts '  -n / --ntriples                    : output RDF N-Triples (instead of RDF Turtle)'
      puts '  -u <uri> / --uri <prefix>          : URI prefix to use'
      puts "                                       (default: #{@@default_uri_prefix})"
      puts '  -b <size>/--batchsize <size>       : process input in batches of the given size'
      puts '                                      (if supported, see below for valid input/rdf pairs;'
      puts "                                       if supported, but not set, default value is #{@@default_batch_size})"
      puts ''
      puts 'Other options:'
      puts '  -v / --version                     : print the Gem\'s version number and exit'
      puts '  -d / --debug                       : turn on debugging output (for stacktraces)'
      puts '  -z / --evaluation                  : use \'RDF\' gem implementation (slow & memory intensive,'
      puts '                                       only included for performance evaluation comparisons)'
      puts '  -h  --help                         : this message'
      puts ''
      puts 'Input-/output-format specific options:'
      reader_writer_pairs.each_index { |reader_writer_pair_index|
        reader_id, writer_id = reader_writer_pairs[reader_writer_pair_index]
        puts "  Input format  : #{reader_id}"
        puts "  Output format : #{writer_id}"
        Registry.options_help(reader_id).each { |option_description|
          option, description = option_description
          puts "    --annotate_#{option}#{' ' * (21 - option.length)} : #{description}"
        }
        puts '' if reader_writer_pair_index + 1 < reader_writer_pairs.length
      }
    
      exit 1
    end
    
    # Print version number and exit:
    if opt['version'] then
      puts "BioInterchange #{Gem.loaded_specs["biointerchange"].version}"
      exit
    end

    # Turn off optimization, if requested. This will generate an RDF graph in memory and
    # at least double memory requirements and runtime.
    @@evaluation = true if opt['evaluation']

    # Switch to N-Triples output:
    @@format = :ntriples if opt['ntriples']

    # Check if the input/rdf options are supported:
    unsupported_combination unless Registry.is_supported?(opt['input'], opt['rdf'])
    
    # If a batchsize is given, then use it. Otherwise, check if the input/rdf combination
    # supports batching and set a default batch value.
    if opt['batchsize'] then
      batching_not_supported unless Registry.is_supporting_batch_processing?(opt['input'], opt['rdf'])
      wrong_type('batchsize', 'a positive integer') unless opt['batchsize'].match(/^[1-9][0-9]*$/)
    elsif Registry.is_supporting_batch_processing?(opt['input'], opt['rdf']) then
      opt['batchsize'] = @@default_batch_size
    end

    # Create a parameter map that can be passed along to Reader implementations:
    map = {
      'input'  => opt['input'],
      'output' => opt['output']
    }
    map['batch_size'] = opt['batchsize'].to_i if opt['batchsize']
    opt.each_key { |key|
      map[key.sub(/^annotate_/, '')] = opt[key] if key.start_with?('annotate_')
    }

    # Generate model from file (deserialization).
    reader_class, *args = Registry.reader(opt['input'])
    reader = reader_class.new(*BioInterchange::get_parameters(map, args))
  
    input_source = nil
    if opt['file'] then
      input_source = File.new(opt['file'], 'r')
    else
      input_source = STDIN
    end
  
    output_source = nil
    if opt['out'] then
      output_source = File.new(opt['out'], 'w')
    else
      output_source = STDOUT
    end

    # Generate rdf from model (serialization).
    writer = Registry.writer(opt['rdf']).new(output_source)
    
    begin
      model = reader.deserialize(input_source)
      writer.serialize(model, opt['uri'])
    end while reader.postponed?

  rescue Interrupt
    # The user hit Ctrl-C, which is okay and does not need error reporting.
    exit 0
  rescue ArgumentError => e
    $stderr.puts e.message
    $stderr.puts e.backtrace if opt['debug']
    exit 1
  rescue Getopt::Long::Error => e
    $stderr.puts e.message
    #$stderr.puts e.backtrace if opt['debug']
    exit 1
  rescue BioInterchange::Exceptions::InputFormatError => e
    $stderr.puts e.message
    $stderr.puts e.backtrace if opt['debug']
    exit 2
  end
end

.evaluation ⇒ Object

# File 'lib/biointerchange/core.rb', line 14

def self.evaluation
  @@evaluation
end

.format ⇒ Object

# File 'lib/biointerchange/core.rb', line 23

def self.format
  @@format
end

.get_parameters(map, parameters) ⇒ Object

Returns the values of several named parameters.

map

a map of named parameters and their values

parameters

the names of the parameter values we are interested in

# File 'lib/biointerchange/core.rb', line 297

def self.get_parameters(map, parameters)
  parameters.map { |parameter|
    if parameter.instance_of? Array then
      parameter[0].call(*BioInterchange::get_parameters(map, parameter[1..-1]))
    else
      map[parameter]
    end
  }
end

.make_safe_label(label) ⇒ Object

Returns a “safe” version of a label that can be used as a Ruby method name.

label

string that should be converted into a “safe” string that can be used as a Ruby method name

# File 'lib/biointerchange/core.rb', line 310

def self.make_safe_label(label)
  label.gsub(/[ '-.<>\/]/, '_').gsub(/\([^\)]*?\)/, '').sub(/^(\d+)/){ "a_#{$1}" }.gsub(/^_+|_+$/, '').gsub(/_+/, '_')
  # This additional call pulled together "whatever_ABC" to "whateverABC";
  # not clear why: .gsub(/_([A-Z]+)/x){ "#{$1}" }
end