module GnCrossmap

Namespace module for crossmapping checklists wth GN sources

rubocop:disable Metrics/ClassLength

Namespace module for crossmapping checklists to GN sources

Constants

INPUT_MODE
MATCH_TYPES
OUTPUT_MODE
VERSION

Attributes

logger[W]

Public Class Methods

find_id(row, name) click to toggle source

# File lib/gn_crossmap.rb, line 65
def find_id(row, name)
  if row.key?(:taxonid) && row[:taxonid]
    row[:taxonid].to_s.strip
  else
    GnUUID.uuid(name.to_s)
  end
end

log(message) click to toggle source

# File lib/gn_crossmap.rb, line 61
def log(message)
  logger.info(message)
end

logger() click to toggle source

rubocop:enable all

# File lib/gn_crossmap.rb, line 57
def logger
  @logger ||= Logger.new(STDERR)
end

opts_struct(opts) click to toggle source

# File lib/gn_crossmap.rb, line 73
def opts_struct(opts)
  resolver_url = "http://resolver.globalnames.org/name_resolvers.json"
  threads = opts[:threads].to_i
  opts[:threads] = threads.between?(1, 10) ? threads : 2
  with_classification = opts[:with_classification] ? true : false
  opts[:with_classification] = with_classification
  data_source_id = opts[:data_source_id].to_i
  opts[:data_source_id] = data_source_id.zero? ? 1 : data_source_id
  OpenStruct.new({ stats: Stats.new, alt_headers: [],
                   resolver_url: resolver_url }.merge(opts))
end

run(opts) click to toggle source

rubocop:disable Metrics/AbcSize

# File lib/gn_crossmap.rb, line 44
def run(opts)
  opts = opts_struct(opts)
  input_io, output_io = io(opts.input, opts.output)
  reader = create_reader(input_io, opts)
  data = block_given? ? reader.read(&Proc.new) : reader.read
  writer = create_writer(reader, output_io, opts)
  resolver = Resolver.new(writer, opts)
  block_given? ? resolver.resolve(data, &Proc.new) : resolver.resolve(data)
  resolver.stats
end

version() click to toggle source

# File lib/gn_crossmap/version.rb, line 7
def self.version
  VERSION
end

Private Class Methods

create_reader(input_io, opts) click to toggle source

# File lib/gn_crossmap.rb, line 92
def create_reader(input_io, opts)
  Reader.new(input_io, input_name(opts.input),
             opts.skip_original, opts.alt_headers, opts.stats)
end

create_writer(reader, output_io, opts) click to toggle source

# File lib/gn_crossmap.rb, line 87
def create_writer(reader, output_io, opts)
  Writer.new(output_io, reader.original_fields,
             output_name(opts.output), opts.with_classification)
end

input_name(input) click to toggle source

# File lib/gn_crossmap.rb, line 120
def input_name(input)
  input.nil? || input == "-" ? "STDIN" : input
end

io(input, output) click to toggle source

# File lib/gn_crossmap.rb, line 97
def io(input, output)
  io_in = iogen(input, INPUT_MODE)
  io_out = iogen(output, OUTPUT_MODE)
  [io_in, io_out]
end

iogen(arg, mode) click to toggle source

# File lib/gn_crossmap.rb, line 103
def iogen(arg, mode)
  if arg.nil? || arg == "-"
    mode == INPUT_MODE ? stdin : STDOUT
  else
    fd_i = IO.sysopen(arg, mode)
    IO.new(fd_i, mode)
  end
end

output_name(output) click to toggle source

# File lib/gn_crossmap.rb, line 124
def output_name(output)
  output.nil? || output == "-" ? "STDOUT" : output
end

stdin() click to toggle source

# File lib/gn_crossmap.rb, line 112
def stdin
  temp = Tempfile.open("stdin")
  return STDIN if File.file?(STDIN)
  IO.copy_stream(STDIN, temp)
  fd_i = IO.sysopen(temp, INPUT_MODE)
  IO.new(fd_i, INPUT_MODE)
end