# require 'shellwords'
# require_relative '../spec_helper'
# require 'bioinform/cli/convert_motif'
# require_relative 'shared_examples/convert_motif/single_motif_specified'
# require_relative 'shared_examples/convert_motif/several_motifs_specified'
# require_relative 'shared_examples/convert_motif/motif_list_empty'
# require_relative 'shared_examples/convert_motif/yield_motif_conversion_error'

# def make_option_list(options = {})
#   result = []
#   result << '--from' << options[:model_from]  if options[:model_from]
#   result << '--to' << options[:model_to]  if options[:model_to]
#   result << '--parser' << options[:parser]  if options[:parser]
#   result << '--formatter' << options[:formatter]  if options[:formatter]
#   result << (options[:silent] ? '--silent' : '--no-silent')  if options.has_key?(:silent)
#   result << (options[:force] ? '--force' : '--no-force')  if options.has_key?(:force)
#   result << '--save' << options[:filename_format]  if options[:filename_format]
#   result << '--algorithm' << options[:algorithm]  if options[:algorithm]
#   result
# end


# shared_context 'most common options' do
#   Given(:parser) { 'plain' }
#   Given(:formatter) { 'plain' }
#   Given(:silent) { true }
#   Given(:force) { false }
#   Given(:filename_format) { nil }
#   Given(:algorithm) { nil }
# end

# shared_context 'completely specified option list' do
#   Given(:options) {
#     make_option_list( model_from: model_from,  model_to: model_to,
#                       parser: parser,  formatter: formatter,
#                       silent: silent,  force: force,
#                       filename_format: filename_format,
#                       algorithm: algorithm ).shelljoin 
#   }
# end

# shared_context 'input filenames are motif_name.motif_type' do
#   Given(:input_filenames) { motif_list.map{|motif| motif_filename(motif, model_from) }.shelljoin }
# end

# ##################################

# describe Bioinform::CLI::ConvertMotif do
#   include FakeFS::SpecHelpers
#   Given(:resulting_stdout) { resulting_io[:stdout] }
#   Given(:resulting_stderr) { resulting_io[:stderr] }
  
#   Given(:command) { options.shellsplit + arguments.shellsplit }
  
#   Given(:sp1_f1){ Fabricate(:SP1_f1_plain_text) }
#   Given(:klf4_f2){ Fabricate(:KLF4_f2_plain_text) }
  
# ########################################################
  
#   context 'when program not piped' do
#     Given(:arguments) { input_filenames }
#     Given(:resulting_io) {
#       capture_io{
#           Bioinform::CLI::ConvertMotif.main(command)
#       }
#     }
#     include_context 'input filenames are motif_name.motif_type'
    
#     context 'with most options specified' do
#       include_context 'completely specified option list'
#       include_context 'most common options'      

#       include_examples 'single motif specified'
#       include_examples 'several motifs specified'
#     end
    
#     include_examples 'motif list is empty'
#   end
  
# ########################################################

#   context 'when program is piped' do
# #    include_context 'completely specified option list'
# #    include_context 'most common options'
#     include_context 'input filenames are motif_name.motif_type'

#     Given(:tty){ false }
#     Given(:stdin_data) { input_filenames }
#     Given(:arguments) { '' }
#     Given(:resulting_io) {
#       capture_io{
#         provide_stdin(stdin_data, tty) {
#           Bioinform::CLI::ConvertMotif.main(command)
#         }
#       }
#     }

#     include_examples 'motif list is empty'
#     context 'with most options specified' do
#       include_context 'completely specified option list'
#       include_context 'most common options'      

#       include_examples 'single motif specified'
#       include_examples 'several motifs specified'
#     end
#   end
# end