init.rb

#!/usr/bin/env ruby

#### TraitDB YML/CSV File validator ####

APP_ROOT = File.dirname(__FILE__) # a constant, based on the directory containing this file

$:.unshift APP_ROOT # puts the directory into the search path

require 'import_template'
require 'validator' # loads once the validator.rb file
require 'downloader'
require 'pp'

# Instantiate a template validator with the first argument
# which should be a YML file

if ARGV.length == 0
  puts "Usage: #{__FILE__} <config.yml> [<dataset.csv>]"
  exit -1
end


import_template = TraitDB::ImportTemplate.new(ARGV[0])
#
#puts "Import Config Continuous Trait Names".center(80,'=')
#PP.pp(import_template.continuous_trait_column_names)
#puts "Import Config Categorical Trait Names".center(80,'=')
#PP.pp(import_template.categorical_trait_column_names)

exit -1 if ARGV.length < 2

# Validator takes a template and a path to a CSV file
  validator = TraitDB::Validator.new(import_template, ARGV[1])
begin
  validation_results = validator.validate
rescue Exception => e
  if e.message == 'invalid byte sequence in UTF-8' && validator.encoding.nil?
    validator.encoding = 'ISO-8859-1'
    validation_results = validator.validate
  else
    puts "ERROR: #{ARGV[1]} is not valid a CSV file".center(80, '=')
    puts e.message
    exit -1
  end
end

extra_columns = validator.extra_columns
puts "Extra columns: #{extra_columns.count} ".ljust(100,'=')
PP.pp(extra_columns)

puts "Validation Results ".ljust(100,'=')
puts ""
PP.pp(validation_results)

parse_results = validator.parse
puts "Parse Issues: #{parse_results[:issues].count} ".ljust(100,'=')
parse_results[:issues].each do |issue|
  pp(issue)
end

datasets = validator.datasets
puts "Datasets: #{datasets.count} ".ljust(100,'=')
puts ""
# PP.pp(datasets)