Ruby port of the BaseSpace Native App test python script

Sample_ruby_native_apps_script.rb

require 'json'

def metadatajson
  json = JSON.parse('
{
  "Name": "",
  "Description": "",
  "HrefAppSession": "",
  "Properties": [
    {
      "Type": "sample[]",
      "Name": "Input.Samples",
      "Items": []
    }
  ]
}
  ')
  return json
end

json_object = JSON.parse(File.read('/data/input/AppSession.json'))
puts ">> json_object"
p json_object
items = json_object['Properties']['Items']
parameters = []
sample_hrefs = []
project_id = nil

items.each do |item|
  case item['Name']
  when 'Input.textbox'
    parameters.push(item['Content'])
  when 'Input.radio'
    parameters.push(item['Content'])
  when 'Input.checkbox'
    parameters.push(item['Items'][0])
  when 'Input.numeric'
    parameters.push(item['Content'])
  when 'Input.Projects'
    project_id = item['Items'][0]['Id']
  end
end

puts ">> parameters"
p parameters
puts ">> project_id"
p project_id

items.each do |item|
  if item['Name'] == 'Input.Samples'
    item['Items'].each do |sample|
      sample_dir = "/data/input/samples/#{sample['Id']}/Data/Intensities/BaseCalls"
      if not File.exists?(sample_dir)
        sample_dir = "/data/input/samples/#{sample['Id']}"
      end
      puts ">> sample_dir"
      p sample_dir
      r1_files = Dir.glob("#{sample_dir}/*_R1_*")
      r2_files = Dir.glob("#{sample_dir}/*_R2_*")
      puts ">> r1_files"
      p r1_files
      puts ">> r2_files"
      p r2_files
      if r1_files.size != r2_files.size
        puts "number of R1 and R2 files do not match"
        exit
      end
      sample_out_dir = "/data/output/appresults/#{project_id}/#{sample['Name']}"
      puts ">> sample_out_dir"
      p sample_out_dir
      system("mkdir -p '#{sample_out_dir}'")
      File.open("#{sample_out_dir}/parameters.csv", "w") do |file|
        parameters.each_with_index do |parameter, count|
          file.puts "#{count},#{parameter}"
        end
      end
      puts ">> parameters.csv"
      p File.read("#{sample_out_dir}/parameters.csv")

      meta_json_object = metadatajson
      meta_json_object['Name'] = sample['Id']
      meta_json_object['Description'] = 'Sample Description'
      meta_json_object['HrefAppSession'] = json_object['Href']
      meta_json_object['Properties'][0]['Items'].push(sample['Href'])

      # not sure why generating a file everytime in a loop 
      File.open("#{sample_out_dir}/_metadata.json", "w") do |file|
        file.puts meta_json_object.to_json
      end
      puts ">> meta_json_object"
      puts File.read("#{sample_out_dir}/_metadata.json")
    end
  end
end

Debug code will print outputs into a "Container log" file (URL for the file can be found in your spacedock log).

Original python script can be found at https://illumina.app.box.com/shared/lv2bnr7rmevufrnnfi0z/1/2616054777