example.rb

# -*- ruby -*-
 
require "json"
require "net/http"
require "uri"
 
class BlastCondition
  attr_accessor :params
  def initialize
    self.params = {
      "querySequence" => nil,
      "datasets"      => nil,
      "database"      => nil,
      "program"       => nil,
      "parameters"    => nil,
      "format"        => nil,
      "result"        => nil,
      "address"       => nil,
    }
  end
end
 
WABI_URL_ROOT = "http://ddbj.nig.ac.jp/wabi"
GET_INTERVAL = 1.0              # Note: 1.0 (sec)
 
def read_blast_condition
  cond = BlastCondition.new
  cond.params["querySequence"] = File.read("blast_condition.fasta")
  File.foreach("blast_condition.txt") do |line|
    tokens = line.chomp.split("\t")
    next unless cond.params.has_key?(tokens[0])
    cond.params[tokens[0]] = tokens[1]
  end
  cond
end
 
def post_to_wabi(blast_condition)
  url = URI.parse("#{WABI_URL_ROOT}/blast")
  res = Net::HTTP.post_form(url, blast_condition.params)
   response = JSON.parse(res.body)
  case res
  when Net::HTTPSuccess
    return response["requestId"]
  when Net::HTTPClientError
    warn "BLAST condition errors: #{response['error-messages'].inspect}"
    exit 1
  else
    warn "WABI server error"
    exit 2
  end
end
 
def get_status(request_id)
  url = URI.parse("#{WABI_URL_ROOT}/blast/#{request_id}?info=status&format=json")
  while true
    sleep GET_INTERVAL
    res = Net::HTTP.get_response(url)
    case res
    when Net::HTTPSuccess
      response = JSON.parse(res.body)
      case response["status"]
      when "waiting"
        puts "#{Time.now}: waiting"
        next
      when "running"
        puts "#{Time.now}: running"
        next
      when "finished"
        puts "#{Time.now}: finished"
        return
      else
        warn "No such Request-id. time-out"
        exit 3
      end
    when Net::HTTPClientError
      warn "No such Request-id. Cause: time-out or wrong Request-ID"
      exit 3
    else
      warn "WABI server error"
      exit 2
    end
  end
end
 
def get_result(request_id)
  url = URI.parse("#{WABI_URL_ROOT}/blast/#{request_id}?info=result&format=bigfile")
  res = Net::HTTP.get_response(url)
  case res
  when Net::HTTPSuccess
    return res.body
  when Net::HTTPClientError
    warn "BLAST result not found. Cause: time-out, not-finished, or wrong Request-ID"
    exit 4
  else
    warn "WABI server error"
    exit 2
  end
end
 
def main
  blast_condition = read_blast_condition
  puts "Load BLAST condition"
 
  request_id = post_to_wabi(blast_condition)
  puts "POST : success (Request-ID=#{request_id})"
 
  get_status request_id
  puts "Request : finished"
 
  blast_result = get_result(request_id)
  puts "GET BLAST result : success"
  File.open("#{request_id}.txt", "w") do |out|
    out.puts blast_result
  end
end
 
main
 
# example.rb ends here