#! /usr/bin/python

# Thomas Trolle, July 2014
# trolle@cbs.dtu.dk

# Tested on Python 2.7.2

import cgi
import subprocess


# Define the path to the program that the server should run. 
# Alternatively, you can define the path in the subprocess.check_output
# function below.
PROGRAM = '/path/to/your/method'

def main():
    # Parse the input data sent in the URL. Note that 
    # the following request format is assumed:
    # '<URL>?peptide=<PEPTIDE>&allele=<ALLELE>'
    arguments = cgi.FieldStorage()
    try:
        peptide = arguments['peptide'].value
        allele = arguments['allele'].value
    except:
        print "Please supply some data in the following format: '<URL>?peptide=PEPTIDE&allele=ALLELE'"
        return

    # Check that the input data makes sense.
    allowed_chars = "ACDEFGHIKLMNPQRSTUVWY,"
    for char in peptide:
        if char not in allowed_chars:
            print "Invalid peptide input"
            return

    supported_alleles = ["DRB1*01:01", 
                         "DRB5*01:01", 
                         "DQA1*06:02/DQB1*03:01",
                         "DQA1*01:02/DQB1*03:01"]

    if allele not in supported_alleles:
        print "Invalid allele input"
        return


    # subprocess.check_output() calls your program. The path to your 
    # program and any command line options or arguements should be 
    # passed as a list of strings. Notice that options (such as -mode) 
    # and arguements (such as peptide) that are separated by 
    # whitespace in the shell go in separate list elements.
    result = subprocess.check_output([PROG, '-mode', 'peptide', allele, peptide]) 

    # Parse the output from your program here if necessary. For the 
    # IEDB benchmark, results for each peptide are expected in the 
    # following format: 
    # Allele\tPeptide\tPrediction\n
    print result


if __name__ == '__main__':
    main()