#!/usr/bin/env python3
# -*- coding: utf-8 -*-

###
# © 2018 The Board of Trustees of the Leland Stanford Junior University
# Nathaniel Watson
# nathankw@stanford.edu
# 2018-10-23
###

"""
Use this script when there are records on the ENCODE Portal for which you know their aliases, but
want to retreive their DCC accessions. This will only work if the record aliases you provided are
registered with the records on the ENCODE Portal. Note that if the particular DCC profile at hand
doesn't support the accession property, then the uuid will be returned. 
"""

import argparse
import encode_utils
from encode_utils.connection import Connection
from encode_utils.parent_argparser import dcc_login_parser
# dcc_login_parser  contains the arguments needed for logging in to the
# ENCODE Portal, including which env.


def get_parser():
    parser = argparse.ArgumentParser(
        parents=[dcc_login_parser],
        description=__doc__,
        formatter_class=argparse.RawTextHelpFormatter)
    parser.add_argument("-i", "--infile", required=True, help="""
        Input file containing record aliases (one per line). Empty lines and lines beginning with 
        a '#' will be ignored.""")

    parser.add_argument("-o", "--outfile", required=True, help="""
        The output file, which is in the same as the input file except for the addition of the
        tab-delimited columns - one for each alias.
  """)
    parser.add_argument("-l", "--submitter-lab", help="""
        The submitting lab alias prefix (i.e. michael-snyder) for these aliases.  No need to set this
        option if your input file's aliases are already prefixed with the submitting lab. Furthermore,
        for any aliases lacking the prefix, the default will be taken from the DCC_LAB environment
        variable if not set here.""")
    return parser


def main():
    """Program
    """
    parser = get_parser()
    args = parser.parse_args()
    infile = args.infile
    outfile = args.outfile
    dcc_mode = args.dcc_mode
    submitter_lab = args.submitter_lab
    if not submitter_lab:
        submitter_lab = encode_utils.LAB_PREFIX.rstrip(":")

    conn = Connection(dcc_mode=dcc_mode)

    fh = open(infile, 'r')
    fout = open(outfile, 'w')
    for line in fh:
        alias = line.strip("\n").split("\t")[0]
        if not alias or alias.startswith("#"):
            fout.write(line)
            continue
        alias_lab_prefix = alias.split(":", 1)
        try:
            lab_prefix, alias_name = alias.split(":", 1)
        except ValueError:
            if not submitter_lab:
                raise Exception("Unknown submitting lab name for alias {}. See description for --submitter-lab  argument.".format(alias))
            alias = submitter_lab + ":" + alias
        rec = conn.get(rec_ids=alias, ignore404=False)
        try:
            dcc_id = rec["accession"]
        except KeyError:
            dcc_id = rec["uuid"]
        line = [line.strip("\n")]
        outline = line.append(dcc_id)
        fout.write("\t".join(line) + "\n")
    fout.close()
    fh.close()

if __name__ == "__main__":
    main()