# -*- coding: utf-8 -*-
# :noTabs=true:

import sys, os, os.path, commands
import json
args = json.load( file('.arguments.py') )

essential = []  # list of essential files for this jobs, rest of files will be deleted in ~30 days after the job finish.


def execute(message, commandline, return_=False):
    print message
    print commandline
    (res, output) = commands.getstatusoutput(commandline)
    print output
    if res:
        print "\nEncounter error while executing: ", commandline
        if return_: return True
        else: sys.exit(1)

    return False


def exit_with_job_failure(failure_message):
    output = dict(status='fail', failure_message=failure_message)
    json.dump(output, file('output.json', 'w') )
    sys.exit(0)

"""
# now lets find all CDR_* regions!
light_chain = file('input/light_chain.fasta').read()
l1 = file('output/query.l1').read().split('\n')[1]
l2 = file('output/query.l2').read().split('\n')[1]
l3 = file('output/query.l3').read().split('\n')[1]

FR_L1, CDR_L1, _     = light_chain.partition(l1)
FR_L2, CDR_L2, _     = _.partition(l2)
FR_L3, CDR_L3, FR_L4 = _.partition(l3)

light_chain_annotated = [('FR_L1',FR_L1), ('CDR_L1', CDR_L1), ('FR_L2', FR_L2), ('CDR_L2', CDR_L2), ('FR_L3', FR_L3), ('CDR_L3',CDR_L3), ('FR_L4', FR_L4)]


heavy_chain = file('input/heavy_chain.fasta').read()
h1 = file('output/query.h1').read().split('\n')[1]
h2 = file('output/query.h2').read().split('\n')[1]
h3 = file('output/query.h3').read().split('\n')[1]

FR_H1, CDR_H1, _     = heavy_chain.partition(h1)
FR_H2, CDR_H2, _     = _.partition(h2)
FR_H3, CDR_H3, FR_H4 = _.partition(h3)

heavy_chain_annotated = [('FR_H1',FR_H1), ('CDR_H1', CDR_H1), ('FR_H2', FR_H2), ('CDR_H2', CDR_H2), ('FR_H3', FR_H3), ('CDR_H3',CDR_H3), ('FR_H4', FR_H4)]


def read_align_file(fname):
    ''' read .align file and produce tuple (CDR_code, [keys] [list_of_top_values]) with top ~20 structures plus one that in the right side of query.matches
        and all keys as a zero row '''

    lines = file(fname).read().split('\n')
    file_cdr_key = lines[2].split('.')[-1]

    for l in file('output/query.matches'):
        if file_cdr_key == l.split()[0]: matched_pdb = l.split()[-3] [3:7]

    alignment_keys = ['No.', 'PDB', 'Identity', 'Alignment length', 'Mismatches', 'Gap openings', 'Q start', 'Q end', 'S start', 'S end', 'E value', 'Bit score']

    res = [alignment_keys]
    for l in lines[4:14]:
        if l:
            d = l.split()
            d[1] = d[1] [3:7]
            if d[1]  == matched_pdb: res.insert(1, d)
            else: res.append(d)
            d[0] = res.index(d)

            '''
            d = dict( zip(alignment_keys, l.split())[1:] )
            d[ alignment_keys[1] ] = d[ alignment_keys[1] ] [3:7]
            if d[ alignment_keys[1] ]  == matched_pdb: res.insert(0, d)
            else: res.append(d)
            d['No.'] = res.index(d) + 1
            '''

    return (file_cdr_key.upper(), res)


alignment = dict( map(lambda f: read_align_file('output/query_%s.align' % f), ['l1', 'l2', 'l3', 'h1', 'h2', 'h3', 'lfr', 'hfr', 'lightheavy', ] ) )
"""

# extract score info if any...
score_table = []
score_table_keys = []
best_decoys = []
score_file = 'score.sf'


if os.path.isfile('output/results.json'): status = 0
else: status = 'fail'

output = dict(json.load( file('output/results.json') ),
              status=status,
              #light_chain_annotated=light_chain_annotated, heavy_chain_annotated=heavy_chain_annotated,
              #alignment=alignment,
              #score_table=score_table, score_table_keys=score_table_keys, best_decoys=best_decoys, cluster_centers=cluster_centers,
              essential=essential)

json.dump(output, file('output.json', 'w') )