import optparse
import os
import shutil
import subprocess
import sys
import tempfile

BUFF_SIZE = 1048576
DESIGN_FILE = 'design.tabular'


def generate_design_file(input_items, filename):
    design_file = open(filename, 'wb')
    for items in input_items:
        filename, ext, signal_control, condition_name, replicate_name, read_distribution_file, fixed_read = items
        # MultiGPS version 0.5 does not support the newer scidx datatype.
        if ext == 'scidx':
            datatype = 'IDX'
        else:
            datatype = ext.upper()
        design_file.write('%s\n' % '\t'.join([filename, signal_control, datatype, condition_name, replicate_name, read_distribution_file, fixed_read]))
    design_file.close()


def get_stderr_exception(tmp_err, tmp_stderr, tmp_out, tmp_stdout, include_stdout=False):
    tmp_stderr.close()
    # Get stderr, allowing for case where it's very large.
    tmp_stderr = open(tmp_err, 'rb')
    stderr_str = ''
    buffsize = BUFF_SIZE
    try:
        while True:
            stderr_str += tmp_stderr.read(buffsize)
            if not stderr_str or len(stderr_str) % buffsize != 0:
                break
    except OverflowError:
        pass
    tmp_stderr.close()
    if include_stdout:
        tmp_stdout = open(tmp_out, 'rb')
        stdout_str = ''
        buffsize = BUFF_SIZE
        try:
            while True:
                stdout_str += tmp_stdout.read(buffsize)
                if not stdout_str or len(stdout_str) % buffsize != 0:
                    break
        except OverflowError:
            pass
    tmp_stdout.close()
    if include_stdout:
        return 'STDOUT\n%s\n\nSTDERR\n%s\n' % (stdout_str, stderr_str)
    return stderr_str


def stop_err(msg):
    sys.stderr.write(msg)
    sys.exit(1)

parser = optparse.OptionParser()
parser.add_option('--input_item', dest='input_items', action='append', nargs=7, help="Input datasets and associated parameters")
parser.add_option('--threads', dest='threads', type="int", default=4, help='The number of threads to run')
parser.add_option('--multigps_jar', dest='multigps_jar', help='Path to the MultiGPS jar file')
parser.add_option('--geninfo', dest='geninfo', help='File listing the lengths of all chromosomes')
parser.add_option('--use_motif', dest='use_motif', help='Perform motif-finding or use a motif-prior')
parser.add_option('--seq_dir', dest='seq_dir', default=None, help='Directory containing fasta files corresponding to every named chromosome')
parser.add_option('--positional_prior', dest='positional_prior', default=None, help='Perform inter-experiment positional prior')
parser.add_option('--events_shared_probability', dest='events_shared_probability', type=float, default=0.9, help='Probability that events are shared across conditions')
parser.add_option('--motifs', dest='motifs', default=None, help='Perform motif-finding and motif priors')
parser.add_option('--motif_finding_only', dest='motif_finding_only', default=None, help='Perform motif-finding only')
parser.add_option('--num_motifs', dest='num_motifs', type="int", default=None, help='Number of motifs MEME should find for each condition')
parser.add_option('--mememinw', dest='mememinw', type="int", default=None, help='Minimum motif width for MEME')
parser.add_option('--mememaxw', dest='mememaxw', type="int", default=None, help='Maximum motif width for MEME')
parser.add_option('--fixedpb', dest='fixedpb', type="int", default=None, help='Fixed per-base limit')
parser.add_option('--poissongausspb', dest='poissongausspb', type="int", default=None, help='Poisson threshold for filtering per base')
parser.add_option('--non_unique_reads', dest='non_unique_reads', default=None, help='Use non-unique reads')
parser.add_option('--minqvalue', dest='minqvalue', type="int", default=None, help='Minimum Q-value (corrected p-value) of reported binding events')
parser.add_option('--minfold', dest='minfold', type="int", default=None, help='Minimum event fold-change vs scaled control')
parser.add_option('--diff_enrichment_tests', dest='diff_enrichment_tests', help='Run differential enrichment tests')
parser.add_option('--edgerod', dest='edgerod', type="int", default=None, help='EdgeR over-dispersion parameter value')
parser.add_option('--diffp', dest='diffp', type="int", default=None, help='Minimum p-value for reporting differential enrichment')
parser.add_option('--noscaling', dest='noscaling', default=None, help='Do not use signal vs control scaling')
parser.add_option('--medianscale', dest='medianscale', default=None, help='Use the median signal/control ratio as the scaling factor')
parser.add_option('--sesscale', dest='sesscale', default=None, help='Estimate scaling factor by SES')
parser.add_option('--scalewin', dest='scalewin', type="int", default=None, help='Window size for estimating scaling ratios')
parser.add_option('--max_training_rounds', dest='max_training_rounds', type="int", default=None, help='Maximum number of training rounds for updating binding event read distributions')
parser.add_option('--exclude_file', dest='exclude_file', default=None, help='File containing a set of regions to ignore during MultiGPS training')
parser.add_option('--binding_model_updates', dest='binding_model_updates', default=None, help='Perform binding model updates')
parser.add_option('--minmodelupdateevents', dest='minmodelupdateevents', type="int", default=None, help='Minimum number of events to support an update of the read distribution')
parser.add_option('--binding_model_smoothing', dest='binding_model_smoothing', default=None, help='Binding model smoothing')
parser.add_option('--spline_smooth', dest='spline_smooth', type="int", default=None, help='Binding model smoothing value')
parser.add_option('--gauss_smooth', dest='gauss_smooth', type="int", default=None, help='Gaussian smoothing std dev')
parser.add_option('--joint_in_model', dest='joint_in_model', default=None, help='Allow joint events in model updates')
parser.add_option('--ml_config_not_shared', dest='ml_config_not_shared', default=None, help='Share component configs in the ML step')
parser.add_option('--output_html_path', dest='output_html_path', help='Output html results file')
parser.add_option('--output_html_files_path', dest='output_html_files_path', help='Output html extra files')
parser.add_option('--output_process_path', dest='output_process_path', default=None, help='Output file for capturing stdout')
options, args = parser.parse_args()

try:
    # Preparation.
    tmp_dir = tempfile.mkdtemp(prefix="tmp-multigps-")
    generate_design_file(options.input_items, DESIGN_FILE)
    # Build the command line.
    cmd_list = ['java -jar %s --verbose' % options.multigps_jar]
    cmd_list.append('--threads %d' % options.threads)
    cmd_list.append('--geninfo %s' % options.geninfo)
    if options.use_motif == 'yes':
        cmd_list.append('--seq %s' % options.seq_dir)
        if options.positional_prior == 'no':
            cmd_list.append('--noposprior')
        cmd_list.append('--probshared %3f' % options.events_shared_probability)
        if options.motifs == 'no':
            cmd_list.append('--nomotifs')
        if options.motif_finding_only == 'yes':
            cmd_list.append('--nomotifprior')
        if options.num_motifs is not None:
            cmd_list.append('--memenmotifs %d' % options.num_motifs)
        if options.mememinw is not None:
            cmd_list.append('--mememinw %d' % options.mememinw)
        if options.mememaxw is not None:
            cmd_list.append('--mememaxw %d' % options.mememaxw)
    if options.fixedpb is not None:
        cmd_list.append('--fixedpb %d' % options.fixedpb)
    if options.poissongausspb is not None:
        cmd_list.append('--poissongausspb %d' % options.poissongausspb)
    if options.non_unique_reads == 'yes':
        cmd_list.append('--nonunique')
    if options.minqvalue is not None:
        cmd_list.append('--q %d' % options.minqvalue)
    if options.minfold is not None:
        cmd_list.append('--minfold %d' % options.minfold)
    if options.diff_enrichment_tests == 'no':
        cmd_list.append('--nodifftests')
    if options.edgerod is not None:
        cmd_list.append('--edgerod %d' % options.edgerod)
    if options.diffp is not None:
        cmd_list.append('--diffp %d' % options.diffp)
    if options.noscaling == 'no':
        cmd_list.append('--noscaling')
    if options.medianscale == "yes":
        cmd_list.append('--medianscale')
    if options.sesscale == "yes":
        cmd_list.append('--sesscale')
    if options.scalewin is not None:
        cmd_list.append('--scalewin %d' % options.scalewin)
    if options.max_training_rounds is not None:
        cmd_list.append('--r %d' % options.max_training_rounds)
    if options.exclude_file not in [None, 'None']:
        cmd_list.append('--exclude %s' % options.exclude_file)
    if options.binding_model_updates == 'no':
        cmd_list.append('--nomodelupdate')
    if options.minmodelupdateevents is not None:
        cmd_list.append('--minmodelupdateevents %d' % options.minmodelupdateevents)
    if options.binding_model_smoothing == 'yes':
        if options.spline_smooth is not None:
            cmd_list.append('--splinesmoothparam %d' % options.spline_smooth)
    else:
        cmd_list.append('--nomodelsmoothing')
        if options.gauss_smooth is not None:
            cmd_list.append('--gaussmodelsmoothing')
            cmd_list.append('--gausssmoothparam %d' % options.gauss_smooth)
    if options.joint_in_model == 'yes':
        cmd_list.append('--jointinmodel')
    if options.ml_config_not_shared == 'no':
        cmd_list.append('--mlconfignotshared')
    cmd_list.append('--design %s' % DESIGN_FILE)
    cmd_list.append('--out %s' % options.output_html_files_path)
    if options.output_process_path is None:
        cmd_list.append('2>/dev/null')
    else:
        cmd_list.append('2>%s' % options.output_process_path)
    cmd = ' '.join(cmd_list)
    # Define command response buffers.
    tmp_out = tempfile.NamedTemporaryFile(dir=tmp_dir).name
    tmp_stdout = open(tmp_out, 'wb')
    tmp_err = tempfile.NamedTemporaryFile(dir=tmp_dir).name
    tmp_stderr = open(tmp_err, 'wb')
    tmp_filename = tempfile.NamedTemporaryFile(dir=tmp_dir).name
    # Execute the command.
    proc = subprocess.Popen(args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True)
    rc = proc.wait()
    if rc != 0:
        error_message = get_stderr_exception(tmp_err, tmp_stderr, tmp_out, tmp_stdout)
        stop_err(error_message)
    # Move the output HTML file to the output dataset path.
    output_html_filename = 'multiGPS_%s_results.html' % os.path.split(options.output_html_files_path)[1]
    shutil.move(os.path.join(options.output_html_files_path, output_html_filename), options.output_html_path)
except Exception, e:
    stop_err('Error running MultiGPS\n%s\n' % str(e))
finally:
    if os.path.exists(tmp_dir):
        shutil.rmtree(tmp_dir)