#!/usr/bin/env python
"""

    test_N_x_M_and_collate.py


        This script takes N pairs of input file pairs
                                (with the suffices .gene and .gwas)
                          and runs them against M sets of simulation data
                                (with the suffix .simulation)
        A summary per input file pair is then produced


    In pseudo-code:

        STEP_1:

        for n_file in NNN_pairs_of_input_files:
            for m_file in MMM_simulation_data:

                [n_file.gene,
                 n_file.gwas,
                 m_file.simulation] -> n_file.m_file.simulation_res


        STEP_2:

        for n_file in NNN_pairs_of_input_files:

            n_file.*.simulation_res -> n_file.mean


        n = CNT_GENE_GWAS_FILES
        m = CNT_SIMULATION_FILES



"""

CNT_GENE_GWAS_FILES     = 2
CNT_SIMULATION_FILES    = 3



import os, sys
exe_path = os.path.split(os.path.abspath(sys.argv[0]))[0]
sys.path.insert(0, os.path.abspath(os.path.join(exe_path,"..", "..")))



from ruffus import *
import random
from itertools import izip


#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888

#   options


#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888

from optparse import OptionParser
parser = OptionParser(version="%prog 1.0")
parser.add_option("-D", "--debug", dest = "debug",
                  action="store_true", default=False,
                  help="Run as unit test with default values.")
parser.add_option("-k", "--keep", dest = "keep",
                  action="store_true", default=False,
                  help="Do not cleanup after unit test runs.")
parser.add_option("-t", "--target_tasks", dest="target_tasks",
                  action="append",
                  default = ["statistical_summary"],
                  metavar="JOBNAME",
                  type="string",
                  help="Target task(s) of pipeline.")
parser.add_option("-f", "--forced_tasks", dest="forced_tasks",
                  action="append",
                  default = list(),
                  metavar="JOBNAME",
                  type="string",
                  help="Pipeline task(s) which will be included even if they are up to date.")
parser.add_option("-j", "--jobs", dest="jobs",
                  default=5,
                  metavar="jobs",
                  type="int",
                  help="Specifies the number of jobs (commands) to run simultaneously.")

parser.add_option("-g", "--gene_data_dir", dest="gene_data_dir",
                  default="%s/temp_gene_data_for_intermediate_example" % exe_path,
                  metavar="PATH",
                  type="string",
                  help="Directory with gene data [*.genes / *.gwas].")
parser.add_option("-s", "--simulation_data_dir", dest="simulation_data_dir",
                  default="%s/temp_simulation_data_for_intermediate_example" % exe_path,
                  metavar="PATH",
                  type="string",
                  help="Directory with simulation data [*.simulation].")
parser.add_option("-w", "--working_dir", dest="working_dir",
                  default="%s/working_dir_for_intermediate_example" % exe_path,
                  metavar="PATH",
                  type="string",
                  help="Working directory.")


parser.add_option("-v", "--verbose", dest = "verbose",
                  action="count", default=0,
                  help="Print more verbose messages for each additional verbose level.")
parser.add_option("-d", "--dependency", dest="dependency_file",
                  metavar="FILE",
                  type="string",
                  help="Print a dependency graph of the pipeline that would be executed "
                        "to FILE, but do not execute it.")
parser.add_option("-F", "--dependency_graph_format", dest="dependency_graph_format",
                  metavar="FORMAT",
                  type="string",
                  default = 'svg',
                  help="format of dependency graph file. Can be 'ps' (PostScript), "+
                  "'svg' 'svgz' (Structured Vector Graphics), " +
                  "'png' 'gif' (bitmap  graphics) etc ")
parser.add_option("-n", "--just_print", dest="just_print",
                    action="store_true", default=False,
                    help="Print a description of the jobs that would be executed, "
                        "but do not execute them.")





#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888

#   imports


#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888

import StringIO
import re
import operator
import sys
from collections import defaultdict
import glob
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888

#   Functions


#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888

#_________________________________________________________________________________________
#
#   get gene gwas file pairs
#
#_________________________________________________________________________________________
def get_gene_gwas_file_pairs(  ):
    """
    Helper function to get all *.gene, *.gwas from the direction specified
        in --gene_data_dir

    Returns
        file pairs with both .gene and .gwas extensions,
        corresponding roots (no extension) of each file
    """


    gene_files = glob.glob(os.path.join(options.gene_data_dir, "*.gene"))
    gwas_files = glob.glob(os.path.join(options.gene_data_dir, "*.gwas"))

    common_roots = set(map(lambda x: os.path.splitext(os.path.split(x)[1])[0], gene_files))
    common_roots &=set(map(lambda x: os.path.splitext(os.path.split(x)[1])[0], gwas_files))
    common_roots = list(common_roots)

    p = os.path; g_dir = options.gene_data_dir

    file_pairs = [[p.join(g_dir, x + ".gene"), p.join(g_dir, x + ".gwas")] for x in common_roots]

    return file_pairs, common_roots

#_________________________________________________________________________________________
#
#   get simulation files
#
#_________________________________________________________________________________________
def get_simulation_files(  ):
    """
    Helper function to get all *.simulation from the direction specified
        in --simulation_data_dir
        Returns
            file with .simulation extensions,
            corresponding roots (no extension) of each file
    """
    simulation_files = glob.glob(os.path.join(options.simulation_data_dir, "*.simulation"))
    simulation_roots =map(lambda x: os.path.splitext(os.path.split(x)[1])[0], simulation_files)
    return simulation_files, simulation_roots



#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888

#   Main logic


#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888





# get help string
f =StringIO.StringIO()
parser.print_help(f)
helpstr = f.getvalue()
(options, remaining_args) = parser.parse_args()


working_dir = options.working_dir




#_________________________________________________________________________________________
#
#   setup_simulation_data
#
#_________________________________________________________________________________________

#
# mkdir: makes sure output directories exist before task
#
@follows(mkdir(options.gene_data_dir, options.simulation_data_dir))
def setup_simulation_data ():
    """
    create simulation files
    """
    for i in range(CNT_GENE_GWAS_FILES):
        open(os.path.join(options.gene_data_dir, "%03d.gene" % i), "w")
        open(os.path.join(options.gene_data_dir, "%03d.gwas" % i), "w")

    # gene files without corresponding gwas and vice versa
    open(os.path.join(options.gene_data_dir, "orphan1.gene"), "w")
    open(os.path.join(options.gene_data_dir, "orphan2.gwas"), "w")
    open(os.path.join(options.gene_data_dir, "orphan3.gwas"), "w")

    for i in range(CNT_SIMULATION_FILES):
        open(os.path.join(options.simulation_data_dir, "%03d.simulation" % i), "w")




#_________________________________________________________________________________________
#
#   cleanup_simulation_data
#
#_________________________________________________________________________________________
def try_rmdir (d):
    if os.path.exists(d):
        try:
            os.rmdir(d)
        except OSError:
            sys.stderr.write("Warning:\t%s is not empty and will not be removed.\n" % d)

def cleanup_simulation_data ():
    """
    cleanup files
    """
    if options.verbose:
        sys.stderr.write("Cleanup working directory and simulation files.\n")

    #
    #   cleanup gene and gwas files
    #
    for f in glob.glob(os.path.join(options.gene_data_dir, "*.gene")):
        os.unlink(f)
    for f in glob.glob(os.path.join(options.gene_data_dir, "*.gwas")):
        os.unlink(f)
    try_rmdir(options.gene_data_dir)

    #
    #   cleanup simulation
    #
    for f in glob.glob(os.path.join(options.simulation_data_dir, "*.simulation")):
        os.unlink(f)
    try_rmdir(options.simulation_data_dir)


    #
    #   cleanup working_dir
    #
    for f in glob.glob(os.path.join(working_dir, "simulation_results", "*.simulation_res")):
        os.unlink(f)
    try_rmdir(os.path.join(working_dir, "simulation_results"))

    for f in glob.glob(os.path.join(working_dir, "*.mean")):
        os.unlink(f)
    try_rmdir(working_dir)


#_________________________________________________________________________________________
#
#   Step 1:
#
#        for n_file in NNN_pairs_of_input_files:
#            for m_file in MMM_simulation_data:
#
#                [n_file.gene,
#                 n_file.gwas,
#                 m_file.simulation] -> working_dir/n_file.m_file.simulation_res
#
#_________________________________________________________________________________________
def generate_simulation_params ():
    """
    Custom function to generate
    file names for gene/gwas simulation study
    """

    simulation_files, simulation_file_roots    = get_simulation_files()
    gene_gwas_file_pairs, gene_gwas_file_roots =  get_gene_gwas_file_pairs()

    for sim_file, sim_file_root in izip(simulation_files, simulation_file_roots):
        for (gene, gwas), gene_file_root in izip(gene_gwas_file_pairs, gene_gwas_file_roots):

            result_file = "%s.%s.simulation_res" % (gene_file_root, sim_file_root)
            result_file_path = os.path.join(working_dir, "simulation_results", result_file)

            yield [gene, gwas, sim_file], result_file_path, gene_file_root, sim_file_root, result_file

#
# mkdir: makes sure output directories exist before task
#
@follows(mkdir(options.working_dir, os.path.join(working_dir, "simulation_results")))
@files(generate_simulation_params)
def gwas_simulation(input_files, result_file_path, gene_file_root, sim_file_root, result_file):
    """
    Dummy calculation of gene gwas vs simulation data
    Normally runs in parallel on a computational cluster
    """
    (gene_file,
    gwas_file,
    simulation_data_file) = input_files

    simulation_res_file = open(result_file_path, "w")
    simulation_res_file.write("%s + %s -> %s\n" % (gene_file_root, sim_file_root, result_file))


#_________________________________________________________________________________________
#
#   Step 2:
#
#       Statistical summary per gene/gwas file pair
#
#        for n_file in NNN_pairs_of_input_files:
#            working_dir/simulation_results/n.*.simulation_res
#               -> working_dir/n.mean
#
#_________________________________________________________________________________________


@collate(gwas_simulation, regex(r"simulation_results/(\d+).\d+.simulation_res"), r"\1.mean")
@posttask(lambda : sys.stdout.write("\nOK\n"))
def statistical_summary (result_files, summary_file):
    """
    Simulate statistical summary
    """

    summary_file = open(summary_file, "w")
    for f in result_files:
        summary_file.write(open(f).read())









#888888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
#
#   print pipeline or run pipeline
#

#
#   Necessary to protect the "entry point" of the program under windows.
#       see: http://docs.python.org/library/multiprocessing.html#multiprocessing-programming
#
if __name__ == '__main__':
    try:
        if options.debug:
            if not len(options.target_tasks):
                options.target_tasks.append([statistical_summary])
            pipeline_run([setup_simulation_data], [setup_simulation_data], multiprocess = options.jobs, verbose = 0)
        else:
            if (not len(get_gene_gwas_file_pairs(  )[0]) or
                not len (get_simulation_files(  )[0])):
                print "Warning!!\n\n\tNo *.gene / *.gwas or *.simulation: Run --debug to create simulation files first\n\n"
                sys.exit(1)


        if options.just_print:
            pipeline_printout(sys.stdout, options.target_tasks, options.forced_tasks, verbose=options.verbose)

        elif options.dependency_file:
            graph_printout (     open(options.dependency_file, "w"),
                                 options.dependency_graph_format,
                                 options.target_tasks,
                                 options.forced_tasks)
        else:
            pipeline_run(options.target_tasks, options.forced_tasks, multiprocess = options.jobs, verbose = options.verbose)


        if options.debug and not options.keep:
            cleanup_simulation_data ()

    except Exception, e:
        print e.args
        raise