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

    ruffus_template.py
                        [--log_file PATH]
                        [--verbose]
                        [--target_tasks]
                        [--jobs]
                        [--just_print]
                        [--flowchart]
                        [--key_legend_in_graph]
                        [--forced_tasks]

"""
import sys, os


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#   options


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if __name__ == '__main__':
    from optparse import OptionParser
    import StringIO

    parser = OptionParser(version="%prog 1.0", usage = "\n\n    %progs [options]")



    #
    #   general options: verbosity / logging
    #
    parser.add_option("-v", "--verbose", dest = "verbose",
                      action="count", default=0,
                      help="Print more verbose messages for each additional verbose level.")
    parser.add_option("-L", "--log_file", dest="log_file",
                      metavar="FILE",
                      type="string",
                      help="Name and path of log file")




    #
    #   pipeline
    #
    parser.add_option("-t", "--target_tasks", dest="target_tasks",
                        action="append",
                        default = list(),
                        metavar="JOBNAME",
                        type="string",
                        help="Target task(s) of pipeline.")
    parser.add_option("-j", "--jobs", dest="jobs",
                        default=1,
                        metavar="N",
                        type="int",
                        help="Allow N jobs (commands) to run simultaneously.")
    parser.add_option("-n", "--just_print", dest="just_print",
                        action="store_true", default=False,
                        help="Don't actually run any commands; just print the pipeline.")
    parser.add_option("--flowchart", dest="flowchart",
                        metavar="FILE",
                        type="string",
                        help="Don't actually run any commands; just print the pipeline "
                             "as a flowchart.")

    #
    #   Less common pipeline options
    #
    parser.add_option("--key_legend_in_graph", dest="key_legend_in_graph",
                        action="store_true", default=False,
                        help="Print out legend and key for dependency graph.")
    parser.add_option("--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.")

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


    #vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
    #                                             #
    #   Change this if necessary                  #
    #                                             #
    #^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

    #
    #   Add names of mandatory options,
    #       strings corresponding to the "dest" parameter
    #       in the options defined above
    #
    mandatory_options = [ ]

    #vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
    #                                             #
    #   Change this if necessary                  #
    #                                             #
    #^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^


    def check_mandatory_options (options, mandatory_options, helpstr):
        """
        Check if specified mandatory options have b een defined
        """
        missing_options = []
        for o in mandatory_options:
            if not getattr(options, o):
                missing_options.append("--" + o)

        if not len(missing_options):
            return

        raise Exception("Missing mandatory parameter%s: %s.\n\n%s\n\n" %
                        ("s" if len(missing_options) > 1 else "",
                         ", ".join(missing_options),
                         helpstr))
    check_mandatory_options (options, mandatory_options, helpstr)


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#   imports


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from ruffus import *
from ruffus.ruffus_exceptions import JobSignalledBreak

#from json import dumps
#from collections import defaultdict



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#   Functions


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#   Logger


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if __name__ == '__main__':
    import logging
    import logging.handlers

    MESSAGE = 15
    logging.addLevelName(MESSAGE, "MESSAGE")

    def setup_std_logging (logger, log_file, verbose):
        """
        set up logging using programme options
        """
        class debug_filter(logging.Filter):
            """
            Ignore INFO messages
            """
            def filter(self, record):
                return logging.INFO != record.levelno

        class NullHandler(logging.Handler):
            """
            for when there is no logging
            """
            def emit(self, record):
                pass

        # We are interesting in all messages
        logger.setLevel(logging.DEBUG)
        has_handler = False

        # log to file if that is specified
        if log_file:
            handler = logging.FileHandler(log_file, delay=False)
            handler.setFormatter(logging.Formatter("%(asctime)s - %(name)s - %(levelname)6s - %(message)s"))
            handler.setLevel(MESSAGE)
            logger.addHandler(handler)
            has_handler = True

        # log to stderr if verbose
        if verbose:
            stderrhandler = logging.StreamHandler(sys.stderr)
            stderrhandler.setFormatter(logging.Formatter("    %(message)s"))
            stderrhandler.setLevel(logging.DEBUG)
            if log_file:
                stderrhandler.addFilter(debug_filter())
            logger.addHandler(stderrhandler)
            has_handler = True

        # no logging
        if not has_handler:
            logger.addHandler(NullHandler())


    #
    #   set up log
    #
    logger = logging.getLogger(module_name)
    setup_std_logging(logger, options.log_file, options.verbose)

    #
    #   Allow logging across Ruffus pipeline
    #
    def get_logger (logger_name, args):
        return logger

    from ruffus.proxy_logger import *
    (logger_proxy,
     logging_mutex) = make_shared_logger_and_proxy (get_logger,
                                                    module_name,
                                                    {})


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#   Pipeline


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#       Put pipeline code here







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#   Main logic


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

    elif options.flowchart:
        pipeline_printout_graph (   open(options.flowchart, "w"),
                                    # use flowchart file name extension to decide flowchart format
                                    #   e.g. svg, jpg etc.
                                    os.path.splitext(options.flowchart)[1][1:],
                                    options.target_tasks,
                                    options.forced_tasks,
                                    no_key_legend   = not options.key_legend_in_graph)
    else:
        pipeline_run(options.target_tasks, options.forced_tasks,
                            multiprocess    = options.jobs,
                            logger          = stderr_logger,
                            verbose         = options.verbose)