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#!/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
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# options
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
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)
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# imports
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
from ruffus import *
from ruffus.ruffus_exceptions import JobSignalledBreak
#from json import dumps
#from collections import defaultdict
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# Functions
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# Logger
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
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,
{})
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# Pipeline
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# Put pipeline code here
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# Main logic
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
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)
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