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#################################################################################
# Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * Neither the name of Pacific Biosciences nor the names of its
# contributors may be used to endorse or promote products derived from
# this software without specific prior written permission.
#
# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
# BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
# IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
#################################################################################
import argparse, cProfile, logging, pstats
LOG_FORMAT = "%(asctime)s [%(levelname)s] %(message)s"
class PBToolRunner(object):
#
# Interface to be overridden in subclasses (client code)
#
def getVersion(self):
raise NotImplementedError()
def run(self):
raise NotImplementedError()
def validateArgs(self):
'''
Method to validate args
'''
pass
#
# Methods below should not be overriden
#
def __init__(self, description):
self._setupParsers(description)
self._addStandardArguments()
def _addStandardArguments(self):
self.parser.add_argument(
"--verbose", "-v",
dest="verbosity", action="count",
help="Set the verbosity level")
self.parser.add_argument(
'--version',
action='version', version= '%(prog)s ' + self.getVersion())
self.parser.add_argument(
"--profile", action="store_true",
help="Print runtime profile at exit")
self.parser.add_argument(
"--debug", action="store_true",
help="Catch exceptions in debugger (requires ipdb)")
def _setupParsers(self, description):
self.parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description=description)
def _parseArgs(self):
self.args = self.parser.parse_args()
def _setupLogging(self):
if self.args.verbosity >= 2:
logLevel = logging.DEBUG
elif self.args.verbosity == 1:
logLevel = logging.INFO
else:
logLevel = logging.WARN
logging.basicConfig(level=logLevel, format=LOG_FORMAT)
def start(self):
self._parseArgs()
self._setupLogging()
self.validateArgs()
if self.args.debug:
try:
import ipdb
except ImportError:
print "--debug requires module 'ipdb'"
return -1
with ipdb.launch_ipdb_on_exception():
self.run()
elif self.args.profile:
l = locals()
cProfile.runctx("_rv=self.run()", globals(), l, "profile.out")
pstats.Stats("profile.out").sort_stats("time").print_stats(20)
return l["_rv"]
else:
return self.run()
class PBMultiToolRunner(PBToolRunner):
def _setupParsers(self, description):
self.parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description=description)
self.subParsers = self.parser.add_subparsers(dest="subCommand")
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