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#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
"""
Messaging, logging and support.
"""
import sys
import os
import logging
import textwrap
from dendropy.utility import metavar
###############################################################################
## metavar.LOGGING
def get_logging_level():
if metavar.LOGGING_LEVEL_ENVAR in os.environ:
if os.environ[metavar.LOGGING_LEVEL_ENVAR].upper() == "NOTSET":
level = logging.NOTSET
elif os.environ[metavar.LOGGING_LEVEL_ENVAR].upper() == "DEBUG":
level = logging.DEBUG
elif os.environ[metavar.LOGGING_LEVEL_ENVAR].upper() == "INFO":
level = logging.INFO
elif os.environ[metavar.LOGGING_LEVEL_ENVAR].upper() == "WARNING":
level = logging.WARNING
elif os.environ[metavar.LOGGING_LEVEL_ENVAR].upper() == "ERROR":
level = logging.ERROR
elif os.environ[metavar.LOGGING_LEVEL_ENVAR].upper() == "CRITICAL":
level = logging.CRITICAL
else:
level = logging.NOTSET
else:
level = logging.NOTSET
return level
def get_logger(name="dendropy"):
"""
Returns a logger with name set as given, and configured
to the level given by the environment variable metavar.LOGGING_LEVEL_ENVAR.
"""
# package_dir = os.path.dirname(module_path)
# config_filepath = os.path.join(package_dir, metavar.LOGGING_CONFIG_FILE)
# if os.path.exists(config_filepath):
# try:
# logging.config.fileConfig(config_filepath)
# logger_set = True
# except:
# logger_set = False
logger = logging.getLogger(name)
if not hasattr(logger, 'is_configured'):
logger.is_configured = False
if not logger.is_configured:
level = get_logging_level()
rich_formatter = logging.Formatter("[%(asctime)s] %(filename)s (%(lineno)d): %(levelname) 8s: %(message)s")
simple_formatter = logging.Formatter("%(levelname) 8s: %(message)s")
raw_formatter = logging.Formatter("%(message)s")
default_formatter = None
logging_formatter = default_formatter
if metavar.LOGGING_FORMAT_ENVAR in os.environ:
if os.environ[metavar.LOGGING_FORMAT_ENVAR].upper() == "RICH":
logging_formatter = rich_formatter
elif os.environ[metavar.LOGGING_FORMAT_ENVAR].upper() == "SIMPLE":
logging_formatter = simple_formatter
elif os.environ[metavar.LOGGING_FORMAT_ENVAR].upper() == "NONE":
logging_formatter = None
else:
logging_formatter = default_formatter
else:
logging_formatter = default_formatter
if logging_formatter is not None:
logging_formatter.datefmt='%H:%M:%S'
logger.setLevel(level)
ch = logging.StreamHandler()
ch.setLevel(level)
ch.setFormatter(logging_formatter)
logger.addHandler(ch)
logger.is_configured = True
return logger
class ConsoleMessenger(object):
ERROR_MESSAGING_LEVEL = 2000
WARNING_MESSAGING_LEVEL = 1000
INFO_MESSAGING_LEVEL = 100
def __init__(self,
name="DendroPy",
messaging_level=None,
dest=sys.stderr):
self.name = name
if messaging_level is None:
self.messaging_level = ConsoleMessenger.INFO_MESSAGING_LEVEL
else:
self.messaging_level = messaging_level
self.primary_out = dest
self.text_wrapper = textwrap.TextWrapper(width=78, initial_indent= "", subsequent_indent=" " * (len(self.name) + 2))
self.message_leader = {
ConsoleMessenger.ERROR_MESSAGING_LEVEL : self.error_leader,
ConsoleMessenger.WARNING_MESSAGING_LEVEL : self.warning_leader,
ConsoleMessenger.INFO_MESSAGING_LEVEL : self.info_leader
}
self.silent = False
def error_leader(self):
return self.name + ": [ERROR] "
def warning_leader(self):
return self.name + ": [WARNING] "
def info_leader(self):
return self.name + ": "
def format_message(self, msg, level, wrap=True, prefix=""):
if not wrap:
msg = self.message_leader[level]() + prefix + msg
else:
if prefix:
full_leader = self.message_leader[level]() + prefix
msg = textwrap.fill(
msg,
width=self.text_wrapper.width,
initial_indent=full_leader,
subsequent_indent=" " * len(full_leader))
else:
msg = self.text_wrapper.fill(self.message_leader[level]() + msg)
return msg
def log(self, msg, level=0, wrap=True, prefix="", newline=True):
if self.silent:
return
if level >= self.messaging_level:
msg = self.format_message(msg, level, wrap=wrap, prefix=prefix)
self.primary_out.write(msg)
if newline:
self.primary_out.write("\n")
def log_lines(self, msg, level=None, wrap=True, prefix=""):
for line in msg:
self.log(msg=line, level=level, wrap=wrap, prefix=prefix)
def error(self, msg, wrap=True, prefix=""):
self.log(msg, level=ConsoleMessenger.ERROR_MESSAGING_LEVEL, wrap=wrap, prefix=prefix)
def warning(self, msg, wrap=True, prefix=""):
self.log(msg, level=ConsoleMessenger.WARNING_MESSAGING_LEVEL, wrap=wrap, prefix=prefix)
def info(self, msg, wrap=True, prefix=""):
self.log(msg, level=ConsoleMessenger.INFO_MESSAGING_LEVEL, wrap=wrap, prefix=prefix)
def info_lines(self, msg, wrap=True, prefix=""):
for line in msg:
self.log(msg=line, level=ConsoleMessenger.INFO_MESSAGING_LEVEL, wrap=wrap, prefix=prefix)
def info_raw(self, msg):
if self.messaging_level <= ConsoleMessenger.INFO_MESSAGING_LEVEL:
self.primary_out.write(self.info_leader() + msg)
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