# Copyright (C) 2015-2021 Regents of the University of California
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import gzip
import io
import json
import logging
import os
import time
from argparse import ArgumentParser, Namespace
from logging.handlers import RotatingFileHandler
from threading import Event, Thread
from typing import IO, TYPE_CHECKING, Any, Callable, List, Optional, Union
from toil.lib.conversions import strtobool
from toil.lib.expando import Expando
from toil.lib.resources import ResourceMonitor
if TYPE_CHECKING:
from toil.common import Config
from toil.jobStores.abstractJobStore import AbstractJobStore
logger = logging.getLogger(__name__)
root_logger = logging.getLogger()
toil_logger = logging.getLogger('toil')
DEFAULT_LOGLEVEL = logging.INFO
__loggingFiles = []
[docs]
class StatsAndLogging:
"""A thread to aggregate statistics and logging."""
def __init__(self, jobStore: 'AbstractJobStore', config: 'Config') -> None:
self._stop = Event()
self._worker = Thread(target=self.statsAndLoggingAggregator,
args=(jobStore, self._stop, config),
daemon=True)
[docs]
def start(self) -> None:
"""Start the stats and logging thread."""
self._worker.start()
[docs]
@classmethod
def writeLogFiles(cls, jobNames: List[str], jobLogList: List[str], config: 'Config', failed: bool = False) -> None:
def createName(logPath: str, jobName: str, logExtension: str, failed: bool = False) -> str:
logName = jobName.replace('-', '--')
logName = logName.replace('/', '-')
logName = logName.replace(' ', '_')
logName = logName.replace("'", '')
logName = logName.replace('"', '')
# Add a "failed_" prefix to logs from failed jobs.
logName = ('failed_' if failed else '') + logName
counter = 0
while True:
suffix = '_' + str(counter).zfill(3) + logExtension
fullName = os.path.join(logPath, logName + suffix)
# The maximum file name size in the default HFS+ file system is 255 UTF-16 encoding units, so basically 255 characters
if len(fullName) >= 255:
return fullName[:(255 - len(suffix))] + suffix
if not os.path.exists(fullName):
return fullName
counter += 1
mainFileName = jobNames[0]
extension = '.log'
writeFn: Callable[..., Any]
if config.writeLogs:
path = config.writeLogs
writeFn = open
elif config.writeLogsGzip:
path = config.writeLogsGzip
writeFn = gzip.open
extension += '.gz'
else:
# we don't have anywhere to write the logs, return now
return
# Make sure the destination exists
os.makedirs(path, exist_ok=True)
fullName = createName(path, mainFileName, extension, failed)
with writeFn(fullName, 'wb') as f:
for l in jobLogList:
if isinstance(l, bytes):
l = l.decode('utf-8')
if not l.endswith('\n'):
l += '\n'
f.write(l.encode('utf-8'))
for alternateName in jobNames[1:]:
# There are chained jobs in this output - indicate this with a symlink
# of the job's name to this file
name = createName(path, alternateName, extension, failed)
if not os.path.exists(name):
os.symlink(os.path.relpath(fullName, path), name)
[docs]
@classmethod
def statsAndLoggingAggregator(cls, jobStore: 'AbstractJobStore', stop: Event, config: 'Config') -> None:
"""
The following function is used for collating stats/reporting log messages from the workers.
Works inside of a thread, collates as long as the stop flag is not True.
"""
# Overall timing
startTime = time.time()
startClock = ResourceMonitor.get_total_cpu_time()
def callback(fileHandle: Union[IO[bytes], IO[str]]) -> None:
statsStr = fileHandle.read()
if not isinstance(statsStr, str):
statsStr = statsStr.decode()
stats = json.loads(statsStr, object_hook=Expando)
if not stats:
return
try:
# Handle all the log_to_leader messages
logs = stats.workers.logs_to_leader
except AttributeError:
# To be expected if there were no calls to log_to_leader()
pass
else:
for message in logs:
logger.log(int(message.level),
'Got message from job at time %s: %s',
time.strftime('%m-%d-%Y %H:%M:%S'), message.text)
try:
# Handle all the user-level text streams reported back (command output, etc.)
user_logs = stats.workers.logging_user_streams
except AttributeError:
# To be expected if there were no calls to log_user_stream()
pass
else:
for stream_entry in user_logs:
try:
# Unpack the stream name and text.
name, text = stream_entry.name, stream_entry.text
except AttributeError:
# Doesn't have a user-provided stream name and stream
# text, so skip it.
continue
# Since this is sent as inline text we need to pretend to stream it.
# TODO: Save these as individual files if they start to get too big?
cls.logWithFormatting(name, io.StringIO(text), logger.info)
# Save it as a log file, as if it were a Toil-level job.
cls.writeLogFiles([name], [text], config=config)
try:
logs = stats.logs
except AttributeError:
pass
else:
# we may have multiple jobs per worker
jobNames = logs.names
messages = logs.messages
cls.logWithFormatting(f'Log from job "{jobNames[0]}"', messages,
message='Received Toil worker log. Disable debug level logging to hide this output')
cls.writeLogFiles(jobNames, messages, config=config)
while True:
# This is a indirect way of getting a message to the thread to exit
if stop.is_set():
jobStore.read_logs(callback)
break
if jobStore.read_logs(callback) == 0:
time.sleep(0.5) # Avoid cycling too fast
# Finish the stats file
text = json.dumps(dict(total_time=str(time.time() - startTime),
total_clock=str(ResourceMonitor.get_total_cpu_time() - startClock)), ensure_ascii=True)
jobStore.write_logs(text)
[docs]
def check(self) -> None:
"""
Check on the stats and logging aggregator.
:raise RuntimeError: If the underlying thread has quit.
"""
if not self._worker.is_alive():
raise RuntimeError("Stats and logging thread has quit")
[docs]
def shutdown(self) -> None:
"""Finish up the stats/logging aggregation thread."""
logger.debug('Waiting for stats and logging collator thread to finish ...')
startTime = time.time()
self._stop.set()
self._worker.join()
logger.debug('... finished collating stats and logs. Took %s seconds', time.time() - startTime)
# in addition to cleaning on exceptions, onError should clean if there are any failed jobs
[docs]
def set_log_level(level: str, set_logger: Optional[logging.Logger] = None) -> None:
"""Sets the root logger level to a given string level (like "INFO")."""
level = "CRITICAL" if level.upper() == "OFF" else level.upper()
set_logger = set_logger if set_logger else root_logger
set_logger.setLevel(level)
# Suppress any random loggers introduced by libraries we use.
# Especially boto/boto3. They print too much. -__-
suppress_exotic_logging(__name__)
[docs]
def install_log_color(set_logger: Optional[logging.Logger] = None) -> None:
"""Make logs colored."""
# Most of this code is taken from miniwdl
# delayed import
import coloredlogs # type: ignore[import-untyped]
level_styles = dict(coloredlogs.DEFAULT_LEVEL_STYLES)
level_styles["debug"]["color"] = 242
level_styles["notice"] = {"color": "green", "bold": True}
level_styles["error"]["bold"] = True
level_styles["warning"]["bold"] = True
level_styles["info"] = {}
field_styles = dict(coloredlogs.DEFAULT_FIELD_STYLES)
field_styles["asctime"] = {"color": "blue"}
field_styles["name"] = {"color": "magenta"}
field_styles["levelname"] = {"color": "blue"}
field_styles["threadName"] = {"color": "blue"}
fmt = "[%(asctime)s] [%(threadName)s] [%(levelname).1s] [%(name)s] %(message)s" # mimic old toil logging format
set_logger = set_logger if set_logger else root_logger
coloredlogs.install(
level=set_logger.getEffectiveLevel(),
logger=set_logger,
level_styles=level_styles,
field_styles=field_styles,
datefmt="%Y-%m-%dT%H:%M:%S%z", # mimic old toil date format
fmt=fmt,
)
[docs]
def add_logging_options(parser: ArgumentParser, default_level: Optional[int] = None) -> None:
"""
Add logging options to set the global log level.
:param default_level: A logging level, like logging.INFO, to use as the default.
"""
if default_level is None:
# Make sure we have a log levle to make the default
default_level = DEFAULT_LOGLEVEL
default_level_name = logging.getLevelName(default_level)
group = parser.add_argument_group("Logging Options")
levels = ['Critical', 'Error', 'Warning', 'Debug', 'Info']
for level in levels:
group.add_argument(f"--log{level}", dest="logLevel", default=default_level_name, action="store_const",
const=level, help=f"Turn on loglevel {level}. Default: {default_level_name}.")
levels += [l.lower() for l in levels] + [l.upper() for l in levels]
group.add_argument("--logOff", dest="logLevel", default=default_level_name,
action="store_const", const="CRITICAL", help="Same as --logCRITICAL.")
# Maybe deprecate the above in favor of --logLevel?
group.add_argument("--logLevel", dest="logLevel", default=default_level_name, choices=levels,
help=f"Set the log level. Default: {default_level_name}. Options: {levels}.")
group.add_argument("--logFile", dest="logFile", help="File to log in.")
group.add_argument("--rotatingLogging", dest="logRotating", action="store_true", default=False,
help="Turn on rotating logging, which prevents log files from getting too big.")
group.add_argument("--logColors", dest="colored_logs", default=True, type=strtobool, metavar="BOOL",
help="Enable or disable colored logging. Default: %(default)s")
[docs]
def log_to_file(log_file: Optional[str], log_rotation: bool) -> None:
if log_file and log_file not in __loggingFiles:
logger.debug(f"Logging to file '{log_file}'.")
__loggingFiles.append(log_file)
handler: Union[RotatingFileHandler, logging.FileHandler]
if log_rotation:
handler = RotatingFileHandler(log_file, maxBytes=1000000, backupCount=1)
else:
handler = logging.FileHandler(log_file)
root_logger.addHandler(handler)
[docs]
def set_logging_from_options(options: Union["Config", Namespace]) -> None:
configure_root_logger()
options.logLevel = options.logLevel or logging.getLevelName(root_logger.getEffectiveLevel())
set_log_level(options.logLevel)
if options.colored_logs:
install_log_color()
logger.debug(f"Root logger is at level '{logging.getLevelName(root_logger.getEffectiveLevel())}', "
f"'toil' logger at level '{logging.getLevelName(toil_logger.getEffectiveLevel())}'.")
# start logging to log file if specified
log_to_file(options.logFile, options.logRotating)
[docs]
def suppress_exotic_logging(local_logger: str) -> None:
"""
Attempts to suppress the loggers of all non-Toil packages by setting them to CRITICAL.
For example: 'requests_oauthlib', 'google', 'boto', 'websocket', 'oauthlib', etc.
This will only suppress loggers that have already been instantiated and can be seen in the environment,
except for the list declared in "always_suppress".
This is important because some packages, particularly boto3, are not always instantiated yet in the
environment when this is run, and so we create the logger and set the level preemptively.
"""
never_suppress = ['toil', '__init__', '__main__', 'toil-rt', 'cwltool']
always_suppress = ['boto3', 'boto', 'botocore'] # ensure we suppress even before instantiated
top_level_loggers: List[str] = []
# Due to https://stackoverflow.com/questions/61683713
for pkg_logger in list(logging.Logger.manager.loggerDict.keys()) + always_suppress:
if pkg_logger != local_logger:
# many sub-loggers may exist, like "boto.a", "boto.b", "boto.c"; we only want the top_level: "boto"
top_level_logger = pkg_logger.split('.')[0] if '.' in pkg_logger else pkg_logger
if top_level_logger not in top_level_loggers + never_suppress:
top_level_loggers.append(top_level_logger)
logging.getLogger(top_level_logger).setLevel(logging.CRITICAL)
logger.debug(f'Suppressing the following loggers: {set(top_level_loggers)}')
