__author__ = "Johannes Köster"
__copyright__ = "Copyright 2022, Johannes Köster"
__email__ = "johannes.koester@uni-due.de"
__license__ = "MIT"
import logging as _logging
import platform
import time
import datetime
import sys
import os
import json
import threading
from functools import partial
import inspect
import textwrap
[docs]
def get_default_exec_mode():
from snakemake_interface_executor_plugins.settings import ExecMode
return ExecMode.DEFAULT
[docs]
class ColorizingStreamHandler(_logging.StreamHandler):
BLACK, RED, GREEN, YELLOW, BLUE, MAGENTA, CYAN, WHITE = range(8)
RESET_SEQ = "\033[0m"
COLOR_SEQ = "\033[%dm"
BOLD_SEQ = "\033[1m"
colors = {
"WARNING": YELLOW,
"INFO": GREEN,
"DEBUG": BLUE,
"CRITICAL": MAGENTA,
"ERROR": RED,
}
[docs]
def __init__(self, nocolor=False, stream=sys.stderr, mode=None):
super().__init__(stream=stream)
if mode is None:
mode = get_default_exec_mode()
self._output_lock = threading.Lock()
self.nocolor = nocolor or not self.can_color_tty(mode)
def can_color_tty(self, mode):
from snakemake_interface_executor_plugins.settings import ExecMode
if "TERM" in os.environ and os.environ["TERM"] == "dumb":
return False
if mode == ExecMode.SUBPROCESS:
return True
return self.is_tty and not platform.system() == "Windows"
@property
def is_tty(self):
isatty = getattr(self.stream, "isatty", None)
return isatty and isatty()
def emit(self, record):
with self._output_lock:
try:
self.format(record) # add the message to the record
self.stream.write(self.decorate(record))
self.stream.write(getattr(self, "terminator", "\n"))
self.flush()
except BrokenPipeError as e:
raise e
except (KeyboardInterrupt, SystemExit):
# ignore any exceptions in these cases as any relevant messages have been printed before
pass
except Exception as e:
self.handleError(record)
def decorate(self, record):
message = record.message
message = [message]
if not self.nocolor and record.levelname in self.colors:
message.insert(0, self.COLOR_SEQ % (30 + self.colors[record.levelname]))
message.append(self.RESET_SEQ)
return "".join(message)
[docs]
class SlackLogger:
[docs]
def __init__(self):
from slack_sdk import WebClient
self.token = os.getenv("SLACK_TOKEN")
if not self.token:
print(
"The use of slack logging requires the user to set a user specific slack User OAuth token to the SLACK_TOKEN environment variable. Set this variable by 'export SLACK_TOKEN=your_token'. To generate your token please visit https://api.slack.com/authentication/token-types#user."
)
exit(-1)
self.slack = WebClient(self.token)
# Check for success
try:
auth = self.slack.auth_test().data
except Exception:
print(
"Slack connection failed. Please compare your provided slack token exported in the SLACK_TOKEN environment variable with your online token (app). This token can be tested at https://api.slack.com/methods/auth.test/test. A different token can be set up by 'export SLACK_TOKEN=your_token'."
)
exit(-1)
self.own_id = auth["user_id"]
self.error_occured = False
self.slack.chat_postMessage(
channel=self.own_id, text="Snakemake has connected."
)
def log_handler(self, msg):
if "error" in msg["level"] and not self.error_occured:
self.slack.chat_postMessage(
channel=self.own_id, text="At least one error occurred."
)
self.error_occured = True
if msg["level"] == "progress" and msg["done"] == msg["total"]:
# workflow finished
self.slack.chat_postMessage(channel=self.own_id, text="Workflow complete.")
[docs]
class WMSLogger:
[docs]
def __init__(self, address=None, args=None, metadata=None):
"""A WMS monitor is a workflow management system logger to enable
monitoring with something like Panoptes. The address corresponds to
the --wms-monitor argument, and args should be a list of key/value
pairs with extra arguments to send to identify the workflow. We require
the logging server to exist and receive creating a workflow to start
the run, but we don't exit with error if any updates fail, as the
workflow will already be running and it would not be worth stopping it.
"""
from snakemake.resources import DefaultResources
self.address = address or "http:127.0.0.1:5000"
self.args = list(map(DefaultResources.decode_arg, args)) if args else []
self.args = {item[0]: item[1] for item in list(self.args)}
self.metadata = metadata or {}
# A token is suggested but not required, depends on server
self.token = os.getenv("WMS_MONITOR_TOKEN")
self.service_info()
# Create or retrieve the existing workflow
self.create_workflow()
def service_info(self):
"""Service Info ensures that the server is running. We exit on error
if this isn't the case, so the function can be called in init.
"""
import requests
# We first ensure that the server is running, period
response = requests.get(
f"{self.address}/api/service-info", headers=self._headers
)
if response.status_code != 200:
sys.stderr.write(f"Problem with server: {self.address} {os.linesep}")
sys.exit(-1)
# And then that it's ready to be interacted with
if response.json().get("status") != "running":
sys.stderr.write(
f"The status of the server {self.address} is not in 'running' mode {os.linesep}"
)
sys.exit(-1)
def create_workflow(self):
"""Creating a workflow means pinging the wms server for a new id, or
if providing an argument for an existing workflow, ensuring that
it exists and receiving back the same identifier.
"""
import requests
# Send the working directory to the server
workdir = (
os.getcwd()
if not self.metadata.get("directory")
else os.path.abspath(self.metadata["directory"])
)
# Prepare a request that has metadata about the job
metadata = {
"command": self.metadata.get("command"),
"workdir": workdir,
}
response = requests.get(
f"{self.address}/create_workflow",
headers=self._headers,
params=self.args,
data=metadata,
)
# Extract the id from the response
id = response.json()["id"]
# Check the response, will exit on any error
self.check_response(response, "/create_workflow")
# Provide server parameters to the logger
headers = (
{"Content-Type": "application/json"}
if self._headers is None
else {**self._headers, **{"Content-Type": "application/json"}}
)
# Send the workflow name to the server
response_change_workflow_name = requests.put(
f"{self.address }/api/workflow/{id}",
headers=headers,
data=json.dumps(self.args),
)
# Check the response, will exit on any error
self.check_response(response_change_workflow_name, f"/api/workflow/{id}")
# Provide server parameters to the logger
self.server = {"url": self.address, "id": id}
def check_response(self, response, endpoint="wms monitor request"):
"""A helper function to take a response and check for an expected set of
error codes, 404 (not found), 401 (requires authorization), 403 (permission
denied), 500 (server error) and 200 (success).
"""
status_code = response.status_code
# Cut out early on success
if status_code == 200:
return
if status_code == 404:
sys.stderr.write(f"The wms {endpoint} endpoint was not found")
sys.exit(-1)
elif status_code == 401:
sys.stderr.write(
"Authorization is required with a WMS_MONITOR_TOKEN in the environment"
)
sys.exit(-1)
elif status_code == 500:
sys.stderr.write(
f"There was a server error when trying to access {endpoint}"
)
sys.exit(-1)
elif status_code == 403:
sys.stderr.write("Permission is denied to %s." % endpoint)
sys.exit(-1)
# Any other response code is not acceptable
sys.stderr.write(
f"The {endpoint} response code {response.status_code} is not recognized."
)
@property
def _headers(self):
"""return authenticated headers if the user has provided a token"""
headers = None
if self.token:
headers = {"Authorization": "Bearer %s" % self.token}
return headers
def _parse_message(self, msg):
"""Given a message dictionary, we want to loop through the key, value
pairs and convert some attributes to strings (e.g., jobs are fine to be
represented as names) and return a dictionary.
"""
result = {}
for key, value in msg.items():
# For a job, the name is sufficient
if key == "job":
result[key] = str(value)
# For an exception, return the name and a message
elif key == "exception":
result[key] = "{}: {}".format(
msg["exception"].__class__.__name__,
msg["exception"] or "Exception",
)
# All other fields are json serializable
else:
result[key] = value
# Return a json dumped string
return json.dumps(result)
def log_handler(self, msg):
"""Custom wms server log handler.
Sends the log to the server.
Args:
msg (dict): the log message dictionary
"""
import requests
url = self.server["url"] + "/update_workflow_status"
server_info = {
"msg": self._parse_message(msg),
"timestamp": time.asctime(),
"id": self.server["id"],
}
response = requests.post(url, data=server_info, headers=self._headers)
self.check_response(response, "/update_workflow_status")
[docs]
class Logger:
[docs]
def __init__(self):
from snakemake_interface_executor_plugins.settings import ExecMode
self.logger = _logging.getLogger(__name__)
self.log_handler = [self.text_handler]
self.stream_handler = None
self.printshellcmds = False
self.printreason = False
self.debug_dag = False
self.quiet = set()
self.logfile = None
self.last_msg_was_job_info = False
self.mode = ExecMode.DEFAULT
self.show_failed_logs = False
self.logfile_handler = None
self.dryrun = False
def setup_logfile(self):
from snakemake_interface_executor_plugins.settings import ExecMode
if self.mode == ExecMode.DEFAULT and not self.dryrun:
os.makedirs(os.path.join(".snakemake", "log"), exist_ok=True)
self.logfile = os.path.abspath(
os.path.join(
".snakemake",
"log",
datetime.datetime.now().isoformat().replace(":", "")
+ ".snakemake.log",
)
)
self.logfile_handler = _logging.FileHandler(self.logfile)
self.logger.addHandler(self.logfile_handler)
def cleanup(self):
from snakemake_interface_executor_plugins.settings import ExecMode
if self.mode == ExecMode.DEFAULT and self.logfile_handler is not None:
self.logger.removeHandler(self.logfile_handler)
self.logfile_handler.close()
self.log_handler = [self.text_handler]
def get_logfile(self):
if self.logfile is not None:
self.logfile_handler.flush()
return self.logfile
def handler(self, msg):
msg["timestamp"] = time.time()
for handler in self.log_handler:
handler(msg)
def set_stream_handler(self, stream_handler):
if self.stream_handler is not None:
self.logger.removeHandler(self.stream_handler)
self.stream_handler = stream_handler
self.logger.addHandler(stream_handler)
def set_level(self, level):
self.logger.setLevel(level)
def logfile_hint(self):
from snakemake_interface_executor_plugins.settings import ExecMode
if self.mode == ExecMode.DEFAULT and not self.dryrun:
logfile = self.get_logfile()
self.info(f"Complete log: {os.path.relpath(logfile)}")
def location(self, msg):
callerframerecord = inspect.stack()[1]
frame = callerframerecord[0]
info = inspect.getframeinfo(frame)
self.debug(
"{}: {info.filename}, {info.function}, {info.lineno}".format(msg, info=info)
)
def info(self, msg, indent=False):
self.handler(dict(level="info", msg=msg, indent=indent))
def warning(self, msg, *fmt_items):
if fmt_items:
msg = msg % fmt_items
self.handler(dict(level="warning", msg=msg))
def debug(self, msg):
self.handler(dict(level="debug", msg=msg))
def error(self, msg):
self.handler(dict(level="error", msg=msg))
def progress(self, done=None, total=None):
self.handler(dict(level="progress", done=done, total=total))
def resources_info(self, msg):
self.handler(dict(level="resources_info", msg=msg))
def run_info(self, msg):
self.handler(dict(level="run_info", msg=msg))
def group_info(self, **msg):
msg["level"] = "group_info"
self.handler(msg)
def job_info(self, **msg):
msg["level"] = "job_info"
self.handler(msg)
def job_error(self, **msg):
msg["level"] = "job_error"
self.handler(msg)
def group_error(self, **msg):
msg["level"] = "group_error"
self.handler(msg)
def dag_debug(self, msg):
self.handler(dict(level="dag_debug", **msg))
def shellcmd(self, msg, indent=False):
if msg is not None:
msg = dict(level="shellcmd", msg=msg)
msg["indent"] = indent
self.handler(msg)
def job_finished(self, **msg):
msg["level"] = "job_finished"
self.handler(msg)
def rule_info(self, **msg):
msg["level"] = "rule_info"
self.handler(msg)
def d3dag(self, **msg):
msg["level"] = "d3dag"
self.handler(msg)
def is_quiet_about(self, msg_type: str):
from snakemake.settings import Quietness
return (
Quietness.ALL in self.quiet
or Quietness.parse_choice(msg_type) in self.quiet
)
def text_handler(self, msg):
"""The default snakemake log handler.
Prints the output to the console.
Args:
msg (dict): the log message dictionary
"""
if self.is_quiet_about("all"):
# do not log anything
return
def job_info(msg):
def format_item(item, omit=None, valueformat=str):
value = msg[item]
if value != omit:
return f" {item}: {valueformat(value)}"
yield "{}{} {}:".format(
"local" if msg["local"] else "",
"checkpoint" if msg["is_checkpoint"] else "rule",
msg["name"],
)
for item in ["input", "output", "log"]:
fmt = format_item(item, omit=[], valueformat=", ".join)
if fmt != None:
yield fmt
singleitems = ["jobid", "benchmark"]
if self.printreason:
singleitems.append("reason")
for item in singleitems:
fmt = format_item(item, omit=None)
if fmt != None:
yield fmt
wildcards = format_wildcards(msg["wildcards"])
if wildcards:
yield f" wildcards: {wildcards}"
for item, omit in zip("priority threads".split(), [0, 1]):
fmt = format_item(item, omit=omit)
if fmt != None:
yield fmt
resources = format_resources(msg["resources"])
if resources:
yield f" resources: {resources}"
def show_logs(logs):
for f in logs:
try:
content = open(f, "r").read()
except FileNotFoundError:
yield f"Logfile {f} not found."
return
lines = content.splitlines()
logfile_header = f"Logfile {f}:"
if not lines:
logfile_header += " empty file"
yield logfile_header
return
yield logfile_header
# take the length of the longest line, but limit to max 80
max_len = min(max(max(len(l) for l in lines), len(logfile_header)), 80)
yield "=" * max_len
yield from lines
yield "=" * max_len
def indent(item):
if msg.get("indent"):
return f" {item}"
else:
return item
def timestamp():
self.logger.info(indent(f"[{time.asctime()}]"))
level = msg["level"]
if level == "job_info" and not self.is_quiet_about("rules"):
if not self.last_msg_was_job_info:
self.logger.info("")
timestamp()
if msg["msg"] is not None:
self.logger.info(indent("Job {}: {}".format(msg["jobid"], msg["msg"])))
if self.printreason:
self.logger.info(indent("Reason: {}".format(msg["reason"])))
else:
self.logger.info("\n".join(map(indent, job_info(msg))))
if msg["is_checkpoint"]:
self.logger.warning(
indent("DAG of jobs will be updated after completion.")
)
if msg["is_handover"]:
self.logger.warning("Handing over execution to foreign system...")
self.logger.info("")
self.last_msg_was_job_info = True
elif level == "group_info" and not self.is_quiet_about("rules"):
timestamp()
msg = "group job {} (jobs in lexicogr. order):".format(msg["groupid"])
if not self.last_msg_was_job_info:
msg = "\n" + msg
self.logger.info(msg)
elif level == "job_error":
def job_error():
yield "Error in rule {}:".format(msg["name"])
if msg["msg"]:
yield " message: {}".format(msg["msg"])
yield " jobid: {}".format(msg["jobid"])
if msg["input"]:
yield " input: {}".format(", ".join(msg["input"]))
if msg["output"]:
yield " output: {}".format(", ".join(msg["output"]))
if msg["log"]:
yield " log: {} (check log file(s) for error details)".format(
", ".join(msg["log"])
)
if msg["conda_env"]:
yield " conda-env: {}".format(msg["conda_env"])
if msg["shellcmd"]:
yield " shell:\n {}\n (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)".format(
msg["shellcmd"]
)
for item in msg["aux"].items():
yield " {}: {}".format(*item)
if self.show_failed_logs and msg["log"]:
yield from show_logs(msg["log"])
yield ""
timestamp()
self.logger.error("\n".join(map(indent, job_error())))
elif level == "group_error":
def group_error():
yield f"Error in group {msg['groupid']}:"
if msg["msg"]:
yield f" message: {msg['msg']}"
if msg["aux_logs"]:
yield f" log: {', '.join(msg['aux_logs'])} (check log file(s) for error details)"
yield " jobs:"
for info in msg["job_error_info"]:
yield f" rule {info['name']}:"
yield f" jobid: {info['jobid']}"
if info["output"]:
yield f" output: {', '.join(info['output'])}"
if info["log"]:
yield f" log: {', '.join(info['log'])} (check log file(s) for error details)"
logs = msg["aux_logs"] + [
f for info in msg["job_error_info"] for f in info["log"]
]
if self.show_failed_logs and logs:
yield from show_logs(logs)
yield ""
timestamp()
self.logger.error("\n".join(group_error()))
else:
if level == "info" and not self.is_quiet_about("progress"):
self.logger.warning(msg["msg"])
if level == "warning":
self.logger.critical(msg["msg"])
elif level == "error":
self.logger.error(msg["msg"])
elif level == "debug":
self.logger.debug(msg["msg"])
elif level == "resources_info" and not self.is_quiet_about("progress"):
self.logger.warning(msg["msg"])
elif level == "run_info" and not self.is_quiet_about("progress"):
self.logger.warning(msg["msg"])
elif level == "progress" and not self.is_quiet_about("progress"):
done = msg["done"]
total = msg["total"]
self.logger.info(
"{} of {} steps ({}) done".format(
done, total, format_percentage(done, total)
)
)
elif level == "shellcmd":
if self.printshellcmds:
self.logger.warning(indent(msg["msg"]))
elif level == "job_finished" and not self.is_quiet_about("progress"):
timestamp()
self.logger.info("Finished job {}.".format(msg["jobid"]))
pass
elif level == "rule_info":
self.logger.info(msg["name"])
if msg["docstring"]:
self.logger.info(" " + msg["docstring"])
elif level == "d3dag":
print(json.dumps({"nodes": msg["nodes"], "links": msg["edges"]}))
elif level == "dag_debug":
if self.debug_dag:
if "file" in msg:
self.logger.warning(
"file {file}:\n {msg}\n{exception}".format(
file=msg["file"],
msg=msg["msg"],
exception=textwrap.indent(
str(msg["exception"]), " "
),
)
)
else:
job = msg["job"]
self.logger.warning(
"{status} job {name}\n wildcards: {wc}".format(
status=msg["status"],
name=job.rule.name,
wc=format_wildcards(job.wildcards),
)
)
self.last_msg_was_job_info = False
format_resources = partial(format_dict, omit_keys={"_cores", "_nodes"})
format_wildcards = format_dict
logger = Logger()
[docs]
def setup_logger(
handler=[],
quiet=False,
printshellcmds=False,
printreason=True,
debug_dag=False,
nocolor=False,
stdout=False,
debug=False,
mode=None,
show_failed_logs=False,
dryrun=False,
):
from snakemake.settings import Quietness
if mode is None:
mode = get_default_exec_mode()
if quiet is None:
# not quiet at all
quiet = set()
elif isinstance(quiet, bool):
if quiet:
quiet = {Quietness.PROGRESS, Quietness.RULES}
else:
quiet = set()
elif not isinstance(quiet, set):
raise ValueError(
"Unsupported value provided for quiet mode (either bool, None or list allowed)."
)
logger.log_handler.extend(handler)
# console output only if no custom logger was specified
stream_handler = ColorizingStreamHandler(
nocolor=nocolor,
stream=sys.stdout if stdout else sys.stderr,
mode=mode,
)
logger.set_stream_handler(stream_handler)
logger.set_level(_logging.DEBUG if debug else _logging.INFO)
logger.quiet = quiet
logger.printshellcmds = printshellcmds
logger.printreason = printreason
logger.debug_dag = debug_dag
logger.mode = mode
logger.dryrun = dryrun
logger.show_failed_logs = show_failed_logs