Source code for snakemake.logging

__author__ = "Johannes Köster"
__copyright__ = "Copyright 2021, Johannes Köster"
__email__ = ""
__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

from snakemake.common import DYNAMIC_FILL
from snakemake.common import Mode

[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": RED, "ERROR": RED, } def __init__( self, nocolor=False, stream=sys.stderr, use_threads=False, mode=Mode.default ): super().__init__(stream=stream) self._output_lock = threading.Lock() self.nocolor = nocolor or not self.can_color_tty(mode)
[docs] def can_color_tty(self, mode): if "TERM" in os.environ and os.environ["TERM"] == "dumb": return False if mode == Mode.subprocess: return True return self.is_tty and not platform.system() == "Windows"
@property def is_tty(self): isatty = getattr(, "isatty", None) return isatty and isatty()
[docs] def emit(self, record): with self._output_lock: try: self.format(record) # add the message to the record, "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)
[docs] 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: def __init__(self): from slacker import Slacker 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 legacy token to the SLACK_TOKEN environment variable. Set this variable by 'export SLACK_TOKEN=your_token'. To generate your token please visit" ) exit(-1) self.slack = Slacker(self.token) # Check for success try: auth = self.slack.auth.test().body except Exception: print( "Slack connection failed. Please compare your provided slack token exported in the SLACK_TOKEN environment variable with your online token at 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
[docs] def log_handler(self, msg): if msg["level"] == "error" and not self.error_occured: self.own_id, text="At least one error occured.", username="snakemake" ) self.error_occured = True if msg["level"] == "progress" and msg["done"] == msg["total"]: # workflow finished self.own_id, text="Workflow complete.", username="snakemake" )
[docs]class WMSLogger: 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:" self.args = map(DefaultResources.decode_arg, args) if args else [] 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()
[docs] 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( self.address + "/api/service-info", headers=self._headers ) if response.status_code != 200: sys.stderr.write( "Problem with server: {} {}".format(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( "The status of the server {} is not in 'running' mode {}".format( self.address, os.linesep ) ) sys.exit(-1)
[docs] 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 = { "snakefile": os.path.join(workdir, self.metadata.get("snakefile")), "command": self.metadata.get("command"), "workdir": workdir, } response = requests.get( self.address + "/create_workflow", headers=self._headers, params=self.args, data=metadata, ) # Check the response, will exit on any error self.check_response(response, "/create_workflow") # Provide server parameters to the logger self.server = {"url": self.address, "id": response.json()["id"]}
[docs] 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("The wms %s endpoint was not found" % endpoint) 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( "There was a server error when trying to access %s" % 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( "The %s response code %s is not recognized." % (endpoint, response.status_code) )
@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 represnted 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] = "%s: %s" % ( 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)
[docs] 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 =, data=server_info, headers=self._headers) self.check_response(response, "/update_workflow_status")
[docs]class Logger: def __init__(self): 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 = False self.logfile = None self.last_msg_was_job_info = False self.mode = Mode.default self.show_failed_logs = False self.logfile_handler = None
[docs] def setup_logfile(self): if self.mode == Mode.default: os.makedirs(os.path.join(".snakemake", "log"), exist_ok=True) self.logfile = os.path.abspath( os.path.join( ".snakemake", "log",":", "") + ".snakemake.log", ) ) self.logfile_handler = _logging.FileHandler(self.logfile) self.logger.addHandler(self.logfile_handler)
[docs] def cleanup(self): if self.mode == Mode.default and self.logfile_handler is not None: self.logger.removeHandler(self.logfile_handler) self.logfile_handler.close() self.log_handler = [self.text_handler]
[docs] def get_logfile(self): if self.logfile is not None: self.logfile_handler.flush() return self.logfile
[docs] def remove_logfile(self): if self.mode == Mode.default: self.logfile_handler.close() os.remove(self.logfile)
[docs] def handler(self, msg): for handler in self.log_handler: handler(msg)
[docs] 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)
[docs] def set_level(self, level): self.logger.setLevel(level)
[docs] def logfile_hint(self): if self.mode == Mode.default: logfile = self.get_logfile()"Complete log: {}".format(logfile))
[docs] 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) )
[docs] def info(self, msg, indent=False): self.handler(dict(level="info", msg=msg, indent=indent))
[docs] def warning(self, msg): self.handler(dict(level="warning", msg=msg))
[docs] def debug(self, msg): self.handler(dict(level="debug", msg=msg))
[docs] def error(self, msg): self.handler(dict(level="error", msg=msg))
[docs] def progress(self, done=None, total=None): self.handler(dict(level="progress", done=done, total=total))
[docs] def resources_info(self, msg): self.handler(dict(level="resources_info", msg=msg))
[docs] def run_info(self, msg): self.handler(dict(level="run_info", msg=msg))
[docs] def group_info(self, **msg): msg["level"] = "group_info" self.handler(msg)
[docs] def job_info(self, **msg): msg["level"] = "job_info" self.handler(msg)
[docs] def job_error(self, **msg): msg["level"] = "job_error" self.handler(msg)
[docs] def group_error(self, **msg): msg["level"] = "group_error" self.handler(msg)
[docs] def dag_debug(self, msg): self.handler(dict(level="dag_debug", **msg))
[docs] def shellcmd(self, msg, indent=False): if msg is not None: msg = dict(level="shellcmd", msg=msg) msg["indent"] = indent self.handler(msg)
[docs] def job_finished(self, **msg): msg["level"] = "job_finished" self.handler(msg)
[docs] def rule_info(self, **msg): msg["level"] = "rule_info" self.handler(msg)
[docs] def d3dag(self, **msg): msg["level"] = "d3dag" self.handler(msg)
[docs] def text_handler(self, msg): """The default snakemake log handler. Prints the output to the console. Args: msg (dict): the log message dictionary """ def job_info(msg): def format_item(item, omit=None, valueformat=str): value = msg[item] if value != omit: return " {}: {}".format(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 " 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 " resources: " + resources def indent(item): if msg.get("indent"): return " " + item else: return item def timestamp():"[{}]".format(time.asctime()))) level = msg["level"] if level == "job_info" and not self.quiet: if not self.last_msg_was_job_info:"") timestamp() if msg["msg"] is not None:"Job {}: {}".format(msg["jobid"], msg["msg"]))) if self.printreason:"Reason: {}".format(msg["reason"]))) else:"\n".join(map(indent, job_info(msg)))) if msg["is_checkpoint"]: self.logger.warning( indent("Downstream jobs will be updated " "after completion.") ) if msg["is_handover"]: self.logger.warning("Handing over execution to foreign system...")"") self.last_msg_was_job_info = True elif level == "group_info" and not self.quiet: timestamp() if not self.last_msg_was_job_info:"") "group job {} (jobs in lexicogr. order):".format(msg["groupid"]) ) elif level == "job_error": timestamp() self.logger.error(indent("Error in rule {}:".format(msg["name"]))) self.logger.error(indent(" jobid: {}".format(msg["jobid"]))) if msg["output"]: self.logger.error( indent(" output: {}".format(", ".join(msg["output"]))) ) if msg["log"]: self.logger.error( indent( " log: {} (check log file(s) for error message)".format( ", ".join(msg["log"]) ) ) ) if msg["conda_env"]: self.logger.error(indent(" conda-env: {}".format(msg["conda_env"]))) if msg["shellcmd"]: self.logger.error( indent( " 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(): self.logger.error(indent(" {}: {}".format(*item))) if self.show_failed_logs and msg["log"]: for f in msg["log"]: try: self.logger.error("Logfile {}:\n{}".format(f, open(f).read())) except FileNotFoundError: self.logger.error("Logfile {} not found.".format(f)) self.logger.error("") elif level == "group_error": timestamp() self.logger.error("Error in group job {}:".format(msg["groupid"])) else: if level == "info" and not self.quiet: self.logger.warning(msg["msg"]) if level == "warning": self.logger.warning(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.quiet: self.logger.warning(msg["msg"]) elif level == "run_info": self.logger.warning(msg["msg"]) elif level == "progress" and not self.quiet: done = msg["done"] total = msg["total"] "{} 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.quiet: timestamp()"Finished job {}.".format(msg["jobid"])) pass elif level == "rule_info":["name"]) if msg["docstring"]:" " + 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"],, wc=format_wildcards(job.wildcards), ) ) self.last_msg_was_job_info = False
[docs]def format_dict(dict_like, omit_keys=[], omit_values=[]): from import Namedlist if isinstance(dict_like, Namedlist): items = dict_like.items() elif isinstance(dict_like, dict): items = dict_like.items() else: raise ValueError( "bug: format_dict applied to something neither a dict nor a Namedlist" ) return ", ".join( "{}={}".format(name, str(value)) for name, value in items if name not in omit_keys and value not in omit_values )
format_resources = partial(format_dict, omit_keys={"_cores", "_nodes"}) format_wildcards = partial(format_dict, omit_values={DYNAMIC_FILL})
[docs]def format_resource_names(resources, omit_resources="_cores _nodes".split()): return ", ".join(name for name in resources if name not in omit_resources)
[docs]def format_percentage(done, total): """Format percentage from given fraction while avoiding superflous precision.""" if done == total: return "100%" if done == 0: return "0%" precision = 0 fraction = done / total fmt_precision = "{{:.{}%}}".format fmt = lambda fraction: fmt_precision(precision).format(fraction) while fmt(fraction) == "100%" or fmt(fraction) == "0%": precision += 1 return fmt(fraction)
logger = Logger()
[docs]def setup_logger( handler=[], quiet=False, printshellcmds=False, printreason=False, debug_dag=False, nocolor=False, stdout=False, debug=False, use_threads=False, mode=Mode.default, show_failed_logs=False, ): 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, use_threads=use_threads, 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.show_failed_logs = show_failed_logs