Merge pull request #1893 from cmu-delphi/release/indicators_v0.3.46_u…

…tils_v0.3.20

Release covidcast-indicators 0.3.46

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.45
+current_version = 0.3.46
 commit = True
 message = chore: bump covidcast-indicators to {new_version}
 tag = False

_delphi_utils_python/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.19
+current_version = 0.3.20
 commit = True
 message = chore: bump delphi_utils to {new_version}
 tag = False

_delphi_utils_python/delphi_utils/__init__.py

@@ -15,4 +15,4 @@
 from .nancodes import Nans
 from .weekday import Weekday
 
-__version__ = "0.3.19"
+__version__ = "0.3.20"

_delphi_utils_python/delphi_utils/logger.py

@@ -1,21 +1,45 @@
-"""Structured logger utility for creating JSON logs in Delphi pipelines."""
+"""Structured logger utility for creating JSON logs."""
+
+# the Delphi group uses two ~identical versions of this file.
+# try to keep them in sync with edits, for sanity.
+#   https://github.com/cmu-delphi/covidcast-indicators/blob/main/_delphi_utils_python/delphi_utils/logger.py  # pylint: disable=line-too-long
+#   https://github.com/cmu-delphi/delphi-epidata/blob/dev/src/common/logger.py
+
+import contextlib
 import logging
+import multiprocessing
+import os
 import sys
 import threading
+from traceback import format_exception
+
 import structlog
 
 
 def handle_exceptions(logger):
     """Handle exceptions using the provided logger."""
-    def exception_handler(etype, value, traceback):
+
+    def exception_handler(scope, etype, value, traceback):
         logger.exception("Top-level exception occurred",
-                         exc_info=(etype, value, traceback))
+                         scope=scope, exc_info=(etype, value, traceback))
+
+    def sys_exception_handler(etype, value, traceback):
+        exception_handler("sys", etype, value, traceback)
 
-    def multithread_exception_handler(args):
-        exception_handler(args.exc_type, args.exc_value, args.exc_traceback)
+    def threading_exception_handler(args):
+        if args.exc_type == SystemExit and args.exc_value.code == 0:
+            # `sys.exit(0)` is considered "successful termination":
+            #   https://docs.python.org/3/library/sys.html#sys.exit
+            logger.debug("normal thread exit", thread=args.thread,
+                        stack="".join(
+                            format_exception(
+                                args.exc_type, args.exc_value, args.exc_traceback)))
+        else:
+            exception_handler(f"thread: {args.thread}",
+                              args.exc_type, args.exc_value, args.exc_traceback)
 
-    sys.excepthook = exception_handler
-    threading.excepthook = multithread_exception_handler
+    sys.excepthook = sys_exception_handler
+    threading.excepthook = threading_exception_handler
 
 
 def get_structured_logger(name=__name__,
@@ -40,12 +64,21 @@ def get_structured_logger(name=__name__,
     is a good choice.
     filename: An (optional) file to write log output.
     """
-    # Configure the basic underlying logging configuration
+    # Set the underlying logging configuration
+    if "LOG_DEBUG" in os.environ:
+        log_level = logging.DEBUG
+    else:
+        log_level = logging.INFO
+
     logging.basicConfig(
         format="%(message)s",
-        level=logging.INFO,
-        handlers=[logging.StreamHandler()]
-    )
+        level=log_level,
+        handlers=[logging.StreamHandler()])
+
+    def add_pid(_logger, _method_name, event_dict):
+        """Add current PID to the event dict."""
+        event_dict["pid"] = os.getpid()
+        return event_dict
 
     # Configure structlog. This uses many of the standard suggestions from
     # the structlog documentation.
@@ -57,6 +90,8 @@ def get_structured_logger(name=__name__,
             structlog.stdlib.add_logger_name,
             # Include log level in output.
             structlog.stdlib.add_log_level,
+            # Include PID in output.
+            add_pid,
             # Allow formatting into arguments e.g., logger.info("Hello, %s",
             # name)
             structlog.stdlib.PositionalArgumentsFormatter(),
@@ -68,7 +103,7 @@ def get_structured_logger(name=__name__,
             # Decode unicode characters
             structlog.processors.UnicodeDecoder(),
             # Render as JSON
-            structlog.processors.JSONRenderer()
+            structlog.processors.JSONRenderer(),
         ],
         # Use a dict class for keeping track of data.
         context_class=dict,
@@ -84,10 +119,136 @@ def get_structured_logger(name=__name__,
     system_logger = logging.getLogger(name)
     if filename and not system_logger.handlers:
         system_logger.addHandler(logging.FileHandler(filename))
-    system_logger.setLevel(logging.INFO)
+    system_logger.setLevel(log_level)
     logger = structlog.wrap_logger(system_logger)
 
     if log_exceptions:
         handle_exceptions(logger)
 
     return logger
+
+
+class LoggerThread():
+    """
+    A construct to use a logger from multiprocessing workers/jobs.
+
+    the bare structlog loggers are thread-safe but not multiprocessing-safe.
+    a `LoggerThread` will spawn a thread that listens to a mp.Queue
+    and logs messages from it with the provided logger,
+    so other processes can send logging messages to it
+    via the logger-like `SubLogger` interface.
+    the SubLogger even logs the pid of the caller.
+
+    this is good to use with a set of jobs that are part of a mp.Pool,
+    but isnt recommended for general use
+    because of overhead from threading and multiprocessing,
+    and because it might introduce lag to log messages.
+
+    somewhat inspired by:
+    docs.python.org/3/howto/logging-cookbook.html#logging-to-a-single-file-from-multiple-processes
+    """
+
+    class SubLogger():
+        """MP-safe logger-like interface to convey log messages to a listening LoggerThread."""
+
+        def __init__(self, queue):
+            """Create SubLogger with a bound queue."""
+            self.queue = queue
+
+        def _log(self, level, *args, **kwargs):
+            kwargs_plus = {'sub_pid': multiprocessing.current_process().pid}
+            kwargs_plus.update(kwargs)
+            self.queue.put([level, args, kwargs_plus])
+
+        def debug(self, *args, **kwargs):
+            """Log a DEBUG level message."""
+            self._log(logging.DEBUG, *args, **kwargs)
+
+        def info(self, *args, **kwargs):
+            """Log an INFO level message."""
+            self._log(logging.INFO, *args, **kwargs)
+
+        def warning(self, *args, **kwargs):
+            """Log a WARNING level message."""
+            self._log(logging.WARNING, *args, **kwargs)
+
+        def error(self, *args, **kwargs):
+            """Log an ERROR level message."""
+            self._log(logging.ERROR, *args, **kwargs)
+
+        def critical(self, *args, **kwargs):
+            """Log a CRITICAL level message."""
+            self._log(logging.CRITICAL, *args, **kwargs)
+
+
+    def get_sublogger(self):
+        """Retrieve SubLogger for this LoggerThread."""
+        return self.sublogger
+
+    def __init__(self, logger, q=None):
+        """Create and start LoggerThread with supplied logger, creating a queue if not provided."""
+        self.logger = logger
+        if q:
+            self.msg_queue = q
+        else:
+            self.msg_queue = multiprocessing.Queue()
+
+        def logger_thread_worker():
+            logger.info('thread started')
+            while True:
+                msg = self.msg_queue.get()
+                if msg == 'STOP':
+                    logger.debug('received stop signal')
+                    break
+                level, args, kwargs = msg
+                if level in [logging.DEBUG, logging.INFO, logging.WARNING,
+                             logging.ERROR, logging.CRITICAL]:
+                    logger.log(level, *args, **kwargs)
+                else:
+                    logger.error('received unknown logging level!  exiting...',
+                                 level=level, args_kwargs=(args, kwargs))
+                    break
+            logger.debug('stopping thread')
+
+        self.thread = threading.Thread(target=logger_thread_worker,
+                                       name="LoggerThread__"+logger.name)
+        logger.debug('starting thread')
+        self.thread.start()
+
+        self.sublogger = LoggerThread.SubLogger(self.msg_queue)
+        self.running = True
+
+    def stop(self):
+        """Terminate this LoggerThread."""
+        if not self.running:
+            self.logger.warning('thread already stopped')
+            return
+        self.logger.debug('sending stop signal')
+        self.msg_queue.put('STOP')
+        self.thread.join()
+        self.running = False
+        self.logger.info('thread stopped')
+
+
+@contextlib.contextmanager
+def pool_and_threadedlogger(logger, *poolargs):
+    """
+    Provide (to a context) a multiprocessing Pool and a proxy to the supplied logger.
+
+    Emulates the multiprocessing.Pool() context manager,
+    but also provides (via a LoggerThread) a SubLogger proxy to logger
+    that can be safely used by pool workers.
+    The SubLogger proxy interface supports these methods: debug, info, warning, error,
+    and critical.
+    Also "cleans up" the pool by waiting for workers to complete
+    as it exits the context.
+    """
+    with multiprocessing.Manager() as manager:
+        logger_thread = LoggerThread(logger, manager.Queue())
+        try:
+            with multiprocessing.Pool(*poolargs) as pool:
+                yield pool, logger_thread.get_sublogger()
+                pool.close()
+                pool.join()
+        finally:
+            logger_thread.stop()

_delphi_utils_python/setup.py

@@ -27,7 +27,7 @@
 
 setup(
     name="delphi_utils",
-    version="0.3.19",
+    version="0.3.20",
     description="Shared Utility Functions for Indicators",
     long_description=long_description,
     long_description_content_type="text/markdown",

changehc/version.cfg

@@ -1 +1 @@
-current_version = 0.3.45
+current_version = 0.3.46

claims_hosp/version.cfg

@@ -1 +1 @@
-current_version = 0.3.45
+current_version = 0.3.46

doctor_visits/version.cfg

@@ -1 +1 @@
-current_version = 0.3.45
+current_version = 0.3.46

google_symptoms/version.cfg

@@ -1 +1 @@
-current_version = 0.3.45
+current_version = 0.3.46

hhs_hosp/version.cfg

@@ -1 +1 @@
-current_version = 0.3.45
+current_version = 0.3.46

nchs_mortality/version.cfg

@@ -1 +1 @@
-current_version = 0.3.45
+current_version = 0.3.46

nowcast/version.cfg

@@ -1 +1 @@
-current_version = 0.3.45
+current_version = 0.3.46