release commit

biocypher/_logger.py

@@ -0,0 +1,121 @@
+#!/usr/bin/env python
+
+#
+# Copyright 2021, Heidelberg University Clinic
+#
+# File author(s): Sebastian Lobentanzer
+#                 ...
+#
+# Distributed under MIT licence, see the file `LICENSE`.
+#
+"""
+Configuration of the module logger.
+"""
+
+__all__ = ["get_logger", "log", "logfile"]
+
+from datetime import datetime
+import os
+import pydoc
+import logging
+
+from biocypher import _config
+from biocypher._metadata import __version__
+
+
+def get_logger(name: str = "biocypher") -> logging.Logger:
+    """
+    Access the module logger, create a new one if does not exist yet.
+
+    Method providing central logger instance to main module. Is called
+    only from main submodule, :mod:`biocypher.driver`. In child modules,
+    the standard Python logging facility is called
+    (using ``logging.getLogger(__name__)``), automatically inheriting
+    the handlers from the central logger.
+
+    The file handler creates a log file named after the current date and
+    time. Levels to output to file and console can be set here.
+
+    Args:
+        name:
+            Name of the logger instance.
+
+    Returns:
+        An instance of the Python :py:mod:`logging.Logger`.
+    """
+
+    if not logging.getLogger(name).hasHandlers():
+        # create logger
+        logger = logging.getLogger(name)
+        logger.setLevel(logging.DEBUG)
+        logger.propagate = True
+
+        # formatting
+        file_formatter = logging.Formatter(
+            "%(asctime)s\t%(levelname)s\tmodule:%(module)s\n%(message)s",
+        )
+        stdout_formatter = logging.Formatter("%(levelname)s -- %(message)s")
+
+        # file name and creation
+        now = datetime.now()
+        date_time = now.strftime("%Y%m%d-%H%M%S")
+
+        log_to_disk = _config.config("biocypher").get("log_to_disk")
+
+        if log_to_disk:
+            logdir = (
+                _config.config("biocypher").get("log_directory")
+                or "biocypher-log"
+            )
+            os.makedirs(logdir, exist_ok=True)
+            logfile = os.path.join(logdir, f"biocypher-{date_time}.log")
+
+            # file handler
+            file_handler = logging.FileHandler(logfile)
+
+            if _config.config("biocypher").get("debug"):
+                file_handler.setLevel(logging.DEBUG)
+            else:
+                file_handler.setLevel(logging.INFO)
+
+            file_handler.setFormatter(file_formatter)
+
+            logger.addHandler(file_handler)
+
+        # handlers
+        # stream handler
+        stdout_handler = logging.StreamHandler()
+        stdout_handler.setLevel(logging.INFO)
+        stdout_handler.setFormatter(stdout_formatter)
+
+        # add handlers
+        logger.addHandler(stdout_handler)
+
+        # startup message
+        logger.info(f"This is BioCypher v{__version__}.")
+        if log_to_disk:
+            logger.info(f"Logging into `{logfile}`.")
+        else:
+            logger.info("Logging into stdout.")
+
+    return logging.getLogger(name)
+
+
+def logfile() -> str:
+    """
+    Path to the log file.
+    """
+
+    return get_logger().handlers[0].baseFilename
+
+
+def log():
+    """
+    Browse the log file.
+    """
+
+    with open(logfile()) as fp:
+        pydoc.pager(fp.read())
+
+
+logger = get_logger()