Add centralized logger.

CHANGELOG.md

@@ -1,10 +1,14 @@
 ## Release notes
 
+### 0.13.6 -- Jun 13, 2022
+* Add - unified package level logger for package (#667) PR #1031
+* Update - swap various datajoint messages, warnings, etc. to use the new logger. (#667) PR #1031
+
 ### 0.13.5 -- May 19, 2022
 * Update - Import ABC from collections.abc for Python 3.10 compatibility
 * Bugfix - Fix multiprocessing value error (#1013) PR #1026
 
-### 0.13.4 -- March, 28 2022
+### 0.13.4 -- Mar, 28 2022
 * Add - Allow reading blobs produced by legacy 32-bit compiled mYm library for matlab. PR #995
 * Bugfix - Add missing `jobs` argument for multiprocessing PR #997
 * Add - Test for multiprocessing PR #1008

LNX-docker-compose.yml

@@ -32,7 +32,7 @@ services:
       interval: 1s
   fakeservices.datajoint.io:
     <<: *net
-    image: datajoint/nginx:v0.1.1
+    image: datajoint/nginx:v0.2.1
     environment:
     - ADD_db_TYPE=DATABASE
     - ADD_db_ENDPOINT=db:3306

datajoint/__init__.py

@@ -52,6 +52,7 @@
     "key_hash",
 ]
 
+from .logging import logger
 from .version import __version__
 from .settings import config
 from .connection import conn, Connection

datajoint/autopopulate.py

@@ -13,7 +13,7 @@
 
 # noinspection PyExceptionInherit,PyCallingNonCallable
 
-logger = logging.getLogger(__name__)
+logger = logging.getLogger(__name__.split(".")[0])
 
 
 # --- helper functions for multiprocessing --
@@ -159,7 +159,7 @@ def populate(
         max_calls=None,
         display_progress=False,
         processes=1,
-        make_kwargs=None
+        make_kwargs=None,
     ):
         """
         ``table.populate()`` calls ``table.make(key)`` for every primary key in
@@ -207,7 +207,7 @@ def handler(signum, frame):
         elif order == "random":
             random.shuffle(keys)
 
-        logger.info("Found %d keys to populate" % len(keys))
+        logger.debug("Found %d keys to populate" % len(keys))
 
         keys = keys[:max_calls]
         nkeys = len(keys)
@@ -275,7 +275,7 @@ def _populate1(
                 if jobs is not None:
                     jobs.complete(self.target.table_name, self._job_key(key))
             else:
-                logger.info("Populating: " + str(key))
+                logger.debug(f"Making {key} -> {self.target.full_table_name}")
                 self.__class__._allow_insert = True
                 try:
                     make(dict(key), **(make_kwargs or {}))
@@ -288,6 +288,9 @@ def _populate1(
                         exception=error.__class__.__name__,
                         msg=": " + str(error) if str(error) else "",
                     )
+                    logger.debug(
+                        f"Error making {key} -> {self.target.full_table_name} - {error_message}"
+                    )
                     if jobs is not None:
                         # show error name and error message (if any)
                         jobs.error(
@@ -303,6 +306,9 @@ def _populate1(
                         return key, error if return_exception_objects else error_message
                 else:
                     self.connection.commit_transaction()
+                    logger.debug(
+                        f"Success making {key} -> {self.target.full_table_name}"
+                    )
                     if jobs is not None:
                         jobs.complete(self.target.table_name, self._job_key(key))
                 finally:

datajoint/connection.py

@@ -17,7 +17,7 @@
 from .hash import uuid_from_buffer
 from .plugin import connection_plugins
 
-logger = logging.getLogger(__name__)
+logger = logging.getLogger(__name__.split(".")[0])
 query_log_max_length = 300
 
 
@@ -187,7 +187,7 @@ def __init__(self, host, user, password, port=None, init_fun=None, use_tls=None)
         self.conn_info["ssl_input"] = use_tls
         self.conn_info["host_input"] = host_input
         self.init_fun = init_fun
-        print("Connecting {user}@{host}:{port}".format(**self.conn_info))
+        logger.info("Connecting {user}@{host}:{port}".format(**self.conn_info))
         self._conn = None
         self._query_cache = None
         connect_host_hook(self)
@@ -341,7 +341,7 @@ def query(
         except errors.LostConnectionError:
             if not reconnect:
                 raise
-            warnings.warn("MySQL server has gone away. Reconnecting to the server.")
+            logger.warning("MySQL server has gone away. Reconnecting to the server.")
             connect_host_hook(self)
             if self._in_transaction:
                 self.cancel_transaction()
@@ -382,15 +382,15 @@ def start_transaction(self):
             raise errors.DataJointError("Nested connections are not supported.")
         self.query("START TRANSACTION WITH CONSISTENT SNAPSHOT")
         self._in_transaction = True
-        logger.info("Transaction started")
+        logger.debug("Transaction started")
 
     def cancel_transaction(self):
         """
         Cancels the current transaction and rolls back all changes made during the transaction.
         """
         self.query("ROLLBACK")
         self._in_transaction = False
-        logger.info("Transaction cancelled. Rolling back ...")
+        logger.debug("Transaction cancelled. Rolling back ...")
 
     def commit_transaction(self):
         """
@@ -399,7 +399,7 @@ def commit_transaction(self):
         """
         self.query("COMMIT")
         self._in_transaction = False
-        logger.info("Transaction committed and closed.")
+        logger.debug("Transaction committed and closed.")
 
     # -------- context manager for transactions
     @property

datajoint/declare.py

@@ -75,7 +75,7 @@ def match_type(attribute_type):
         )
 
 
-logger = logging.getLogger(__name__)
+logger = logging.getLogger(__name__.split(".")[0])
 
 
 def build_foreign_key_parser_old():
@@ -207,7 +207,7 @@ def compile_foreign_key(
         )
 
     if obsolete:
-        warnings.warn(
+        logger.warning(
             'Line "{line}" uses obsolete syntax that will no longer be supported in datajoint 0.14. '
             "For details, see issue #780 https://github.com/datajoint/datajoint-python/issues/780".format(
                 line=line

datajoint/diagram.py

@@ -2,10 +2,14 @@
 import re
 import functools
 import io
-import warnings
+import logging
 import inspect
 from .table import Table
 from .dependencies import unite_master_parts
+from .user_tables import Manual, Imported, Computed, Lookup, Part
+from .errors import DataJointError
+from .table import lookup_class_name
+
 
 try:
     from matplotlib import pyplot as plt
@@ -21,11 +25,8 @@
 except:
     diagram_active = False
 
-from .user_tables import Manual, Imported, Computed, Lookup, Part
-from .errors import DataJointError
-from .table import lookup_class_name
-
 
+logger = logging.getLogger(__name__.split(".")[0])
 user_table_classes = (Manual, Lookup, Computed, Imported, Part)
 
 
@@ -63,7 +64,7 @@ class Diagram:
         """
 
         def __init__(self, *args, **kwargs):
-            warnings.warn(
+            logger.warning(
                 "Please install matplotlib and pygraphviz libraries to enable the Diagram feature."
             )
 

datajoint/expression.py

@@ -17,7 +17,7 @@
 )
 from .declare import CONSTANT_LITERALS
 
-logger = logging.getLogger(__name__)
+logger = logging.getLogger(__name__.split(".")[0])
 
 
 class QueryExpression:

datajoint/fetch.py

@@ -1,6 +1,6 @@
 from functools import partial
 from pathlib import Path
-import warnings
+import logging
 import pandas
 import itertools
 import re
@@ -12,6 +12,8 @@
 from .settings import config
 from .utils import safe_write
 
+logger = logging.getLogger(__name__.split(".")[0])
+
 
 class key:
     """
@@ -209,7 +211,7 @@ def __call__(
                 )
 
         if limit is None and offset is not None:
-            warnings.warn(
+            logger.warning(
                 "Offset set, but no limit. Setting limit to a large number. "
                 "Consider setting a limit explicitly."
             )

datajoint/heading.py

@@ -14,7 +14,7 @@
 from .attribute_adapter import get_adapter, AttributeAdapter
 
 
-logger = logging.getLogger(__name__)
+logger = logging.getLogger(__name__.split(".")[0])
 
 default_attribute_properties = (
     dict(  # these default values are set in computed attributes

datajoint/logging.py

@@ -0,0 +1,32 @@
+import logging
+import os
+import sys
+import io
+
+logger = logging.getLogger(__name__.split(".")[0])
+
+log_level = os.getenv("DJ_LOG_LEVEL", "info").upper()
+
+log_format = logging.Formatter("[%(asctime)s][%(levelname)s]: %(message)s")
+
+stream_handler = logging.StreamHandler()  # default handler
+stream_handler.setFormatter(log_format)
+
+logger.setLevel(level=log_level)
+logger.handlers = [stream_handler]
+
+
+def excepthook(exc_type, exc_value, exc_traceback):
+    if issubclass(exc_type, KeyboardInterrupt):
+        sys.__excepthook__(exc_type, exc_value, exc_traceback)
+        return
+
+    if logger.getEffectiveLevel() == 10:
+        logger.debug(
+            "Uncaught exception", exc_info=(exc_type, exc_value, exc_traceback)
+        )
+    else:
+        logger.error(f"Uncaught exception: {exc_value}")
+
+
+sys.excepthook = excepthook

datajoint/plugin.py

@@ -3,6 +3,9 @@
 from pathlib import Path
 from cryptography.exceptions import InvalidSignature
 from otumat import hash_pkg, verify
+import logging
+
+logger = logging.getLogger(__name__.split(".")[0])
 
 
 def _update_error_stack(plugin_name):
@@ -12,13 +15,13 @@ def _update_error_stack(plugin_name):
         plugin_meta = pkg_resources.get_distribution(plugin_name)
 
         data = hash_pkg(pkgpath=str(Path(plugin_meta.module_path, plugin_name)))
-        signature = plugin_meta.get_metadata("{}.sig".format(plugin_name))
-        pubkey_path = str(Path(base_meta.egg_info, "{}.pub".format(base_name)))
+        signature = plugin_meta.get_metadata(f"{plugin_name}.sig")
+        pubkey_path = str(Path(base_meta.egg_info, f"{base_name}.pub"))
         verify(pubkey_path=pubkey_path, data=data, signature=signature)
-        print("DataJoint verified plugin `{}` detected.".format(plugin_name))
+        logger.info(f"DataJoint verified plugin `{plugin_name}` detected.")
         return True
     except (FileNotFoundError, InvalidSignature):
-        print("Unverified plugin `{}` detected.".format(plugin_name))
+        logger.warning(f"Unverified plugin `{plugin_name}` detected.")
         return False
 
 

datajoint/s3.py

@@ -4,13 +4,12 @@
 from io import BytesIO
 import minio  # https://docs.minio.io/docs/python-client-api-reference
 import urllib3
-import warnings
 import uuid
 import logging
 from pathlib import Path
 from . import errors
 
-logger = logging.getLogger(__name__)
+logger = logging.getLogger(__name__.split(".")[0])
 
 
 class Folder:

datajoint/schemas.py

@@ -16,7 +16,7 @@
 from .table import lookup_class_name, Log, FreeTable
 import types
 
-logger = logging.getLogger(__name__)
+logger = logging.getLogger(__name__.split(".")[0])
 
 
 def ordered_dir(class_):
@@ -134,7 +134,7 @@ def activate(
                     )
                 )
             # create database
-            logger.info("Creating schema `{name}`.".format(name=schema_name))
+            logger.debug("Creating schema `{name}`.".format(name=schema_name))
             try:
                 self.connection.query(
                     "CREATE DATABASE `{name}`".format(name=schema_name)
@@ -360,12 +360,12 @@ def drop(self, force=False):
             )
             == "yes"
         ):
-            logger.info("Dropping `{database}`.".format(database=self.database))
+            logger.debug("Dropping `{database}`.".format(database=self.database))
             try:
                 self.connection.query(
                     "DROP DATABASE `{database}`".format(database=self.database)
                 )
-                logger.info(
+                logger.debug(
                     "Schema `{database}` was dropped successfully.".format(
                         database=self.database
                     )

datajoint/settings.py

@@ -49,7 +49,7 @@
     }
 )
 
-logger = logging.getLogger(__name__)
+logger = logging.getLogger(__name__.split(".")[0])
 log_levels = {
     "INFO": logging.INFO,
     "WARNING": logging.WARNING,
@@ -104,7 +104,7 @@ def save(self, filename, verbose=False):
         with open(filename, "w") as fid:
             json.dump(self._conf, fid, indent=4)
         if verbose:
-            print("Saved settings in " + filename)
+            logger.info("Saved settings in " + filename)
 
     def load(self, filename):
         """
@@ -240,8 +240,8 @@ def __getitem__(self, key):
             return self._conf[key]
 
         def __setitem__(self, key, value):
-            logger.log(
-                logging.INFO, "Setting {0:s} to {1:s}".format(str(key), str(value))
+            logger.debug(
+                logging.DEBUG, "Setting {0:s} to {1:s}".format(str(key), str(value))
             )
             if validators[key](value):
                 self._conf[key] = value