Add runfolder name to logger, remove timestamp

Author: RachelDuffin

samplesheet_validator/__main__.py

@@ -101,7 +101,7 @@ def is_valid_dir(parser: argparse.ArgumentParser, dir: str) -> str:
 if __name__ == "__main__":
     parsed_args = get_arguments()
     if not parsed_args.no_stream_handler:
-        set_root_logger()  # Adds stream handler
+        set_root_logger(__package__)  # Adds stream handler
     sscheck_obj = SamplesheetCheck(
         parsed_args.samplesheet_path,
         parsed_args.sequencer_ids,

samplesheet_validator/config.py

@@ -3,7 +3,7 @@
 TIMESTAMP = str(f"{datetime.datetime.now():%Y%m%d_%H%M%S}")
 
 # Specifies the layout of log records in the final output
-LOGGING_FORMATTER = "%(asctime)s - SAMPLESHEET_VALIDATOR - %(levelname)s - %(message)s"
+LOGGING_FORMATTER = "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
 
 LOG_MSGS = {
     "ss_present": "Samplesheet with supplied name exists (%s)",

samplesheet_validator/samplesheet_validator.py

@@ -124,8 +124,8 @@ def get_logger(self):
         runfolder_name = (self.samplesheet_path.split("/")[-1]).split(
             "_SampleSheet.csv"
         )[0]
-        logfile_path = f"{os.path.join(self.logdir, runfolder_name)}_{config.TIMESTAMP}_samplesheet_validator.log"
-        return SSLogger(logfile_path).get_logger()
+        logfile_path = f"{os.path.join(self.logdir, runfolder_name)}_samplesheet_validator.log"
+        return SSLogger(__package__, logfile_path, runfolder_name).get_logger()
 
     def ss_checks(self) -> None:
         """

samplesheet_validator/ss_logger.py

@@ -8,12 +8,15 @@
 import logging.handlers
 
 
-def set_root_logger():
+def set_root_logger(script: str):
     """
     Set up root logger and add stream handler - we only want to add stream handler once
     else it will duplicate log messages to the terminal
+        :param script (str):    Script from which the base logger was setup
+                                (named in same way to ensure it uses the root syslog / stream handler)
     """
-    logger = logging.getLogger()
+    logger = logging.getLogger(script)
+    logger.name=__package__
     logger.setLevel(logging.DEBUG)
     stream_handler = logging.StreamHandler(sys.stdout)
     stream_handler.setLevel(logging.DEBUG)
@@ -28,7 +31,10 @@ class SSLogger:
 
     Attributes
         timestamp (str):                        Timestamp from config
+        script (str):                           Script from which the base logger was setup
+                                                (named in same way to ensure it uses the root syslog / stream handler)
         logfile_path (str):                     Name of filepath to provide to _file_handler()
+        runfolder_name (str):                   Runfolder name
         logging_formatter (logging.Formatter):  Specifies the layout of log records in the final output
 
     Methods
@@ -40,22 +46,27 @@ class SSLogger:
             Get syslog handler for the logger
     """
 
-    def __init__(self, logfile_path: str):
+    def __init__(self, script: str, logfile_path: str, runfolder_name: str):
         """
         Constructor for the Logger class
+            :param script (str):            Script from which the base logger was setup
+                                            (named in same way to ensure it uses the root syslog / stream handler)
             :param logfile_path (str):      Path to logfile location
+            :param runfolder_name (str):    Runfolder name
         """
         # Timestamp used for naming log files with datetime, format %Y%m%d_%H%M%S
         self.timestamp = config.TIMESTAMP
+        self.script = script
         self.logfile_path = logfile_path
+        self.runfolder_name = runfolder_name
         self.logging_formatter = logging.Formatter(config.LOGGING_FORMATTER)
 
     def get_logger(self) -> logging.Logger:
         """
         Returns a Python logging object, and give it a name
             :return logger (object):    Python logging object with custom attributes
         """
-        logger = logging.getLogger()
+        logger = logging.getLogger(f"{__package__}.{self.runfolder_name}")
         logger.filepath = self.logfile_path
         logger.setLevel(logging.DEBUG)
         logger.addHandler(self._get_file_handler())

setup.py

@@ -3,7 +3,7 @@
 
 setup(
     name="samplesheet_validator",
-    version=git_tag(),
+    version="TEST",
     description="Python library for samplesheet validation",
     url="https://github.com/moka-guys/samplesheet_validator",
     author="Rachel Duffin",