Neil F. Abernethy

24 papers A 2C 1Misc 5Journal 12Unranked 4
YearRankTypeTitle / Venue / Authors
2025 J jnl
npj Digit. Medicine
Neil F. Abernethy, Kylie McCloskey, Meg Trahey, Laurie Rinn, Gail Broder, Michele Andrasik, Rebecca Laborde, Daniel McGhan, Scott Spendolini, Senthil Marimuthu, Adam Kanzmeier, Jayson Hanes, James G. Kublin
2025 J jnl
CoRR
Tianmai M. Zhang, Neil F. Abernethy
2025 J jnl
CoRR
Tianmai M. Zhang, Zhaoyi Sun, Sihang Zeng, Chenxi Li, Neil F. Abernethy, Barbara D. Lam, Fei Xia, Meliha Yetisgen
2024 J jnl
CoRR
Tianmai M. Zhang, Neil F. Abernethy
2019 J jnl
PLoS Comput. Biol.
John E. Mittler, James T. Murphy, Sarah E. Stansfield, Kathryn Peebles, Geoffrey S. Gottlieb, Neil F. Abernethy, Molly C. Reid, Steven M. Goodreau, Joshua T. Herbeck
2016 conf
ICBO/BioCreative
Lucy Lu Wang, John H. Gennari, Neil F. Abernethy
2016 Misc conf
AMIA
Lucy Lu Wang, John H. Gennari, Neil F. Abernethy
2015 J jnl
J. Biomed. Informatics
Casey Lynnette Overby, Emily Beth Devine, Neil F. Abernethy, Jeannine S. McCune, Peter Tarczy-Hornoch
2015 Misc conf
AMIA
Kate Zinszer, Anya Okhmatovskaia, Arash Shaban-Nejad, Lauren N. Carroll, Neil F. Abernethy, David L. Buckeridge
2014 J jnl
Int. J. Medical Informatics
Emily Beth Devine, Chia-Ju Lee, Casey Lynnette Overby, Neil F. Abernethy, Jeannine McCune, Joe W. Smith, Peter Tarczy-Hornoch
2014 J jnl
J. Biomed. Informatics
Lauren N. Carroll, Alan P. Au, Landon T. Detwiler, Tsung-chieh Fu, Ian S. Painter, Neil F. Abernethy
2013 J jnl
BioData Min.
Deanna Petrochilos, Ali Shojaie, John H. Gennari, Neil F. Abernethy
2012 C conf
CIBCB
Deanna Petrochilos, Neil F. Abernethy
2012 Misc conf
AMIA
Casey Lynnette Overby, Emily Beth Devine, Neil F. Abernethy, Jeannine McCune, Peter Tarczy-Hornoch
2012 J jnl
J. Biomed. Informatics
Daniel R. Masys, Gail P. Jarvik, Neil F. Abernethy, Nicholas R. Anderson, George J. Papanicolaou, Dina N. Paltoo, Mark A. Hoffman, Isaac S. Kohane, Howard P. Levy
2012 Misc conf
AMIA
Rebecca A. Hills, Debra Revere, Rita Altamore, Neil F. Abernethy, William B. Lober
2010 conf
IHI
Rebecca A. Hills, Blaine Reeder, Debra Revere, William B. Lober, Neil F. Abernethy
2010 conf
IHI
Alicia F. Guidry, Judd L. Walson, Neil F. Abernethy
2000 A conf
ISMB
Robin McEntire, Peter D. Karp, Neil F. Abernethy, David Benton, Gregg Helt, Matt DeJongh, Robert Kent, Anthony Kosky, Suzanna Lewis, Dan Hodnett, Eric P. Neumann, Frank Olken, Dhiraj K. Pathak, Peter Tarczy-Hornoch, Luca Toldo, Thodoros Topaloglou
1999 J jnl
IEEE Intell. Syst.
Russ B. Altman, Michael Bada, Xiaoqian J. Chai, Michelle Whirl Carrillo, Richard O. Chen, Neil F. Abernethy
1999 J jnl
IEEE Intell. Syst.
Neil F. Abernethy, Julie J. Wu, Micheal Hewett, Russ B. Altman
1998 Misc conf
AMIA
Lawrence S. Hon, Neil F. Abernethy, Vladimir Brusic, Jenny Chai, Russ B. Altman
1998 conf
KRDB
Neil F. Abernethy, Russ B. Altman
1997 A conf
ISMB
Russ B. Altman, Neil F. Abernethy, Richard O. Chen
redb/logging_utils.py
← Index redb/logging_utils.py python
"""
Logging utilities and shared enums for REDB.

Contains the ImportResult enum, log formatters, and logger setup functions
used across the ingestor pipeline.
"""
import logging
from logging.handlers import QueueHandler
import os
from enum import Enum


class ImportResult(Enum):
    CORRECTLY = 0
    PARTIALLY = 1
    FAILED = 2
    PENDING = 3
    SKIPPED = 4


class FileNameFormatter(logging.Formatter):
    def format(self, record):
        record.filenameinfo = getattr(record, "filenameinfo", "unknown")
        return super().format(record)


def setup_logger(log_queue, filename):
    logger = logging.getLogger(filename)
    if not logger.handlers:
        if os.getenv("SERVER_ENV") == "prod":
            logger.setLevel(logging.INFO)
        else:
            logger.setLevel(logging.DEBUG)
        handler = QueueHandler(log_queue)
        logger.addHandler(handler)
        logger.propagate = False  # Prevent propagation to parent loggers
    return logger


def logger_thread(log_queue, log_file):
    handler = logging.FileHandler(log_file)
    formatter = FileNameFormatter(
        "%(asctime)s - %(filenameinfo)s - %(levelname)s - %(message)s"
    )
    handler.setFormatter(formatter)

    while True:
        try:
            record = log_queue.get()
            if record is None:
                break
            # Format and write the log record
            message = formatter.format(record)
            handler.stream.write(message + "\n")
            handler.stream.flush()
        except Exception:
            import traceback
            import sys

            print("[ERR] Error in logger thread:", file=sys.stderr)
            traceback.print_exc(file=sys.stderr)


def setup_direct_logger(log_file, filename, pid=None):
    """Setup a logger that writes directly to the log file without using a queue."""
    # Create a unique logger name using the process ID
    logger_name = f"{filename}_{pid}" if pid else filename
    logger = logging.getLogger(logger_name)

    if not logger.handlers:
        handler = logging.FileHandler(log_file)
        formatter = logging.Formatter("%(asctime)s - %(filenameinfo)s - %(levelname)s - %(message)s")
        handler.setFormatter(formatter)
        logger.addHandler(handler)

        if os.getenv("SERVER_ENV") == "prod":
            logger.setLevel(logging.INFO)
        else:
            logger.setLevel(logging.DEBUG)

    # Add filename info to the logger's extra info
    extra = {"filenameinfo": filename}
    logger = logging.LoggerAdapter(logger, extra)

    return logger