C. Jessica E. Metcalf

11 papers Journal 11
YearRankTypeTitle / Venue / Authors
2026 J jnl
PLoS Comput. Biol.
Prerna Singh, Justin Sheen, Chadi M. Saad-Roy, Michael Z. Levy, C. Jessica E. Metcalf
2025 J jnl
PLoS Comput. Biol.
Justin Sheen, Lee Kennedy-Shaffer, Michael Z. Levy, C. Jessica E. Metcalf
2025 J jnl
PLoS Comput. Biol.
Nathanaël Hozé, Margarita Pons-Salort, C. Jessica E. Metcalf, Michael White, Henrik Salje, Simon Cauchemez
2024 J jnl
PLoS Comput. Biol.
Chadi M. Saad-Roy, Sinead E. Morris, Mike Boots, Rachel E. Baker, Bryan L. Lewis, Jeremy Farrar, Madhav V. Marathe, Andrea L. Graham, Simon A. Levin, Caroline E. Wagner, C. Jessica E. Metcalf, Bryan T. Grenfell
2023 J jnl
CoRR
Marc Lipsitch, Mary T. Bassett, John S. Brownstein, Paul Elliott, David Eyre, M. Kate Grabowski, James A. Hay, Michael A. Johansson, Stephen M. Kissler, Daniel B. Larremore, Jennifer Layden, Justin Lessler, Ruth Lynfield, Duncan MacCannell, Lawrence C. Madoff, C. Jessica E. Metcalf, Lauren Ancel Meyers, Sylvia K. Ofori, Celia Quinn, Ana I. Ramos Bento, Nick Reich, Steven Riley, Roni Rosenfeld, Matthew H. Samore, Rangarajan Sampath, Rachel B. Slayton, David L. Swerdlow, Shaun Truelove, Jay K. Varma, Yonatan H. Grad
2023 J jnl
PLoS Comput. Biol.
Arthur Menezes, Saki Takahashi, Isobel Routledge, C. Jessica E. Metcalf, Andrea L. Graham, James A. Hay
2022 J jnl
PLoS Comput. Biol.
Max S. Y. Lau, Alexander D. Becker, Wyatt Madden, Lance A. Waller, C. Jessica E. Metcalf, Bryan T. Grenfell
2021 J jnl
PLoS Comput. Biol.
Alexander E. Downie, Andreas Mayer, C. Jessica E. Metcalf, Andrea L. Graham
2021 J jnl
PLoS Comput. Biol.
John R. Giles, Derek A. T. Cummings, Bryan T. Grenfell, Andrew J. Tatem, Elisabeth Zu Erbach-Schoenberg, C. Jessica E. Metcalf, Amy Wesolowski
2017 J jnl
PLoS Comput. Biol.
Max S. Y. Lau, Gavin J. Gibson, Hola Adrakey, Amanda McClelland, Steven Riley, Jon Zelner, George Streftaris, Sebastian Funk, C. Jessica E. Metcalf, Benjamin D. Dalziel, Bryan T. Grenfell
2016 J jnl
PLoS Comput. Biol.
Benjamin D. Dalziel, Ottar N. Bjørnstad, Willem G. van Panhuis, Donald S. Burke, C. Jessica E. Metcalf, Bryan T. Grenfell
redb/utils/wrapper_run_sort_files.py
← Index redb/utils/wrapper_run_sort_files.py python
import os
import subprocess
import multiprocessing
import logging
from concurrent.futures import ThreadPoolExecutor
import signal

# Variables (replace these with actual values)
src_root_folder_path = "/mnt/samples/consilience/malware/vx-bazaar-expanded/"
dst_root_folder_path = "/mnt/samples/consilience/malware/_sorted_samples/vx-bazaar/"
log_folder_path = "/mnt/samples/consilience/malware/ops-logs/"
folder_names = ["Bazaar.2022.01", "Bazaar.2022.02", "Bazaar.2022.03", "Bazaar.2022.04"]  # List of folder names
script_name = "sort_files_by_type.py"
dry_run = True  # Set to True for testing without execution


# Ensure the log folder exists
os.makedirs(log_folder_path, exist_ok=True)

# Configure logging
main_log_name = "20241229-main_script.log"
main_log_file = os.path.join(log_folder_path, main_log_name)
if not os.path.exists(main_log_file):
    open(main_log_file, 'a').close()  # Create the log file if it doesn't exist
# main_log_file = os.path.join(log_folder_path, main_log_name)
# try:
#     with open(main_log_file, 'a') as f:
#         print(f"Successfully created/opened log file at: {main_log_file}")
#     # Verify the file exists
#     if os.path.exists(main_log_file):
#         print(f"Confirmed log file exists at: {main_log_file}")
#         print(f"File size: {os.path.getsize(main_log_file)} bytes")
# except Exception as e:
#     print(f"Error with log file: {e}")

# Configure logging
logging.basicConfig(
    filename=main_log_file,
    level=logging.INFO,
    format="%(asctime)s - %(levelname)s - %(message)s",
    force=True,
    filemode='a'
)

logging.info("Logging initialization test message")

# Add logging handler to flush immediately
class FlushableFileHandler(logging.FileHandler):
    def emit(self, record):
        super().emit(record)
        self.flush()

for handler in logging.getLogger().handlers:
    if isinstance(handler, logging.FileHandler):
        handler.flush()

# Global flag for graceful termination
terminate_flag = False

def signal_handler(signum, frame):
    global terminate_flag
    terminate_flag = True
    logging.warning("Termination signal received. Attempting to shut down gracefully.")

# Register signal handler
signal.signal(signal.SIGINT, signal_handler)
signal.signal(signal.SIGTERM, signal_handler)

# Define the worker function
def process_folder(folder):
    global terminate_flag
    if terminate_flag:
        logging.warning(f"Skipping folder {folder} due to termination signal.")
        return

    try:
        # Extract the word and date fields from the folder name
        word, year, month = folder.split('.')

        # Construct source, destination, and log paths
        src_folder = os.path.join(src_root_folder_path, folder)
        dst_folder = os.path.join(dst_root_folder_path, folder)
        log_file = os.path.join(
            log_folder_path, f"20241229-SORT_FILES-bazaar_{year}.{month}.output.log"
        )

        if not os.path.exists(log_file):
            open(log_file, 'a').close()  # Create the log file if it doesn't exist

        # Build the command
        command = ["python3", script_name, src_folder, dst_folder]

        if dry_run:
            logging.info(f"Dry run: Would execute: {command}, log: {log_file}")
            print(f"Dry run: Would execute: {command}, log: {log_file}")
        else:
            logging.info(f"Starting task for folder: {folder}")
            with open(log_file, "w") as log:
                subprocess.run(command, stdout=log, stderr=subprocess.STDOUT, check=True)
            logging.info(f"Task completed for folder: {folder}")

    except subprocess.CalledProcessError as e:
        logging.error(f"Subprocess failed for folder {folder} with return code {e.returncode}: {e}")
        print(f"Subprocess failed for folder {folder}: {e}")
    except Exception as e:
        logging.error(f"Error while processing folder {folder}: {e}")
        print(f"Error while processing folder {folder}: {e}")

# Determine the number of processors
num_processors = multiprocessing.cpu_count()

try:
    # Process folders using ThreadPoolExecutor
    with ThreadPoolExecutor(max_workers=num_processors-1) as executor:
        executor.map(process_folder, folder_names)

except Exception as e:
    logging.critical(f"Critical error in the main execution: {e}")
    print(f"Critical error: {e}")

logging.info("All tasks completed.")
print("All tasks completed.")