Nathan D. Price

29 papers Misc 1Journal 25Unranked 2
YearRankTypeTitle / Venue / Authors
2019 J jnl
PLoS Comput. Biol.
Fangzhou Shen, Renliang Sun, Jie Yao, Jian Li, Qian Liu, Nathan D. Price, Chenguang Liu, Zhuo Wang
2018 J jnl
Bioinform.
Brendan King, Terry Farrah, Matthew A. Richards, Michael B. Mundy, Evangelos Simeonidis, Nathan D. Price
2018 conf
RO
Ravi K. Madduri, Kyle Chard, Michel D'Arcy, Segun Jung, Alexis A. Rodriguez, Dinanath Sulakhe, Eric Deutsch, Cory C. Funk, Benjamin D. Heavner, Matthew A. Richards, Paul Shannon, Gustavo Glusman, Nathan D. Price, Carl Kesselman, Ian T. Foster
2016 conf
IEEE BigData
Kyle Chard, Mike D'Arcy, Benjamin D. Heavner, Ian T. Foster, Carl Kesselman, Ravi K. Madduri, Alexis A. Rodriguez, Stian Soiland-Reyes, Carole A. Goble, Kristi Clark, Eric W. Deutsch, Ivo D. Dinov, Nathan D. Price, Arthur W. Toga
2016 J jnl
Biosyst.
Joseph Xu Zhou, Areejit Samal, Aymeric Fouquier d'Hérouël, Nathan D. Price, Sui Huang
2015 J jnl
J. Am. Medical Informatics Assoc.
Arthur W. Toga, Ian T. Foster, Carl Kesselman, Ravi K. Madduri, Kyle Chard, Eric W. Deutsch, Nathan D. Price, Gustavo Glusman, Benjamin D. Heavner, Ivo D. Dinov, Joseph Ames, John D. Van Horn, Roger Kramer, Leroy E. Hood
2015 J jnl
PLoS Comput. Biol.
Benjamin D. Heavner, Nathan D. Price
2015 J jnl
PLoS Comput. Biol.
Shuyi Ma, Kyle J. Minch, Tige R. Rustad, Samuel Hobbs, Suk-Lin Zhou, David R. Sherman, Nathan D. Price
2014 J jnl
PLoS Comput. Biol.
Matthew N. Benedict, Michael B. Mundy, Christopher S. Henry, Nicholas Chia, Nathan D. Price
2013 J jnl
BMC Bioinform.
John C. Earls, James A. Eddy, Cory C. Funk, Youn-Hee Ko, Andrew T. Magis, Nathan D. Price
2013 J jnl
PLoS Comput. Biol.
Sriram Chandrasekaran, Nathan D. Price
2013 J jnl
PLoS Comput. Biol.
Jaeyun Sung, Pan-Jun Kim, Shuyi Ma, Cory C. Funk, Andrew T. Magis, Yuliang Wang, Leroy E. Hood, Donald Geman, Nathan D. Price
2013 J jnl
Database J. Biol. Databases Curation
Benjamin D. Heavner, Kieran Smallbone, Nathan D. Price, Larry P. Walker
2012 J jnl
Briefings Bioinform.
Gürkan Bebek, Mehmet Koyutürk, Nathan D. Price, Mark R. Chance
2012 J jnl
BMC Syst. Biol.
Yuliang Wang, James A. Eddy, Nathan D. Price
2012 J jnl
BMC Bioinform.
Andrew T. Magis, Nathan D. Price
2011 J jnl
PLoS Comput. Biol.
Pan-Jun Kim, Nathan D. Price
2011 J jnl
Bioinform.
Andrew T. Magis, John C. Earls, Youn-Hee Ko, James A. Eddy, Nathan D. Price
2011 J jnl
BMC Syst. Biol.
Caroline B. Milne, James A. Eddy, Ravali Raju, Soroush Ardekani, Pan-Jun Kim, Ryan S. Senger, Yong-Su Jin, Hans P. Blaschek, Nathan D. Price
2011 Misc conf
Pacific Symposium on Biocomputing
Gürkan Bebek, Mehmet Koyutürk, Mark R. Chance, Nathan D. Price
2010 J jnl
IEEE Trans. Inf. Theory
David J. Galas, Matti Nykter, Gregory W. Carter, Nathan D. Price, Ilya Shmulevich
2010 J jnl
PLoS Comput. Biol.
James A. Eddy, Leroy E. Hood, Nathan D. Price, Donald Geman
2010 J jnl
IEEE Trans. Inf. Theory
Olgica Milenkovic, Gil Alterovitz, Gerard Battail, Todd P. Coleman, Joachim Hagenauer, Sean P. Meyn, Nathan D. Price, Marco Ramoni, Ilya Shmulevich, Wojciech Szpankowski
2009 ch.
Encyclopedia of Complexity and Systems Science
James A. Eddy, Nathan D. Price
2008 J jnl
CoRR
David J. Galas, Matti Nykter, Gregory W. Carter, Nathan D. Price, Ilya Shmulevich
2006 J jnl
PLoS Comput. Biol.
Timothy E. Allen, Nathan D. Price, Andrew R. Joyce, Bernhard Ø. Palsson
2006 J jnl
PLoS Comput. Biol.
Erwin P. Gianchandani, Jason A. Papin, Nathan D. Price, Andrew R. Joyce, Bernhard Ø. Palsson
2006 J jnl
BMC Bioinform.
Scott A. Becker, Nathan D. Price, Bernhard O. Palsson
2006 J jnl
BMC Bioinform.
Christian L. Barrett, Nathan D. Price, Bernhard O. Palsson
redb/utils/sort_files_by_type.py
← Index redb/utils/sort_files_by_type.py python
import os
import sys
from collections import defaultdict
import tempfile
from magika import Magika
import py7zr
import pyzipper
import shutil

"""
This script is used to sort files by their type. 
It reads all the files in the provided directory and splits them into different 
directories based on their type. Mainly, it classifies the files into the following types:
- PE Binaries
- Mach-O Binaries
- ELF Binaries
- APK 
- Other Files

It outputs the count of files for each file extension and file type.

Command line example:
nohup python3 sort_files_by_type.py /mnt/samples/consilience/malware/vx-bazaar-expanded/Bazaar.2020.12 \
    /mnt/samples/consilience/malware/_sorted_samples/vx-bazaar/2020/ > \
    /mnt/samples/consilience/malware/ops-logs/20241014-SORT_FILES-bazaar_2020.12.output.log 2>&1 &
"""


def process_zip_file(filepath):
    print(f"[INFO] - Processing zip file: {filepath}")
    with tempfile.TemporaryDirectory() as temp_dir:
        try:
            with pyzipper.AESZipFile(filepath) as zf:
                zf.pwd = b"infected"
                filename = zf.namelist()[0]
                zf.extractall(temp_dir)
                extracted_zip_path = os.path.join(temp_dir, filename)
                return process_binary_file(extracted_zip_path)
        except Exception as e:
            print(f"[ERR] - Error processing zip file {filepath}: {str(e)}")
            return None


def process_7z_file(filepath):
    print(f"[INFO] - Processing 7z file: {filepath}")
    with tempfile.TemporaryDirectory() as temp_dir:
        try:
            with py7zr.SevenZipFile(filepath, mode="r", password="infected") as z:
                z.extractall(path=temp_dir)
                for root, _, files in os.walk(temp_dir):
                    for file in files:
                        extracted_file_path = os.path.join(root, file)
                        return process_binary_file(extracted_file_path)
        except Exception as e:
            print(f"[ERR] - Error processing 7z file {filepath}: {str(e)}")
            return None


def process_binary_file(filepath):
    print(f"[INFO] - Processing binary file: {filepath}")
    try:
        with open(filepath, "rb") as f:
            data = f.read(512 * 1024)  # 512KB
        return Magika().identify_bytes(data).output.ct_label
    except Exception as e:
        print(f"[ERR] - Error processing binary file {filepath}: {str(e)}")
        return "ERROR"


def count_file_extensions(path, dest_dir):
    # A defaultdict to store file extension counts
    extension_count = defaultdict(int)
    filetype_count = defaultdict(int)
    tot_files = 0

    # Walk through the directory
    for root, dirs, files in os.walk(path):
        for file in files:
            if file.startswith("."):
                continue

            tot_files += 1
            # Split the file extension from the file name
            _, ext = os.path.splitext(file)
            ext = ext.lower()

            # Count the extensions
            extension_count[ext] += 1
            filepath = os.path.join(root, file)
            filetype = ""

            if ext == ".7z":
                filetype = process_7z_file(filepath)
            elif ext == ".zip":
                filetype = process_zip_file(filepath)
            else:
                filetype = process_binary_file(filepath)

            filetype_count[filetype] += 1

            if filetype == "pebin":
                dest = os.path.join(dest_dir, "pebin")
                os.makedirs(dest, exist_ok=True)
                shutil.copy2(filepath, os.path.join(dest, file))
            elif filetype == "macho":
                dest = os.path.join(dest_dir, "macho")
                os.makedirs(dest, exist_ok=True)
                shutil.copy2(filepath, os.path.join(dest, file))
            elif filetype == "elf":
                dest = os.path.join(dest_dir, "elf")
                os.makedirs(dest, exist_ok=True)
                shutil.copy2(filepath, os.path.join(dest, file))
            elif filetype == "apk":
                dest = os.path.join(dest_dir, "apk")
                os.makedirs(dest, exist_ok=True)
                shutil.copy2(filepath, os.path.join(dest, file))
            else:
                dest = os.path.join(dest_dir, "other")
                os.makedirs(dest, exist_ok=True)
                shutil.copy2(filepath, os.path.join(dest, file))
            print(f"[STATUS] - Progres: {tot_files}/{len(files)} files processed")

    # Print the results
    # print("- File Extension Statistics:")
    # for ext, count in extension_count.items():
    #     if ext:  # To exclude files with no extension
    #         print(f"\t{ext}: {count} files")

    # if "" in extension_count:
    #     print(f'\t{extension_count[""]} files with no extension')

    print(f"- Total Number of Files: {tot_files}")
    print("\n- File Type Statistics:")
    for filetype, count in sorted(filetype_count.items()):
        print(f"\t{filetype:<15}{count:>8}")


if __name__ == "__main__":
    # Check if the path was passed as a command-line argument
    if len(sys.argv) != 3:
        print("Usage: python3 script.py <input_path> <dest_dir>")
        sys.exit(1)

    # Get the path from the command-line arguments
    input_path = sys.argv[1]
    dest_dir = sys.argv[2]

    # Check if the provided path is valid
    if not os.path.isdir(input_path):
        print(f"The path '{input_path}' is not a valid directory.")
        sys.exit(1)

    # Call the function to count file extensions
    count_file_extensions(input_path, dest_dir)