Nathan C. Hulse

36 papers B 1Misc 28Journal 4Unranked 3
YearRankTypeTitle / Venue / Authors
2019 Misc conf
AMIA
Nathan C. Hulse, Jaehoon Lee, Jose Benuzillo
2019 Misc conf
AMIA
Jaehoon Lee, Nathan C. Hulse
2018 Misc conf
AMIA
Nathan C. Hulse, Jaehoon Lee, Martin Brownell
2017 Misc conf
AMIA
Jaehoon Lee, Nathan C. Hulse, Stacey Knight
2017 Misc conf
AMIA
Nathan C. Hulse, Jaehoon Lee
2016 Misc conf
AMIA
Nathan C. Hulse, Jaehoon Lee, Tim Borgeson
2016 Misc conf
AMIA
Nathan C. Hulse, Jie Long
2016 Misc conf
AMIA
David P. Taylor, Nathan C. Hulse, Chaitanya K. Mynam, Bhanu Iyer, Matthew Ebert, Jason Gagner, Peter J. Haug
2016 Misc conf
AMIA
Jaehoon Lee, Nathan C. Hulse, Michael G. Newman, Douglas Mitchell, Gyan Sharma, Naveen Maram
2016 Misc conf
AMIA
Jaehoon Lee, Nathan C. Hulse, Grant M. Wood, Thomas A. Oniki, Stanley M. Huff
2016 Misc conf
AMIA
Nathan C. Hulse, Jaehoon Lee, Tim Borgeson
2015 Misc conf
AMIA
Jie Long, Nathan C. Hulse, Cui Tao
2014 Misc conf
AMIA
Jaehoon Lee, Nathan C. Hulse, David P. Taylor, Pallavi Ranade-Kharkar, Grant M. Wood, Peter J. Haug, Stanley M. Huff
2014 Misc conf
AMIA
Nathan C. Hulse, Jie Long, Xiaomin Xu, Cui Tao
2014 Misc conf
AMIA
Nathan C. Hulse, Grant M. Wood, Siew Lam, Michael Segal
2013 Misc conf
AMIA
Jie Long, Nathan C. Hulse, Cui Tao, Guilherme Del Fiol
2013 conf
MedInfo
Pallavi Ranade-Kharkar, Guilherme Del Fiol, Janet L. Williams, Nathan C. Hulse, Peter J. Haug
2013 Misc conf
AMIA
Jaehoon Lee, Nathan C. Hulse, Pallavi Ranade-Kharkar, Grant M. Wood, Peter J. Haug, Stanley M. Huff
2013 Misc conf
AMIA
Nathan C. Hulse, Jie Long, Cui Tao
2013 conf
MedInfo
Guilherme Del Fiol, Clayton Curtis, James J. Cimino, Andrew Iskander, Aditya S. D. Kalluri, Xia Jing, Nathan C. Hulse, Jie Long, Casey Lynnette Overby, Connie Schardt, David M. Douglas
2013 Misc conf
AMIA
James J. Cimino, Casey Lynnette Overby, Emily Beth Devine, Nathan C. Hulse, Xia Jing, Saverio M. Maviglia, Guilherme Del Fiol
2012 Misc conf
AMIA
Jaehoon Lee, Pallavi Ranade-Kharkar, Nathan C. Hulse, Thomas A. Oniki, Grant M. Wood, Jacob S. Tripp, Ning Zhuo, Stanley M. Huff
2012 Misc conf
AMIA
David Yauch, Pamela Kum, Samson W. Tu, Peter J. Haug, Nathan C. Hulse, Emory Fry, Robert A. Greenes, Mary K. Goldstein
2012 Misc conf
AMIA
Nathan C. Hulse, Joel Galland, Emerson P. Borsato
2012 Misc conf
AMIA
Randy Madsen, Richard L. Bradshaw, Nicholas Schultz, Ryan Butcher, Ramkiran Gouripeddi, Nathan C. Hulse, Scott P. Narus, Marc Jackson, Joyce A. Mitchell
2012 Misc conf
AMIA
Peter J. Haug, Nathan C. Hulse, David Yauch, Emory Fry, Samson W. Tu, Mary K. Goldstein, Pamela Kum, Robert A. Greenes
2010 J jnl
J. Biomed. Informatics
Nathan C. Hulse, Grant M. Wood, Peter J. Haug, Marc S. Williams
2009 conf
Nursing Informatics
Lorrie K. Roemer, Emerson P. Borsato, Nathan C. Hulse
2008 J jnl
J. Biomed. Informatics
Nathan C. Hulse, Guilherme Del Fiol, Richard L. Bradshaw, Lorrie K. Roemer, Roberto A. Rocha
2006 B conf
CBMS
Timothy P. Hanna, Roberto A. Rocha, Nathan C. Hulse, Guilherme Del Fiol, Richard L. Bradshaw
2006 Misc conf
AMIA
Roberto A. Rocha, Richard L. Bradshaw, Sharon M. Bigelow, Timothy P. Hanna, Guilherme Del Fiol, Nathan C. Hulse, Lorrie K. Roemer, Steven G. Wilkinson
2005 J jnl
IEEE Trans. Inf. Technol. Biomed.
Guilherme Del Fiol, Roberto A. Rocha, Richard L. Bradshaw, Nathan C. Hulse, Lorrie K. Roemer
2005 J jnl
J. Am. Medical Informatics Assoc.
Nathan C. Hulse, Roberto A. Rocha, Guilherme Del Fiol, Richard L. Bradshaw, Timothy P. Hanna, Lorrie K. Roemer
2005 Misc conf
AMIA
Timothy P. Hanna, Roberto A. Rocha, Nathan C. Hulse, Guilherme Del Fiol, Richard L. Bradshaw, Lorrie K. Roemer
2005 Misc conf
AMIA
Nathan C. Hulse, Guilherme Del Fiol, Roberto A. Rocha
2003 Misc conf
AMIA
Nathan C. Hulse, Roberto A. Rocha, Richard L. Bradshaw, Guilherme Del Fiol, Lorrie K. Roemer
redb/extractors/decompiler/_archive/DecompileGhidra-old.py
← Index redb/extractors/decompiler/_archive/DecompileGhidra-old.py python
from hashlib import sha256
import inspect
from pathlib import Path
import subprocess
import json
import subprocess
import json
import os
import tempfile
import uuid
import shutil
import time

from dotenv import load_dotenv

from redb.extractors.enum import Tag
from redb.models.dataclasses import Decompiled
from redb.extractors.extractor import Extractor


class DecompileGhidra(Extractor):
    def __init__(
        self,
        filepath,
        log,
        index_prefix=None,
        elastic_index=None,
        known_benign=False,
        known_malicious=False,
    ):
        super().__init__(
            filepath, log, index_prefix, elastic_index, known_benign, known_malicious
        )
        self.log.debug(inspect.currentframe().f_code.co_name)
        self.elastic_index = self.index_prefix + "-ghidra"
        self.ghidra_path = "/opt/ghidra"
        self.java_script_path = (
            self.ghidra_path
            + "/Ghidra/Features/Base/ghidra_scripts/GhidraDecompilerScript.java"
        )
        self.decompiled = None
        load_dotenv()
        self.decompiled_folder = os.getenv("DECOMPILED_FOLDER", "/opt/decompiled")
        self.log.debug(f"Decompiled folder: {self.decompiled_folder}")

    def run_command(self, cmd, env=None):
        try:
            self.log.info(f"Starting command: {' '.join(cmd)}")
            start_time = time.time()
            TIMEOUT = 1200  # 20 minutes in seconds
            process = subprocess.Popen(
                cmd, env=env, stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True
            )

            while True:
                output = process.stdout.readline()
                if output:
                    print(output.strip())
                if process.poll() is not None:
                    break
            try:
                stdout, stderr = process.communicate(timeout=TIMEOUT)
            except subprocess.TimeoutExpired:
                process.kill()
                self.log.error(f"Ghidra timed out after {TIMEOUT} seconds")
                # raise subprocess.TimeoutExpired(process.args, TIMEOUT)
                return None
            end_time = time.time()

            self.log.debug(
                f"Command finished. Execution time: {end_time - start_time:.2f} seconds"
            )
            self.log.debug(f"Return code: {process.returncode}")

            if process.returncode != 0:
                self.log.error(f"Error output:\n{stderr}")
                return None
            return stdout
        except Exception as e:
            self.log.error(f"Error running command {' '.join(cmd)}: {e}")
            return None

    def analyze_binary(self):
        self.log.debug(f"Ghidra path: {self.ghidra_path}")
        self.log.debug(f"Binary path: {self.filepath}")
        self.log.debug(f"Java script path: {self.java_script_path}")

        # Check if Java script exists
        if not os.path.exists(self.java_script_path):
            self.log.error(f"Error: Java script not found at {self.java_script_path}")
            return None

        # Set up environment variables
        env = os.environ.copy()
        java_home = "/usr/lib/jvm/java-17-openjdk-amd64"  # Adjust this path if needed
        env["JAVA_HOME"] = java_home
        env["PATH"] = f"{java_home}/bin:{env['PATH']}"
        env["LD_LIBRARY_PATH"] = f"{java_home}/lib:{env.get('LD_LIBRARY_PATH', '')}"
        env["DECOMPILED_FOLDER"] = self.decompiled_folder

        # Print environment variables for debugging
        self.log.debug(f"JAVA_HOME: {env['JAVA_HOME']}")
        self.log.debug(f"PATH: {env['PATH']}")
        self.log.debug(f"LD_LIBRARY_PATH: {env['LD_LIBRARY_PATH']}")

        # Check Ghidra installation
        analyzeHeadless_path = f"{self.ghidra_path}/support/analyzeHeadless"
        self.log.debug(
            f"analyzeHeadless exists: {os.path.exists(analyzeHeadless_path)}"
        )

        # Create a temporary project directory
        project_path = tempfile.gettempdir() + "/ghidra_" + str(uuid.uuid4())
        os.makedirs(project_path, exist_ok=True)
        self.log.debug(f"Created temporary project path: {project_path}")
        output_file = ""

        try:
            # Run Ghidra's headless analyzer
            analyze_cmd = [
                analyzeHeadless_path,
                project_path,
                "TempProject",
                "-import",
                self.filepath,
                "-postScript",
                self.java_script_path,
                self.sha256,
                "-deleteProject",
            ]

            result = self.run_command(analyze_cmd, env=env)
            if result is None:
                return None

            # Read the output JSON file
            output_file = os.path.join(
                self.decompiled_folder, self.sha256 + "-decompiled.json"
            )
            if os.path.exists(output_file):
                with open(output_file, "r") as f:
                    functions = json.load(f)
                return functions
            else:
                self.log.error(
                    f"Output file {output_file} not found. Ghidra analysis may have failed."
                )
                return None
        finally:
            # Clean up
            if os.path.exists(project_path):
                shutil.rmtree(project_path)
                self.log.debug(f"Deleted temporary project path: {project_path}")

    def extract(self):
        self.log.debug(inspect.currentframe().f_code.co_name)
        try:
            functions = self.analyze_binary()

            if functions:
                self.log.info(f"Extracted functions from {self.filepath}:")
                for func in functions:
                    id = sha256(func["address"].encode()).hexdigest()
                    self.decompiled = Decompiled(
                        _id=id,
                        decompiled_function_name=func["name"],
                        decompiled_function_address=func["address"],
                        decompiled_function=func["decompiled"],
                    )
                    self.export_to_elastic([self.decompiled])
            else:
                self.log.error("No decompiled functions extracted.")
            return True
        except Exception as e:
            self.log.error(f"Error extracting decompiled information: {e}")
            return None

    def tag(self):
        return Tag.DECOMPILED.value