Omolola Ogunyemi

37 papers B 2Misc 23Journal 9Unranked 3
YearRankTypeTitle / Venue / Authors
2025 J jnl
J. Am. Medical Informatics Assoc.
Oliver J. Bear Don't Walk IV, Shefali Haldar, Duo Helen Wei, Hu Huang, Rebecca L. Rivera, Jungwei W. Fan, Vipina Kuttichi Keloth, Tiffany I. Leung, Pooja M. Desai, Diane M. Korngiebel, Lisa Grossman Liu, Adrienne Pichon, Vignesh Subbian, Anthony Solomonides, Laura K. Wiley, Omolola Ogunyemi, Gretchen P. Jackson, Irene Dankwa-Mullan, Lisa G. Dirks, Avery Rose Everhart, Andrea G. Parker, Bradley E. Iott, Clair A. Kronk, Randi E. Foraker, Krista G. Martin, Tara Anand, Salvatore G. Volpe, Nathan Yung, Rubina F. Rizvi, Robert Lucero, Tiffani J. Bright
2025 J jnl
npj Digit. Medicine
Yuan Luo, Yikuan Li, Omolola Ogunyemi, Eileen Koski, Blanca E. Himes
2022 Misc conf
AMIA
Meghal Gandhi, Lauren Daskivich, Omolola Ogunyemi
2021 Misc conf
AMIA
Donghua Tao, Duo (Helen) Wei, Rubina F. Rizvi, Deepti Pandita, Bushra Alghamdi, Polina V. Kukhareva, Margarita Sordo, William R. Hersh, Omolola Ogunyemi, Kelly Evans, Gretchen P. Jackson
2021 Misc conf
AMIA
Karmen S. Williams, Mindy K. Ross, Adela Grando, Tiffany Harman, Rachael Howe, Kelly Evans, Wendy M. Ingram, Davina J. Zamanzadeh, Leyla B. Warsame, Zubin Khan, Anita C. Murcko, Omolola Ogunyemi
2019 Misc conf
AMIA
Yan Cheng, April F. Mohanty, Omolola Ogunyemi, Catherine Arnott-Smith, Gondy Leroy, Qing T. Zeng
2019 Misc conf
AMIA
Douglas S. Bell, Spencer L. SooHoo, Ann S. Chang, Alex A. Bui, Marianne Zachariah, Ross Fleischmann, Omolola Ogunyemi, Robert A. Jenders
2018 Misc conf
AMIA
Ricky K. Taira, Omolola Ogunyemi, Hyeoneui Kim
2017 Misc conf
AMIA
Wendy W. Chapman, Murielle S. Beene, Omolola Ogunyemi, Genevieve B. Melton, Laura K. Wiley
2016 Misc conf
AMIA
Marianne Zachariah, Amanda L. Do, Jennifer Imaa, Omolola Ogunyemi, Liz Y. Chen, Spencer L. SooHoo, Kevin Dawson, Robert A. Jenders, Douglas S. Bell
2016 Misc conf
AMIA
Sheba M. George, Erin Moran Hayes, Allison Fish, Lauren Patty Daskovich, Omolola Ogunyemi
2015 Misc conf
AMIA
Omolola Ogunyemi, Dulcie Kermah
2013 Misc conf
AMIA
Romulo de Castro Jr., Sukrit Mukherjee, Omolola Ogunyemi, Paul Robinson, Sebastien Delta, Raquel Ecarma, John McDonough, Preciosa M. Coloma
2013 conf
MedInfo
Omolola Ogunyemi, Senait Teklehaimanot, Lauren Patty, Erin Moran, Sheba M. George
2013 Misc conf
AMIA
Omolola Ogunyemi, Lauren Daskivich, Sheba M. George, Senait Teklehaimanot, Richard Baker
2013 Misc conf
AMIA
Sukrit Mukherjee, Omolola Ogunyemi, John McDonough, Romulo de Castro Jr.
2012 Misc conf
AMIA
Paul Robinson, Sukrit Mukherjee, Omolola Ogunyemi, Sheba M. George, Suzie Baldwin, Melvin Dayrit
2010 conf
MedInfo
Omolola Ogunyemi, Sukrit Mukherjee, Chizobam Ani, David Hindman, Sheba M. George, Ramarao Ilapakurthi, Mary Verma, Melvin Dayrit
2009 J jnl
J. Biomed. Informatics
Bilal A. Ahmed, Michael E. Matheny, Phillip L. Rice, John R. Clarke, Omolola Ogunyemi
2006 J jnl
J. Biomed. Informatics
Omolola Ogunyemi
2005 Misc conf
AMIA
Michael E. Matheny, Omolola Ogunyemi, Phillip L. Rice, John R. Clarke
2004 conf
MedInfo
Margarita Sordo, Aziz A. Boxwala, Omolola Ogunyemi, Robert A. Greenes
2004 J jnl
J. Biomed. Informatics
Dongwen Wang, Mor Peleg, Samson W. Tu, Aziz A. Boxwala, Omolola Ogunyemi, Qing T. Zeng, Robert A. Greenes, Vimla L. Patel, Edward H. Shortliffe
2004 J jnl
J. Biomed. Informatics
Aziz A. Boxwala, Mor Peleg, Samson W. Tu, Omolola Ogunyemi, Qing T. Zeng, Dongwen Wang, Vimla L. Patel, Robert A. Greenes, Edward H. Shortliffe
2004 J jnl
J. Am. Medical Informatics Assoc.
Mor Peleg, Aziz A. Boxwala, Samson W. Tu, Qing T. Zeng, Omolola Ogunyemi, Dongwen Wang, Vimla L. Patel, Robert A. Greenes, Edward H. Shortliffe
2003 Misc conf
AMIA
Margarita Sordo, Omolola Ogunyemi, Aziz A. Boxwala, Robert A. Greenes
2002 Misc conf
AMIA
Mra Thinzar Nyun, Omolola Ogunyemi, Qing T. Zeng
2002 J jnl
J. Am. Medical Informatics Assoc.
Omolola Ogunyemi, John R. Clarke, Nachman Ash, Bonnie L. Webber
2002 Misc conf
AMIA
Yaron Denekamp, Omolola Ogunyemi, Aziz A. Boxwala, Robert A. Greenes
2001 Misc conf
AMIA
Nachman Ash, Omolola Ogunyemi, Qing T. Zeng, Lucila Ohno-Machado
2001 J jnl
J. Biomed. Informatics
Aziz A. Boxwala, Samson W. Tu, Mor Peleg, Qing T. Zeng, Omolola Ogunyemi, Robert A. Greenes, Edward H. Shortliffe, Vimla L. Patel
2001 Misc conf
AMIA
Mor Peleg, Omolola Ogunyemi, Samson W. Tu, Aziz A. Boxwala, Qing T. Zeng, Robert A. Greenes, Edward H. Shortliffe
2000 Misc conf
AMIA
Mor Peleg, Aziz A. Boxwala, Omolola Ogunyemi, Qing T. Zeng, Samson W. Tu, Ronilda Lacson, Elmer V. Bernstam, Nachman Ash, Peter Mork, Lucila Ohno-Machado, Edward H. Shortliffe, Robert A. Greenes
2000 Misc conf
AMIA
Omolola Ogunyemi, John R. Clarke, Bonnie L. Webber, Norman I. Badler
2000 B conf
CBMS
Omolola Ogunyemi, John R. Clarke, Bonnie L. Webber
1998 B conf
CBMS
Omolola Ogunyemi, Bonnie L. Webber, John R. Clarke
1997 Misc conf
AMIA
Omolola Ogunyemi, Bonnie L. Webber, John R. Clarke
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