James P. McGlothlin

20 papers A* 4C 3Misc 2Journal 1Unranked 10
YearRankTypeTitle / Venue / Authors
2025 conf
BIOSTEC (2): HEALTHINF
James P. McGlothlin, Micah Price-Offerman, Robbie Beyer, George Casey, John P. Barile
2025 conf
BIOSTEC (2): HEALTHINF
James P. McGlothlin, Timothy Martens
2019 conf
HEALTHINF
James P. McGlothlin, Hari Srinivasan, Ilija Stojic
2018 Misc conf
AMIA
James P. McGlothlin, Evan Crawford, Ilija Stojic, Timothy Martens
2018 Misc conf
IRI
James P. McGlothlin
2018 conf
HEALTHINF
James P. McGlothlin, Sriveni Vedire, Hari Srinivasan, Amar Madugula, Srinivasan Rajagopalan, Latifur Khan
2017 conf
HEALTHINF
James P. McGlothlin, Evan Crawford, Jesse Wyatt, Carlos Samayoa, Yana Vaks, Brenda Bruneau, Merrick Lopez, Anthony Moretti, Michele Wilson, James Pappas
2017 conf
ITBAM
James P. McGlothlin, Evan Crawford, Hari Srinivasan, Carissa Cianci, Brenda Bruneau, Ihab Dorotta
2017 conf
HEALTHINF
James P. McGlothlin, Amar Madugula, Ilija Stojic
2013 conf
DARE@CIKM
James P. McGlothlin, Latifur Khan
2011 J jnl
IEEE Trans. Knowl. Data Eng.
Mohammad Farhan Husain, James P. McGlothlin, Mohammad M. Masud, Latifur R. Khan, Bhavani M. Thuraisingham
2011 A* conf
IJCAI
James P. McGlothlin, Latifur Khan, Bhavani Thuraisingham
2011 conf
IEEE CLOUD
Mohammad Farhan Husain, James P. McGlothlin, Latifur Khan, Bhavani Thuraisingham
2011 C conf
IDEAS
James P. McGlothlin, Latifur Khan
2010 conf
ISWC (Posters & Demos)
James P. McGlothlin, Latifur Khan
2010 C conf
IDEAS
James P. McGlothlin, Latifur Khan
2010 A* conf
AAAI
James P. McGlothlin
2010 A* conf
AAAI
James P. McGlothlin, Latifur R. Khan
2010 A* conf
AAAI
James P. McGlothlin, Latifur R. Khan
2009 C conf
IDEAS
James P. McGlothlin, Latifur R. Khan
redb/s3_utils.py
← Index redb/s3_utils.py python
"""
S3 and file utility functions for REDB.

Contains MinIO/S3 client creation, S3 key generation,
file download, and archive extraction helpers.
"""
import os
import tempfile
from typing import Optional, List

from minio import Minio
from minio.error import S3Error


def get_minio_client():
    """Create and return a Minio client using credentials from .env file"""
    return Minio(
        endpoint=os.getenv("S3_ENDPOINT"),
        access_key=os.getenv("S3_ACCESS_KEY"),
        secret_key=os.getenv("S3_SECRET_KEY"),
        secure=os.getenv("S3_SECURE", "false").lower() == "true"
    )


def generate_s3_key_from_hash(sample_hash: str) -> str:
    """
    Generate S3 key from hash using sharding structure.
    Example: 09f7d02a3c2382199458c98a62b045145ee54ab6aba86166aecf3d10c3c1444c
    becomes: 09/f7/09f7d02a3c2382199458c98a62b045145ee54ab6aba86166aecf3d10c3c1444c.zip
    """
    if len(sample_hash) < 4:
        raise ValueError(f"Hash too short for sharding: {sample_hash}")

    # Create sharded path: first 2 chars / next 2 chars / full_hash.zip
    return f"{sample_hash[:2]}/{sample_hash[2:4]}/{sample_hash}.zip"


def download_s3_object(s3_bucket: str, s3_key: str, temp_dir: str, logger=None) -> Optional[str]:
    """
    Download an object from S3 to a local temporary directory and return the local path.
    If the .zip file is not found, automatically tries .7z as a fallback for legacy uploads.
    """
    try:
        minio_client = get_minio_client()
        local_path = os.path.join(temp_dir, os.path.basename(s3_key))

        # Download the file
        minio_client.fget_object(s3_bucket, s3_key, local_path)

        return local_path
    except S3Error as e:
        # If .zip not found and error is NoSuchKey, try .7z fallback
        if e.code == 'NoSuchKey' and s3_key.endswith('.zip'):
            s3_key_7z = s3_key[:-4] + '.7z'  # Replace .zip with .7z
            if logger:
                logger.info(f".zip not found, trying .7z fallback: {s3_key_7z}")
            try:
                local_path_7z = os.path.join(temp_dir, os.path.basename(s3_key_7z))
                minio_client.fget_object(s3_bucket, s3_key_7z, local_path_7z)
                if logger:
                    logger.info(f"Successfully downloaded .7z fallback: {s3_key_7z}")
                return local_path_7z
            except S3Error as e2:
                if logger:
                    logger.error(f"Failed to download S3 object {s3_key} (tried both .zip and .7z): {e2}")
                else:
                    print(f"[ERROR] Failed to download S3 object {s3_key} (tried both .zip and .7z): {e2}")
                return None
        else:
            if logger:
                logger.error(f"Failed to download S3 object {s3_key}: {e}")
            else:
                print(f"[ERROR] Failed to download S3 object {s3_key}: {e}")
            return None


def extract_fat_slices(macho, output_dir: str, logger) -> List[tuple]:
    """
    Extract slices from FAT Mach-O binary using machofile's dump_slices() API.

    Args:
        macho: Parsed machofile.UniversalMachO object
        output_dir: Directory to write slice files
        logger: Logger instance

    Returns:
        List of (arch_name, slice_path, slice_sha256, slice_md5, slice_sha1) tuples
    """
    result = []
    try:
        # Use machofile's dump_slices API (v2026.2.5+)
        slices = macho.dump_slices(output_dir=output_dir)
        logger.debug(f"Extracted {len(slices)} slices from FAT binary")

        for arch_name, slice_path in slices:
            # Get hash info for this slice from machofile
            general_info = macho.get_general_info(arch=arch_name)
            slice_sha256 = general_info.get('SHA256')
            slice_md5 = general_info.get('MD5')
            slice_sha1 = general_info.get('SHA1')
            result.append((arch_name, slice_path, slice_sha256, slice_md5, slice_sha1))
            logger.debug(f"Slice {arch_name}: {slice_sha256}")

    except Exception as e:
        logger.error(f"Error extracting FAT slices: {e}")

    return result