James D. Berry

13 papers A 3Misc 2Journal 5Unranked 3
YearRankTypeTitle / Venue / Authors
2025 J jnl
npj Digit. Medicine
Michele Merler, Carla Agurto, Julian Peller, Esteban Roitberg, Alan Taitz, Marcos A. Trevisan, Indu Navar, James D. Berry, Ernest Fraenkel, Lyle W. Ostrow, Guillermo A. Cecchi, Raquel Norel
2024 conf
ICDH
Carla Agurto, Michele Merler, Esteban Roitberg, Alan Taitz, Marcos A. Trevisan, Diego E. Shalom, Julian Peller, Lyle W. Ostrow, Indu Navar, Ernest Fraenkel, James D. Berry, Guillermo A. Cecchi, Raquel Norel
2023 conf
ICDH
Carla Agurto, Guillermo A. Cecchi, Bo Wen, Ernest Fraenkel, James D. Berry, Indu Navar, Raquel Norel
2023 J jnl
CoRR
Carla Agurto, Guillermo A. Cecchi, Bo Wen, Ernest Fraenkel, James D. Berry, Indu Navar, Raquel Norel
2023 J jnl
npj Digit. Medicine
Stephen A. Johnson, Marta Karas, Katherine M. Burke, Marcin Straczkiewicz, Zoe A. Scheier, Alison P. Clark, Satoshi Iwasaki, Amir Lahav, Amrita S. Iyer, Jukka-Pekka Onnela, James D. Berry
2022 Misc conf
AMIA
Aria Anvar, James D. Berry, Ernest Fraenkel, Indu Navar, Guillermo A. Cecchi, Raquel Norel
2022 J jnl
Nat. Comput. Sci.
Divya Ramamoorthy, Kristen Severson, Soumya Ghosh, Karen Sachs, Emily G. Baxi, Alyssa N. Coyne, Elizabeth Mosmiller, Lindsey Hayes, Aianna Cerezo, Omar Ahmad, Promit Roy, Steven Zeiler, John W. Krakauer, Jonathan Li, Aneesh Donde, Nhan Huynh, Miriam Adam, Brook T. Wassie, Alexander LeNail, Natasha Leanna Patel-Murray, Yogindra Raghav, Velina Kozareva, Stanislav Tsitkov, Tobias Ehrenberger, Julia A. Kaye, Leandro Lima, Stacia K. Wyman, Edward Vertudes, Naufa Amirani, Krishna Raja, Reuben Thomas, Ryan G. Lim, Ricardo Miramontes, Jie Wu, Vineet Vaibhav, Andrea Matlock, Vidya Venkatraman, Ronald Holewenski, Niveda Sundararaman, Rakhi Pandey, Danica-Mae Manalo, Aaron Frank, Loren Ornelas, Lindsey Panther, Emilda Gomez, Erick Galvez, Daniel Pérez, Imara Meepe, Susan Lei, Louis Pinedo, Chunyan Liu, Ruby Moran, Dhruv Sareen, Barry Landin, Carla Agurto, Guillermo A. Cecchi, Raquel Norel, Sara Thrower, Sarah Luppino, Alanna Farrar, Lindsay Pothier, Hong Yu, Ervin Sinani, Prasha Vigneswaran, Alexander V. Sherman, S. Michelle Farr, Berhan Mandefro, Hannah Trost, Maria G. Banuelos, Veronica Garcia, Michael Workman, Richie Ho, Robert Baloh, Jennifer Roggenbuck, Matthew B. Harms, Carolyn Prina, Sarah Heintzman, Stephen Kolb, Jennifer Stocksdale, Keona Wang, Todd Morgan, Daragh Heitzman, Arish Jamil, Jennifer Jockel-Balsarotti, Elizabeth Karanja, Jesse Markway, Molly McCallum, Tim Miller, Ben Joslin, Deniz Alibazoglu, Senda Ajroud-Driss, Jay C. Beavers, Mary Bellard, Elizabeth Bruce, Nicholas J. Maragakis, Merit E. Cudkowicz, James D. Berry, Terri Thompson, Steven Finkbeiner, Leslie M. Thompson, Jennifer E. Van Eyk, Clive N. Svendsen, Jeffrey D. Rothstein, Jonathan D. Glass, Christina N. Fournier, Alexander Sherman, Christian Lunetta, David Walk, Ghazala Hayat, James Wymer, Kelly Gwathmey, Nicholas Olney, Terry Heiman-Patterson, Ximena Arcila-Londono, Kenneth Faulconer, Ervin Sanani, Alex Berger, Julia Mirochnick, Todd M. Herrington, Kenney Ng, Ernest Fraenkel
2021 A conf
Interspeech
Michael Neumann, Oliver Roesler, Jackson Liscombe, Hardik Kothare, David Suendermann-Oeft, David Pautler, Indu Navar, Aria Anvar, Jochen Kumm, Raquel Norel, Ernest Fraenkel, Alexander V. Sherman, James D. Berry, Gary L. Pattee, Jun Wang, Jordan R. Green, Vikram Ramanarayanan
2021 J jnl
CoRR
Michael Neumann, Oliver Roesler, Jackson Liscombe, Hardik Kothare, David Suendermann-Oeft, David Pautler, Indu Navar, Aria Anvar, Jochen Kumm, Raquel Norel, Ernest Fraenkel, Alexander V. Sherman, James D. Berry, Gary L. Pattee, Jun Wang, Jordan R. Green, Vikram Ramanarayanan
2020 Misc conf
AMIA
Carla Agurto, Guillermo A. Cecchi, Mary Pietrowicz, Divya Ramamoorthy, Lorin Wilde, Elizabeth Mosmiller, Emily G. Baxi, Nicholas J. Maragakis, James D. Berry, Ernest Fraenkel, Jeffrey D. Rothstein, Raquel Norel
2019 conf
EMBC
Carla Agurto, Mary Pietrowicz, Elif K. Eyigöz, Elizabeth Mosmiller, Emily G. Baxi, Jeffrey D. Rothstein, Promit Roy, James D. Berry, Nicholas J. Maragakis, Omar Ahmad, Guillermo A. Cecchi, Raquel Norel
2019 A conf
INTERSPEECH
Kathryn P. Connaghan, Jordan R. Green, Sabrina Paganoni, James Chan, Harli Weber, Ella Collins, Brian Richburg, Marziye Eshghi, Jukka-Pekka Onnela, James D. Berry
2014 A conf
INTERSPEECH
Panying Rong, Yana Yunusova, James D. Berry, Lorne Zinman, Jordan R. Green
tests/unit/conftest.py
← Index tests/unit/conftest.py python
"""
Unit test configuration.

Replaces the redb.extractors package with a minimal stub so that
``from redb.extractors.database_exporters import ...`` works without
pulling in the heavy __init__.py import chain (pefile, elftools,
signify, magic, etc.).

Also stubs out redb.settings so that Elasticsearch / ClickHouse
clients are never actually created during unit tests.

Additionally installs binaryninja stubs for decompiler unit tests.

Stubs heavy third-party packages (pefile, magic, psutil, etc.) so that
redb.workers, redb.queries, redb.ingestor, and redb.s3_utils can all
be imported and patched in unit tests without requiring the real packages.
"""
import sys
import types
from pathlib import Path
from unittest.mock import MagicMock

# ---------------------------------------------------------------------------
# 0. Install binaryninja stubs FIRST — must happen before any decompiler
#    module is imported (triggered by __init__.py chain).
# ---------------------------------------------------------------------------
from tests.unit.conftest_binja_stubs import install_binja_stubs as _install_binja_stubs
_install_binja_stubs()

# ---------------------------------------------------------------------------
# 1. Stub external packages required by database_exporters.py itself,
#    the decompiler chain, and the workers/ingestor modules.
# ---------------------------------------------------------------------------
_heavy_deps = [
    # Database / networking
    "elasticsearch", "clickhouse_connect", "dotenv",
    # Binary analysis — top-level packages
    "pefile", "magic", "machofile",
    # Archive handling
    "py7zr", "pyzipper",
    # File type detection
    "magika",
    # System monitoring
    "psutil",
    # S3 / MinIO (submodule paths needed for `from minio.error import S3Error`)
    "minio", "minio.error",
    # YARA
    "yara_x",
    # Binary parsing — elftools tree
    "elftools", "elftools.elf", "elftools.elf.elffile",
    "elftools.common", "elftools.common.exceptions",
    # Code signing — signify tree
    "signify", "signify.fingerprinter", "signify.authenticode",
    # LIEF
    "lief",
    # Fuzzy hashing
    "ppdeep",
    # .NET analysis
    "dotnetfile",
    # Crypto / ASN.1
    "asn1crypto", "asn1crypto.cms", "asn1crypto.pem", "asn1crypto.x509", "asn1crypto.core",
    # Hashing
    "xxhash", "blake3", "mmh3", "numpy",
    # APK analysis
    "androguard", "androguard.core", "androguard.core.apk",
    "androguard.core.dex", "androguard.core.api_specific_resources",
    "androguard.misc",
    "permhash",
]
for _mod in _heavy_deps:
    if _mod not in sys.modules:
        try:
            __import__(_mod)
        except (ImportError, ModuleNotFoundError):
            sys.modules[_mod] = MagicMock()

# Stub urllib3 with a real Warning subclass (warnings.filterwarnings needs a class)
if "urllib3" not in sys.modules or isinstance(sys.modules.get("urllib3"), MagicMock):
    try:
        import urllib3  # noqa: F401
    except (ImportError, ModuleNotFoundError):
        _urllib3_mod = types.ModuleType("urllib3")
        _urllib3_exc = types.ModuleType("urllib3.exceptions")

        class _InsecureRequestWarning(UserWarning):
            pass

        _urllib3_exc.InsecureRequestWarning = _InsecureRequestWarning
        _urllib3_mod.exceptions = _urllib3_exc
        sys.modules["urllib3"] = _urllib3_mod
        sys.modules["urllib3.exceptions"] = _urllib3_exc

# Provide a functional ppdeep stub (tests call ppdeep.hash() and expect a string).
# Must overwrite the MagicMock that the loop above may have installed.
_ppdeep_existing = sys.modules.get("ppdeep")
if _ppdeep_existing is None or isinstance(_ppdeep_existing, MagicMock):
    _ppdeep_mod = types.ModuleType("ppdeep")
    _ppdeep_mod.__name__ = "ppdeep"

    def _ppdeep_hash(data):
        """Fake ssdeep hash — returns a deterministic placeholder."""
        if isinstance(data, str):
            data = data.encode("utf-8")
        if len(data) < 50:
            return None
        import hashlib
        h = hashlib.md5(data).hexdigest()
        return f"3:{h[:16]}:{h[16:]}"

    _ppdeep_mod.hash = _ppdeep_hash
    sys.modules["ppdeep"] = _ppdeep_mod

# Stub mmh3 if the C extension is not available
_mmh3_existing = sys.modules.get("mmh3")
if _mmh3_existing is None or isinstance(_mmh3_existing, MagicMock):
    _mmh3_mod = types.ModuleType("mmh3")
    _mmh3_mod.__name__ = "mmh3"

    def _mmh3_hash(data, seed=0):
        """Fake MurmurHash3 — deterministic hash using built-in hashlib."""
        import hashlib
        if isinstance(data, str):
            data = data.encode("utf-8")
        seed_bytes = (seed & 0xFFFFFFFF).to_bytes(8, "little")
        h = hashlib.md5(data + seed_bytes).digest()
        return int.from_bytes(h[:4], "little", signed=True)

    _mmh3_mod.hash = _mmh3_hash
    sys.modules["mmh3"] = _mmh3_mod

# Stub tlsh if the C extension is not available
if "tlsh" not in sys.modules:
    try:
        import tlsh as _real_tlsh  # noqa: F401
    except (ImportError, ModuleNotFoundError):
        _tlsh_mock = types.ModuleType("tlsh")
        _tlsh_mock.__name__ = "tlsh"

        def _tlsh_hash(data):
            """Fake TLSH hash — returns a deterministic placeholder.

            Returns empty string for data < 50 bytes or data with very
            low entropy (e.g. repeating patterns), mimicking the real
            TLSH library's "TNULL" behaviour.
            """
            if isinstance(data, str):
                data = data.encode("utf-8")
            if len(data) < 50:
                return ""
            # Real TLSH returns "" for low-entropy input
            if len(set(data)) < 8:
                return ""
            import hashlib
            return "T1" + hashlib.sha256(data).hexdigest()[:70].upper()

        _tlsh_mock.hash = _tlsh_hash
        sys.modules["tlsh"] = _tlsh_mock

# ---------------------------------------------------------------------------
# 2. Stub redb.settings (package) so module-level code never runs
# ---------------------------------------------------------------------------
_settings_mock = MagicMock()
_settings_mock.__name__ = "redb.settings"
sys.modules["redb.settings"] = _settings_mock
sys.modules["redb.settings.elasticsearch"] = MagicMock()
sys.modules["redb.settings.clickhouse"] = MagicMock()

# ---------------------------------------------------------------------------
# 3. Replace redb.extractors with a minimal package that does NOT eagerly
#    import every extractor (and their heavy deps).  Sub-module imports
#    like ``from redb.extractors.database_exporters import ...`` still work
#    because __path__ points to the real package directory.
# ---------------------------------------------------------------------------
_repo_root = Path(__file__).resolve().parents[2]
_extractors_pkg = types.ModuleType("redb.extractors")
_extractors_pkg.__path__ = [str(_repo_root / "redb" / "extractors")]
_extractors_pkg.__package__ = "redb.extractors"
sys.modules["redb.extractors"] = _extractors_pkg

# ---------------------------------------------------------------------------
# 4. Force-import redb submodules so that @patch('redb.workers.xxx'),
#    @patch('redb.queries.xxx'), etc. can resolve at decoration time.
#    This works because all heavy deps are already stubbed above.
# ---------------------------------------------------------------------------
import redb.logging_utils   # noqa: F401, E402
import redb.s3_utils         # noqa: F401, E402
import redb.queries          # noqa: F401, E402
import redb.workers          # noqa: F401, E402
import redb.ingestor         # noqa: F401, E402