Cezary Czaplewski

25 papers B 1C 1Journal 22Unranked 1
YearRankTypeTitle / Venue / Authors
2024 J jnl
J. Chem. Inf. Model.
Mateusz Lesniewski, Maciej Pyrka, Cezary Czaplewski, Nguyen Truong Co, Yida Jiang, Zhou Gong, Chun Tang, Adam Liwo
2024 J jnl
Comput. Phys. Commun.
Krzysztof M. Ocetkiewicz, Cezary Czaplewski, Henryk Krawczyk, Agnieszka G. Lipska, Adam Liwo, Jerzy Proficz, Adam K. Sieradzan, Pawel Czarnul
2023 J jnl
J. Comput. Chem.
Agnieszka G. Lipska, Adam K. Sieradzan, Cezary Czaplewski, Andrea D. Lipinska, Krzysztof M. Ocetkiewicz, Jerzy Proficz, Pawel Czarnul, Henryk Krawczyk, Adam Liwo
2023 J jnl
J. Comput. Chem.
Adam K. Sieradzan, Jordi Sans-Duñó, Emilia A. Lubecka, Cezary Czaplewski, Agnieszka G. Lipska, Henryk Leszczynski, Krzysztof M. Ocetkiewicz, Jerzy Proficz, Pawel Czarnul, Henryk Krawczyk, Adam Liwo
2023 J jnl
Bioinform.
Krzysztof M. Ocetkiewicz, Cezary Czaplewski, Henryk Krawczyk, Agnieszka G. Lipska, Adam Liwo, Jerzy Proficz, Adam K. Sieradzan, Pawel Czarnul
2021 J jnl
Bioinform.
Pawel Krupa, Agnieszka S. Karczynska, Magdalena A. Mozolewska, Adam Liwo, Cezary Czaplewski
2020 J jnl
J. Chem. Inf. Model.
Agnieszka S. Karczynska, Karolina Zieba, Urszula Uciechowska, Magdalena A. Mozolewska, Pawel Krupa, Emilia A. Lubecka, Agnieszka G. Lipska, Celina Sikorska, Sergey A. Samsonov, Adam K. Sieradzan, Artur Gieldon, Adam Liwo, Rafal Slusarz, Magdalena Slusarz, Jooyoung Lee, Keehyoung Joo, Cezary Czaplewski
2018 J jnl
Supercomput. Front. Innov.
Emilia A. Lubecka, Adam K. Sieradzan, Cezary Czaplewski, Pawel Krupa, Adam Liwo
2018 J jnl
Nucleic Acids Res.
Cezary Czaplewski, Agnieszka S. Karczynska, Adam K. Sieradzan, Adam Liwo
2017 J jnl
J. Comput. Chem.
Agnieszka S. Karczynska, Cezary Czaplewski, Pawel Krupa, Magdalena A. Mozolewska, Keehyoung Joo, Jooyoung Lee, Adam Liwo
2016 J jnl
Bioinform.
Pawel Krupa, Magdalena A. Mozolewska, Marta Wisniewska, Yanping Yin, Yi He, Adam K. Sieradzan, Robert Ganzynkowicz, Agnieszka G. Lipska, Agnieszka S. Karczynska, Magdalena Slusarz, Rafal Slusarz, Artur Gieldon, Cezary Czaplewski, Dawid Jagiela, Bartlomiej Zaborowski, Harold A. Scheraga, Adam Liwo
2016 J jnl
J. Chem. Inf. Model.
Magdalena A. Mozolewska, Pawel Krupa, Bartlomiej Zaborowski, Adam Liwo, Jooyoung Lee, Keehyoung Joo, Cezary Czaplewski
2015 J jnl
J. Chem. Inf. Model.
Bartlomiej Zaborowski, Dawid Jagiela, Cezary Czaplewski, Anna Halabis, Agnieszka Lewandowska, Wioletta Zmudzinska, Stanislaw Oldziej, Agnieszka S. Karczynska, Christian Omieczynski, Tomasz K. Wirecki, Adam Liwo
2015 J jnl
J. Chem. Inf. Model.
Pawel Krupa, Magdalena A. Mozolewska, Keehyoung Joo, Jooyoung Lee, Cezary Czaplewski, Adam Liwo
2010 C conf
BIBE
Stanislaw Oldziej, Cezary Czaplewski, Adam Liwo, Harold A. Scheraga
2006 J jnl
Multiscale Model. Simul.
Maurizio Chinchio, Cezary Czaplewski, Stanislaw Oldziej, Harold A. Scheraga
2006 conf
PARA
Roman Wyrzykowski, Norbert Meyer, Tomasz Olas, Lukasz Kuczynski, Bogdan Ludwiczak, Cezary Czaplewski, Stanislaw Oldziej
2005 J jnl
J. Comput. Chem.
Kyoungrim Lee, Cezary Czaplewski, Seung-Yeon Kim, Jooyoung Lee
2005 J jnl
J. Comput. Chem.
Marian Nanias, Maurizio Chinchio, Stanislaw Oldziej, Cezary Czaplewski, Harold A. Scheraga
2002 J jnl
J. Comput. Chem.
Harold A. Scheraga, Jaroslaw Pillardy, Adam Liwo, Jooyoung Lee, Cezary Czaplewski, Daniel R. Ripoll, William J. Wedemeyer, Yelena A. Arnautova
2000 B conf
RECOMB
Adam Liwo, Jaroslaw Pillardy, Cezary Czaplewski, Jooyoung Lee, Daniel R. Ripoll, Malgorzata Groth, Sylwia Rodziewicz-Motowidlo, Rajmund Kazmierkiewicz, Ryszard J. Wawak, Stanislaw Oldziej, Harold A. Scheraga
1999 J jnl
J. Comput. Aided Mol. Des.
Rajmund Kazmierkiewicz, Cezary Czaplewski, B. Lammek, Jerzy Ciarkowski
1998 J jnl
J. Comput. Aided Mol. Des.
Cezary Czaplewski, Rajmund Kazmierkiewicz, Jerzy Ciarkowski
1998 J jnl
J. Comput. Chem.
Adam Liwo, Rajmund Kazmierkiewicz, Cezary Czaplewski, Malgorzata Groth, Stanislaw Oldziej, Ryszard J. Wawak, Shelly Rackovsky, Matthew R. Pincus, Harold A. Scheraga
1997 J jnl
J. Comput. Aided Mol. Des.
Rajmund Kazmierkiewicz, Cezary Czaplewski, B. Lammek, Jerzy Ciarkowski
tests/conftest.py
← Index tests/conftest.py python
"""
Pytest configuration and shared fixtures for REDB unit tests.
"""
import os
import sys
import pytest
import logging
import tempfile
import hashlib
from unittest.mock import Mock, MagicMock, patch
from pathlib import Path

# Add the project root to the path
sys.path.insert(0, str(Path(__file__).parent.parent))

# Test files directory
TEST_FILES_DIR = Path(__file__).parent.parent / "test_files"


# ============================================================================
# Logger Fixtures
# ============================================================================

@pytest.fixture
def mock_logger():
    """Create a mock logger for testing."""
    logger = Mock()
    logger.debug = Mock()
    logger.info = Mock()
    logger.warning = Mock()
    logger.error = Mock()
    return logger


@pytest.fixture
def real_logger():
    """Create a real logger for testing with debug output."""
    logger = logging.getLogger("test_logger")
    logger.setLevel(logging.DEBUG)
    if not logger.handlers:
        handler = logging.StreamHandler()
        handler.setLevel(logging.DEBUG)
        formatter = logging.Formatter('%(levelname)s - %(message)s')
        handler.setFormatter(formatter)
        logger.addHandler(handler)
    return logger


# ============================================================================
# Test Binary Files Fixtures
# ============================================================================

@pytest.fixture
def elf_binary_path():
    """Path to the ELF test binary."""
    path = TEST_FILES_DIR / "hello"
    if not path.exists():
        pytest.skip(f"Test file not found: {path}")
    return str(path)


@pytest.fixture
def elf_advanced_binary_path():
    """Path to the advanced ELF test binary."""
    path = TEST_FILES_DIR / "hello_advanced"
    if not path.exists():
        pytest.skip(f"Test file not found: {path}")
    return str(path)


@pytest.fixture
def pe_binary_path():
    """Path to the PE test binary (.NET PE)."""
    path = TEST_FILES_DIR / "d8637bdbcfc9112fcb1f0167b398e771"
    if not path.exists():
        pytest.skip(f"Test file not found: {path}")
    return str(path)


@pytest.fixture
def elf_binary_content(elf_binary_path):
    """Read the ELF test binary content."""
    with open(elf_binary_path, "rb") as f:
        return f.read()


@pytest.fixture
def pe_binary_content(pe_binary_path):
    """Read the PE test binary content."""
    with open(pe_binary_path, "rb") as f:
        return f.read()


# ============================================================================
# Temporary Files Fixtures
# ============================================================================

@pytest.fixture
def temp_binary_file():
    """Create a temporary binary file for testing."""
    with tempfile.NamedTemporaryFile(delete=False, suffix=".bin") as f:
        # Write some test data
        f.write(b"\x7fELF" + b"\x00" * 100 + b"test data")
        temp_path = f.name

    yield temp_path

    # Cleanup
    if os.path.exists(temp_path):
        os.unlink(temp_path)


@pytest.fixture
def temp_text_file():
    """Create a temporary text file for testing."""
    with tempfile.NamedTemporaryFile(delete=False, suffix=".txt", mode="w") as f:
        f.write("This is a test file with some text content.")
        temp_path = f.name

    yield temp_path

    # Cleanup
    if os.path.exists(temp_path):
        os.unlink(temp_path)


@pytest.fixture
def temp_pe_like_file():
    """Create a temporary file with PE-like header for testing."""
    with tempfile.NamedTemporaryFile(delete=False, suffix=".exe") as f:
        # MZ header
        f.write(b"MZ" + b"\x00" * 58)
        # e_lfanew pointing to PE header at offset 64
        f.write(b"\x40\x00\x00\x00")
        # PE signature at offset 64
        f.write(b"PE\x00\x00")
        # Minimal COFF header (20 bytes)
        f.write(b"\x4c\x01")  # Machine (i386)
        f.write(b"\x01\x00")  # NumberOfSections
        f.write(b"\x00" * 16)  # Rest of COFF header
        temp_path = f.name

    yield temp_path

    # Cleanup
    if os.path.exists(temp_path):
        os.unlink(temp_path)


# ============================================================================
# Mock Exporter Fixtures
# ============================================================================

@pytest.fixture
def mock_print_exporter(mock_logger):
    """Create a mock PrintExporter."""
    from redb.extractors.database_exporters import PrintExporter
    exporter = PrintExporter(mock_logger, "test_index")
    return exporter


@pytest.fixture
def mock_elasticsearch_exporter(mock_logger):
    """Create a mock ElasticsearchExporter with mocked client."""
    with patch('redb.settings.get_elasticsearch_client') as mock_client:
        mock_client.return_value = Mock()
        from redb.extractors.database_exporters import ElasticsearchExporter
        exporter = ElasticsearchExporter(mock_logger, "test_index")
        return exporter


@pytest.fixture
def mock_clickhouse_exporter(mock_logger):
    """Create a mock ClickHouseExporter with mocked client."""
    with patch('redb.settings.create_clickhouse_client') as mock_client:
        mock_client.return_value = Mock()
        from redb.extractors.database_exporters import ClickHouseExporter
        exporter = ClickHouseExporter(mock_logger, "test_index", client=Mock())
        return exporter


# ============================================================================
# Mock Settings Fixtures
# ============================================================================

@pytest.fixture
def mock_settings():
    """Mock the redb.settings module."""
    with patch.multiple(
        'redb.settings',
        ELASTIC_BINARIES_COLLECTION="test_collection",
        get_elasticsearch_client=Mock(return_value=Mock()),
        create_clickhouse_client=Mock(return_value=Mock()),
    ):
        yield


# ============================================================================
# Hash Fixtures
# ============================================================================

@pytest.fixture
def known_hashes(elf_binary_content):
    """Compute known hashes for the ELF test binary."""
    return {
        'md5': hashlib.md5(elf_binary_content).hexdigest(),
        'sha1': hashlib.sha1(elf_binary_content).hexdigest(),
        'sha256': hashlib.sha256(elf_binary_content).hexdigest(),
    }


@pytest.fixture
def pe_known_hashes(pe_binary_content):
    """Compute known hashes for the PE test binary."""
    return {
        'md5': hashlib.md5(pe_binary_content).hexdigest(),
        'sha1': hashlib.sha1(pe_binary_content).hexdigest(),
        'sha256': hashlib.sha256(pe_binary_content).hexdigest(),
    }


# ============================================================================
# Sample Data Fixtures
# ============================================================================

@pytest.fixture
def sample_binary_data():
    """Sample binary data for entropy and hash testing."""
    return b"\x00\x01\x02\x03\x04\x05\x06\x07\x08\x09\x0a\x0b\x0c\x0d\x0e\x0f" * 16


@pytest.fixture
def high_entropy_data():
    """High entropy random-like data for testing."""
    import random
    random.seed(42)  # Reproducible
    return bytes(random.randint(0, 255) for _ in range(256))


@pytest.fixture
def low_entropy_data():
    """Low entropy repetitive data for testing."""
    return b"\x00" * 256


# ============================================================================
# PE Object Fixtures
# ============================================================================

@pytest.fixture
def pe_object(pe_binary_path):
    """Create a pefile PE object for testing."""
    import pefile
    try:
        pe = pefile.PE(pe_binary_path)
        yield pe
        pe.close()
    except Exception as e:
        pytest.skip(f"Failed to parse PE file: {e}")


# ============================================================================
# ELF Object Fixtures
# ============================================================================

@pytest.fixture
def elf_object(elf_binary_path):
    """Create an ELFFile object for testing."""
    from elftools.elf.elffile import ELFFile
    try:
        with open(elf_binary_path, 'rb') as f:
            elf = ELFFile(f)
            # We need to keep the file open for ELFFile to work
            yield elf
    except Exception as e:
        pytest.skip(f"Failed to parse ELF file: {e}")


# ============================================================================
# Dataclass Fixtures
# ============================================================================

@pytest.fixture
def sample_hash_dataclass():
    """Create a sample Hash dataclass."""
    from redb.models.dataclasses import Hash
    return Hash(
        md5="d41d8cd98f00b204e9800998ecf8427e",
        sha1="da39a3ee5e6b4b0d3255bfef95601890afd80709",
        sha256="e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855"
    )


@pytest.fixture
def sample_hashes_dataclass():
    """Create a sample Hashes dataclass."""
    from redb.models.dataclasses import Hashes
    return Hashes(
        md5="d41d8cd98f00b204e9800998ecf8427e",
        sha1="da39a3ee5e6b4b0d3255bfef95601890afd80709",
        sha256="e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
        ssdeep_hash="3::",
        tlsh_hash=""
    )


@pytest.fixture
def sample_basic_properties():
    """Create a sample BasicProperties dataclass."""
    from redb.models.dataclasses import BasicProperties
    return BasicProperties(
        filename="test.exe",
        sample_name="test.exe",
        filesize=1024,
        filetype="PE32 executable",
        filetype_mime="application/x-dosexec",
        filetype_magika="pebin",
        file_entropy=6.5
    )


# ============================================================================
# Utility Functions for Tests
# ============================================================================

def compute_entropy(data):
    """Compute entropy of data for verification in tests."""
    import math
    from collections import Counter

    if not data:
        return 0.0

    if isinstance(data, str):
        counts = Counter(data)
        frequencies = (i / len(data) for i in counts.values())
        return -sum(f * math.log(f, 2) for f in frequencies)
    else:
        occurrences = Counter(bytearray(data))
        entropy = 0
        for x in occurrences.values():
            p_x = float(x) / len(data)
            entropy -= p_x * math.log(p_x, 2)
        return entropy


# Make the function available as a fixture
@pytest.fixture
def entropy_calculator():
    """Return the entropy calculation function."""
    return compute_entropy


# ============================================================================
# Skip Markers
# ============================================================================

# Mark tests that require external tools
requires_die = pytest.mark.skipif(
    not os.path.exists("/usr/bin/diec") and not os.path.exists("/usr/local/bin/diec"),
    reason="Detect It Easy (diec) not installed"
)

requires_capa = pytest.mark.skipif(
    not os.path.exists("/usr/bin/capa") and not os.path.exists("/usr/local/bin/capa"),
    reason="capa not installed"
)

requires_floss = pytest.mark.skipif(
    not os.path.exists("/usr/bin/floss") and not os.path.exists("/usr/local/bin/floss"),
    reason="floss not installed"
)