James S. Song

14 papers Journal 14
YearRankTypeTitle / Venue / Authors
2023 J jnl
Nucleic Acids Res.
Jiyao Wang, Farideh Chitsaz, Myra K. Derbyshire, Noreen R. Gonzales, Marc Gwadz, Shennan Lu, Gabriele H. Marchler, James S. Song, Narmada Thanki, Roxanne A. Yamashita, Mingzhang Yang, Dachuan Zhang, Chanjuan Zheng, Christopher J. Lanczycki, Aron Marchler-Bauer
2021 J jnl
Nucleic Acids Res.
Wenjun Li, Kathleen O'Neill, Daniel H. Haft, Michael DiCuccio, Vyacheslav Chetvernin, Azat Badretdin, George Coulouris, Farideh Chitsaz, Myra K. Derbyshire, A. Scott Durkin, Noreen R. Gonzales, Marc Gwadz, Christopher J. Lanczycki, James S. Song, Narmada Thanki, Jiyao Wang, Roxanne A. Yamashita, Mingzhang Yang, Chanjuan Zheng, Aron Marchler-Bauer, Françoise Thibaud-Nissen
2020 J jnl
Nucleic Acids Res.
Shennan Lu, Jiyao Wang, Farideh Chitsaz, Myra K. Derbyshire, Renata C. Geer, Noreen R. Gonzales, Marc Gwadz, David I. Hurwitz, Gabriele H. Marchler, James S. Song, Narmada Thanki, Roxanne A. Yamashita, Mingzhang Yang, Dachuan Zhang, Chanjuan Zheng, Christopher J. Lanczycki, Aron Marchler-Bauer
2018 J jnl
Nucleic Acids Res.
Daniel H. Haft, Michael DiCuccio, Azat Badretdin, Vyacheslav Brover, Vyacheslav Chetvernin, Kathleen O'Neill, Wenjun Li, Farideh Chitsaz, Myra K. Derbyshire, Noreen R. Gonzales, Marc Gwadz, Fu Lu, Gabriele H. Marchler, James S. Song, Narmada Thanki, Roxanne A. Yamashita, Chanjuan Zheng, Françoise Thibaud-Nissen, Lewis Y. Geer, Aron Marchler-Bauer, Kim D. Pruitt
2017 J jnl
Nucleic Acids Res.
Aron Marchler-Bauer, Bo Yu, Lianyi Han, Jane He, Christopher J. Lanczycki, Shennan Lu, Farideh Chitsaz, Myra K. Derbyshire, Renata C. Geer, Noreen R. Gonzales, Marc Gwadz, David I. Hurwitz, Fu Lu, Gabriele H. Marchler, James S. Song, Narmada Thanki, Zhouxi Wang, Roxanne A. Yamashita, Dachuan Zhang, Chanjuan Zheng, Lewis Y. Geer, Stephen H. Bryant
2015 J jnl
Nucleic Acids Res.
Aron Marchler-Bauer, Myra K. Derbyshire, Noreen R. Gonzales, Shennan Lu, Farideh Chitsaz, Lewis Y. Geer, Renata C. Geer, Jane He, Marc Gwadz, David I. Hurwitz, Christopher J. Lanczycki, Fu Lu, Gabriele H. Marchler, James S. Song, Narmada Thanki, Zhouxi Wang, Roxanne A. Yamashita, Dachuan Zhang, Chanjuan Zheng, Stephen H. Bryant
2013 J jnl
Nucleic Acids Res.
Aron Marchler-Bauer, Chanjuan Zheng, Farideh Chitsaz, Myra K. Derbyshire, Lewis Y. Geer, Renata C. Geer, Noreen R. Gonzales, Marc Gwadz, David I. Hurwitz, Christopher J. Lanczycki, Fu Lu, Shennan Lu, Gabriele H. Marchler, James S. Song, Narmada Thanki, Roxanne A. Yamashita, Dachuan Zhang, Stephen H. Bryant
2011 J jnl
Nucleic Acids Res.
Aron Marchler-Bauer, Shennan Lu, John B. Anderson, Farideh Chitsaz, Myra K. Derbyshire, Carol DeWeese-Scott, Jessica H. Fong, Lewis Y. Geer, Renata C. Geer, Noreen R. Gonzales, Marc Gwadz, David I. Hurwitz, John D. Jackson, Zhaoxi Ke, Christopher J. Lanczycki, Fu Lu, Gabriele H. Marchler, Mikhail Mullokandov, Marina V. Omelchenko, Cynthia L. Robertson, James S. Song, Narmada Thanki, Roxanne A. Yamashita, Dachuan Zhang, Naigong Zhang, Chanjuan Zheng, Stephen H. Bryant
2009 J jnl
Nucleic Acids Res.
Aron Marchler-Bauer, John B. Anderson, Farideh Chitsaz, Myra K. Derbyshire, Carol DeWeese-Scott, Jessica H. Fong, Lewis Y. Geer, Renata C. Geer, Noreen R. Gonzales, Marc Gwadz, Siqian He, David I. Hurwitz, John D. Jackson, Zhaoxi Ke, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Fu Lu, Shennan Lu, Gabriele H. Marchler, Mikhail Mullokandov, James S. Song, Asba Tasneem, Narmada Thanki, Roxanne A. Yamashita, Dachuan Zhang, Naigong Zhang, Stephen H. Bryant
2007 J jnl
Nucleic Acids Res.
Aron Marchler-Bauer, John B. Anderson, Myra K. Derbyshire, Carol DeWeese-Scott, Noreen R. Gonzales, Marc Gwadz, Luning Hao, Siqian He, David I. Hurwitz, John D. Jackson, Zhaoxi Ke, Dmitri M. Krylov, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Fu Lu, Shennan Lu, Gabriele H. Marchler, Mikhail Mullokandov, James S. Song, Narmada Thanki, Roxanne A. Yamashita, Jodie J. Yin, Dachuan Zhang, Stephen H. Bryant
2005 J jnl
Nucleic Acids Res.
Aron Marchler-Bauer, John B. Anderson, Praveen F. Cherukuri, Carol DeWeese-Scott, Lewis Y. Geer, Marc Gwadz, Siqian He, David I. Hurwitz, John D. Jackson, Zhaoxi Ke, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Fu Lu, Gabriele H. Marchler, Mikhail Mullokandov, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Roxanne A. Yamashita, Jodie J. Yin, Dachuan Zhang, Stephen H. Bryant
2003 J jnl
Nucleic Acids Res.
Aron Marchler-Bauer, John B. Anderson, Carol DeWeese-Scott, Natalie D. Fedorova, Lewis Y. Geer, Siqian He, David I. Hurwitz, John D. Jackson, Aviva R. Jacobs, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Thomas Madej, Gabriele H. Marchler, Raja Mazumder, Anastasia N. Nikolskaya, Anna R. Panchenko, Bachoti S. Rao, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Sona Vasudevan, Yanli Wang, Roxanne A. Yamashita, Jodie J. Yin, Stephen H. Bryant
2003 J jnl
Nucleic Acids Res.
Jie Chen, John B. Anderson, Carol DeWeese-Scott, Natalie D. Fedorova, Lewis Y. Geer, Siqian He, David I. Hurwitz, John D. Jackson, Aviva R. Jacobs, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Thomas Madej, Aron Marchler-Bauer, Gabriele H. Marchler, Raja Mazumder, Anastasia N. Nikolskaya, Bachoti S. Rao, Anna R. Panchenko, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Sona Vasudevan, Yanli Wang, Roxanne A. Yamashita, Jodie J. Yin, Stephen H. Bryant
2002 J jnl
Nucleic Acids Res.
Yanli Wang, John B. Anderson, Jie Chen, Lewis Y. Geer, Siqian He, David I. Hurwitz, Cynthia A. Liebert, Thomas Madej, Gabriele H. Marchler, Aron Marchler-Bauer, Anna R. Panchenko, Benjamin A. Shoemaker, James S. Song, Paul A. Thiessen, Roxanne A. Yamashita, Stephen H. Bryant
tests/integration/test_base_extractor.py
← Index tests/integration/test_base_extractor.py python
"""
Integration tests for the base Extractor class.
"""
import pytest
import hashlib
import math
from unittest.mock import Mock, patch, MagicMock
from collections import Counter

pytestmark = [pytest.mark.integration]


class TestExtractorStaticMethods:
    """Tests for static methods in Extractor class."""

    def test_process_binary_string_printable(self):
        """Test processing a printable binary string."""
        from redb.extractors.extractor import Extractor

        # Test with printable ASCII characters
        input_bytes = b"Hello World\x00\x00\x00"
        result = Extractor.process_binary_string(input_bytes)
        assert result == "Hello World"

    def test_process_binary_string_non_printable(self):
        """Test processing a string with non-printable characters."""
        from redb.extractors.extractor import Extractor

        # Test with non-printable characters
        input_bytes = b"\x01\x02Hello\x00"
        result = Extractor.process_binary_string(input_bytes)
        assert "\\x01" in result
        assert "\\x02" in result
        assert "Hello" in result

    def test_process_binary_string_empty(self):
        """Test processing an empty binary string."""
        from redb.extractors.extractor import Extractor

        input_bytes = b"\x00\x00\x00"
        result = Extractor.process_binary_string(input_bytes)
        assert result == ""

    def test_process_binary_string_all_printable(self):
        """Test processing a fully printable string."""
        from redb.extractors.extractor import Extractor

        input_bytes = b"TestString123"
        result = Extractor.process_binary_string(input_bytes)
        assert result == "TestString123"

    def test_remove_non_utf8_valid(self):
        """Test removing non-UTF8 characters from valid UTF8 string."""
        from redb.extractors.extractor import Extractor

        input_bytes = b"Hello World"
        result = Extractor.remove_non_utf8(input_bytes)
        assert result == b"Hello World"

    def test_remove_non_utf8_with_invalid(self):
        """Test removing non-UTF8 characters from mixed string."""
        from redb.extractors.extractor import Extractor

        # Mix of valid UTF8 and invalid bytes
        input_bytes = b"Hello\xff\xfeWorld"
        result = Extractor.remove_non_utf8(input_bytes)
        # Should remove the invalid bytes
        assert b"\xff" not in result
        assert b"\xfe" not in result
        assert b"Hello" in result
        assert b"World" in result

    def test_remove_non_utf8_empty(self):
        """Test removing non-UTF8 from empty string."""
        from redb.extractors.extractor import Extractor

        result = Extractor.remove_non_utf8(b"")
        assert result == b""


class TestExtractorEntropyCalculation:
    """Tests for entropy calculation in Extractor class."""

    def test_calculate_entropy_empty_data(self, elf_binary_path, mock_logger):
        """Test entropy calculation with empty data."""
        from redb.extractors.basicproperties import BasicPropertiesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = BasicPropertiesExtractor(elf_binary_path, mock_logger)
            result = extractor.calculate_entropy(b"")
            assert result == 0.0

    def test_calculate_entropy_uniform_data(self, elf_binary_path, mock_logger):
        """Test entropy calculation with uniform (low entropy) data."""
        from redb.extractors.basicproperties import BasicPropertiesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = BasicPropertiesExtractor(elf_binary_path, mock_logger)
            # All same bytes = 0 entropy
            uniform_data = b"\x00" * 256
            result = extractor.calculate_entropy(uniform_data)
            assert result == 0.0

    def test_calculate_entropy_random_data(self, elf_binary_path, mock_logger, high_entropy_data):
        """Test entropy calculation with random (high entropy) data."""
        from redb.extractors.basicproperties import BasicPropertiesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = BasicPropertiesExtractor(elf_binary_path, mock_logger)
            result = extractor.calculate_entropy(high_entropy_data)
            # Random data should have entropy close to 8 (max for bytes)
            assert result > 7.0

    def test_calculate_entropy_binary_data(self, elf_binary_path, mock_logger):
        """Test entropy calculation with binary data."""
        from redb.extractors.basicproperties import BasicPropertiesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = BasicPropertiesExtractor(elf_binary_path, mock_logger)
            # Two equally distributed values = 1 bit entropy
            binary_data = b"\x00\x01" * 128
            result = extractor.calculate_entropy(binary_data)
            assert abs(result - 1.0) < 0.01

    def test_calculate_entropy_string_data(self, elf_binary_path, mock_logger):
        """Test entropy calculation with string data."""
        from redb.extractors.basicproperties import BasicPropertiesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = BasicPropertiesExtractor(elf_binary_path, mock_logger)
            # String with two equally distributed characters
            string_data = "ab" * 100
            result = extractor.calculate_entropy(string_data)
            assert abs(result - 1.0) < 0.01


class TestExtractorInitialization:
    """Tests for Extractor initialization."""

    def test_extractor_hashes_computed_on_init(self, elf_binary_path, mock_logger, known_hashes):
        """Test that hashes are computed during initialization."""
        from redb.extractors.basicproperties import BasicPropertiesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = BasicPropertiesExtractor(elf_binary_path, mock_logger)

            assert extractor.md5 == known_hashes['md5']
            assert extractor.sha1 == known_hashes['sha1']
            assert extractor.sha256 == known_hashes['sha256']

    def test_extractor_hash_dataclass_created(self, elf_binary_path, mock_logger, known_hashes):
        """Test that Hash dataclass is created during initialization."""
        from redb.extractors.basicproperties import BasicPropertiesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = BasicPropertiesExtractor(elf_binary_path, mock_logger)

            assert extractor.hash.md5 == known_hashes['md5']
            assert extractor.hash.sha1 == known_hashes['sha1']
            assert extractor.hash.sha256 == known_hashes['sha256']

    def test_extractor_binary_cached_property(self, elf_binary_path, mock_logger, elf_binary_content):
        """Test that binary content is loaded as cached property."""
        from redb.extractors.basicproperties import BasicPropertiesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = BasicPropertiesExtractor(elf_binary_path, mock_logger)

            # Access binary property
            binary = extractor.binary
            assert binary == elf_binary_content

            # Second access should return cached value (same id)
            assert extractor.binary is binary

    def test_extractor_with_exporters(self, elf_binary_path, mock_logger, mock_print_exporter):
        """Test extractor initialization with exporters."""
        from redb.extractors.basicproperties import BasicPropertiesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = BasicPropertiesExtractor(
                elf_binary_path,
                mock_logger,
                exporters=[mock_print_exporter]
            )

            assert len(extractor.exporters) == 1
            assert extractor.exporters[0] is mock_print_exporter

    def test_extractor_with_index_prefix(self, elf_binary_path, mock_logger):
        """Test extractor initialization with custom index prefix."""
        from redb.extractors.basicproperties import BasicPropertiesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = BasicPropertiesExtractor(
                elf_binary_path,
                mock_logger,
                index_prefix="custom_prefix"
            )

            assert "custom_prefix" in extractor.elastic_index

    def test_extractor_known_benign_flag(self, elf_binary_path, mock_logger):
        """Test extractor with known_benign flag."""
        from redb.extractors.basicproperties import BasicPropertiesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = BasicPropertiesExtractor(
                elf_binary_path,
                mock_logger,
                known_benign=True
            )

            assert extractor.known_benign is True
            assert extractor.known_malicious is False

    def test_extractor_known_malicious_flag(self, elf_binary_path, mock_logger):
        """Test extractor with known_malicious flag."""
        from redb.extractors.basicproperties import BasicPropertiesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = BasicPropertiesExtractor(
                elf_binary_path,
                mock_logger,
                known_malicious=True
            )

            assert extractor.known_benign is False
            assert extractor.known_malicious is True


class TestExtractorExportData:
    """Tests for export_data method."""

    def test_export_data_with_print_exporter(self, elf_binary_path, mock_logger, mock_print_exporter, capsys):
        """Test export_data with PrintExporter."""
        from redb.extractors.basicproperties import BasicPropertiesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = BasicPropertiesExtractor(
                elf_binary_path,
                mock_logger,
                exporters=[mock_print_exporter]
            )

            result = extractor.export_data()
            # Should succeed with PrintExporter
            assert result is True

    def test_export_data_no_exporters(self, elf_binary_path, mock_logger):
        """Test export_data with no exporters configured."""
        from redb.extractors.basicproperties import BasicPropertiesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = BasicPropertiesExtractor(
                elf_binary_path,
                mock_logger,
                exporters=[]
            )

            result = extractor.export_data()
            # Should succeed with no exporters (nothing to export)
            assert result is True


class TestExtractorEdgeCases:
    """Tests for edge cases in Extractor class."""

    def test_extractor_with_nonexistent_file(self, mock_logger):
        """Test extractor with non-existent file."""
        from redb.extractors.basicproperties import BasicPropertiesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            with pytest.raises(FileNotFoundError):
                BasicPropertiesExtractor("/nonexistent/file.bin", mock_logger)

    def test_entropy_none_data(self, elf_binary_path, mock_logger):
        """Test entropy calculation with None returns 0."""
        from redb.extractors.basicproperties import BasicPropertiesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = BasicPropertiesExtractor(elf_binary_path, mock_logger)
            result = extractor.calculate_entropy(None)
            assert result == 0.0

    def test_process_binary_string_high_bytes(self):
        """Test processing binary string with high byte values."""
        from redb.extractors.extractor import Extractor

        # Characters above 126 are non-printable
        input_bytes = b"\x7f\x80\x81\xff"
        result = Extractor.process_binary_string(input_bytes)
        assert "\\x7f" in result
        assert "\\x80" in result
        assert "\\xff" in result