James G. R. Gilbert

20 papers Journal 14Unranked 6
YearRankTypeTitle / Venue / Authors
2017 J jnl
IEEE Trans. Instrum. Meas.
Kurt Barbé, Carolyn Ford, Kenlyn Bonn, James G. R. Gilbert
2015 J jnl
IEEE Trans. Ind. Electron.
Xiaosen Liu, Adrian Colli-Menchi, James G. R. Gilbert, Daniel A. Friedrichs, Keith Malang, Edgar Sánchez-Sinencio
2015 conf
EMBC
Kurt Barbé, Carolyn Ford, Kenlyn Bonn, James G. R. Gilbert
2014 conf
BioCAS
Yasmin Hazrat, Carolyn Ford, James G. R. Gilbert, Daniel A. Friedrichs
2014 J jnl
Nucleic Acids Res.
Catherine M. Farrell, Nuala A. O'Leary, Rachel A. Harte, Jane E. Loveland, Laurens G. Wilming, Craig Wallin, Mark Diekhans, Daniel Barrell, Stephen M. J. Searle, Bronwen L. Aken, Susan M. Hiatt, Adam Frankish, Marie-Marthe Suner, Bhanu Rajput, Charles A. Steward, Garth R. Brown, Ruth Bennett, Michael R. Murphy, Wendy Wu, Mike P. Kay, Jennifer Hart, Jeena Rajan, Janet Weber, Catherine Snow, Lillian D. Riddick, Toby Hunt, David Webb, Mark Thomas, Pamela Tamez, Sanjida H. Rangwala, Kelly M. McGarvey, Shashikant Pujar, Andrei Shkeda, Jonathan M. Mudge, Jose M. Gonzalez, James G. R. Gilbert, Stephen J. Trevanion, Robert Baertsch, Jennifer L. Harrow, Tim J. P. Hubbard, James M. Ostell, David Haussler, Kim D. Pruitt
2014 J jnl
Nucleic Acids Res.
Jennifer L. Harrow, Charles A. Steward, Adam Frankish, James G. R. Gilbert, Jose M. Gonzalez, Jane E. Loveland, Jonathan M. Mudge, Daniel Sheppard, Mark Thomas, Stephen J. Trevanion, Laurens G. Wilming
2013 conf
MeMeA
Anup Amin, Daniel A. Friedrichs, Carolyn Ford, Eric Larson, James G. R. Gilbert
2013 conf
BioCAS
Daniel A. Friedrichs, James G. R. Gilbert, Joe Sartor
2013 J jnl
Database J. Biol. Databases Curation
Laurens G. Wilming, Elizabeth A. Hart, Penny C. Coggill, Roger Horton, James G. R. Gilbert, Chris Clee, Matt Jones, Christine Lloyd, Sophie Palmer, Sarah Sims, Siobhan Whitehead, David Wiley, Stephan Beck, Jennifer L. Harrow
2013 J jnl
Database J. Biol. Databases Curation
Charles A. Steward, Jose M. Gonzalez, Stephen J. Trevanion, Daniel Sheppard, Giselle Kerry, James G. R. Gilbert, Linda S. Wicker, Jane Rogers, Jennifer L. Harrow
2012 J jnl
IEEE Trans. Biomed. Circuits Syst.
Daniel A. Friedrichs, Robert W. Erickson, James G. R. Gilbert
2012 J jnl
Database J. Biol. Databases Curation
Jane E. Loveland, James G. R. Gilbert, Ed Griffiths, Jennifer L. Harrow
2011 conf
EMBC
Daniel A. Friedrichs, Robert W. Erickson, James G. R. Gilbert
2008 J jnl
Nucleic Acids Res.
Laurens G. Wilming, James G. R. Gilbert, Kerstin Howe, Stephen J. Trevanion, Tim J. P. Hubbard, Jennifer L. Harrow
2005 J jnl
Nucleic Acids Res.
Tim J. P. Hubbard, D. Andrews, Mario Cáccamo, Graham Cameron, Yuan Chen, Michele E. Clamp, Laura Clarke, Guy Coates, Tony Cox, Fiona Cunningham, Val Curwen, Tim Cutts, Thomas A. Down, Richard Durbin, Xosé M. Fernández-Suárez, James G. R. Gilbert, Martin Hammond, Javier Herrero, H. Hotz, Kevin L. Howe, Vivek Iyer, Kerstin Jekosch, Andreas Kähäri, Arek Kasprzyk, Damian Keefe, Stephen Keenan, Felix Kokocinski, D. London, Ian Longden, Graham P. McVicker, Craig Melsopp, Patrick Meidl, Simon C. Potter, Glenn Proctor, Mark Rae, Daniel Rios, Michael Schuster, Stephen M. J. Searle, Jessica Severin, Guy Slater, Damian Smedley, James A. Smith, William Spooner, Arne Stabenau, Jim Stalker, Roy Storey, Stephen J. Trevanion, Abel Ureta-Vidal, Jan Vogel, Simon White, Cara Woodwark, Ewan Birney
2005 J jnl
Nucleic Acids Res.
J. L. Ashurst, C.-K. Chen, James G. R. Gilbert, Kerstin Jekosch, Stephen Keenan, Patrick Meidl, Stephen M. J. Searle, Jim Stalker, Roy Storey, Stephen J. Trevanion, Laurens G. Wilming, Tim J. P. Hubbard
2004 J jnl
Nucleic Acids Res.
Ewan Birney, T. Daniel Andrews, Paul Bevan, Mario Cáccamo, Graham Cameron, Yuan Chen, Laura Clarke, Guy Coates, Tony Cox, James A. Cuff, Val Curwen, Tim Cutts, Thomas A. Down, Richard Durbin, Eduardo Eyras, Xosé M. Fernández-Suárez, Paul J. Gane, B. Gibbins, James G. R. Gilbert, Martin Hammond, H. Hotz, Vivek Iyer, Andreas Kähäri, Kerstin Jekosch, Arek Kasprzyk, Damian Keefe, Stephen Keenan, Heikki Lehväslaiho, Graham P. McVicker, Craig Melsopp, Patrick Meidl, Emmanuel Mongin, Roger Pettett, Simon C. Potter, Glenn Proctor, Mark Rae, Stephen M. J. Searle, Guy Slater, Damian Smedley, James A. Smith, William Spooner, Arne Stabenau, Jim Stalker, Roy Storey, Abel Ureta-Vidal, Cara Woodwark, Michele E. Clamp, Tim J. P. Hubbard
2003 J jnl
Nucleic Acids Res.
Michele E. Clamp, T. Daniel Andrews, Daniel Barker, Paul Bevan, Graham Cameron, Yuan Chen, Laura Clarke, Tony Cox, James A. Cuff, Val Curwen, Thomas A. Down, Richard Durbin, Eduardo Eyras, James G. R. Gilbert, Martin Hammond, Tim J. P. Hubbard, Arek Kasprzyk, Damian Keefe, Heikki Lehväslaiho, Vivek Iyer, Craig Melsopp, Emmanuel Mongin, Roger Pettett, Simon C. Potter, Alistair G. Rust, Esther Schmidt, Stephen M. J. Searle, Guy Slater, James A. Smith, William Spooner, Arne Stabenau, Jim Stalker, Elia Stupka, Abel Ureta-Vidal, Imre Vastrik, Ewan Birney
2002 J jnl
Nucleic Acids Res.
Tim J. P. Hubbard, Daniel Barker, Ewan Birney, Graham Cameron, Yuan Chen, Laura Clarke, Tony Cox, James A. Cuff, Val Curwen, Thomas A. Down, Richard Durbin, Eduardo Eyras, James G. R. Gilbert, Martin Hammond, Lukasz Huminiecki, Arek Kasprzyk, Heikki Lehväslaiho, Philip Lijnzaad, Craig Melsopp, Emmanuel Mongin, Roger Pettett, Matthew R. Pocock, Simon C. Potter, Alistair G. Rust, Esther Schmidt, Stephen M. J. Searle, Guy Slater, James A. Smith, William Spooner, Arne Stabenau, Jim Stalker, Elia Stupka, Abel Ureta-Vidal, Imre Vastrik, Michele E. Clamp
1999 conf
VRML
Geoff Leach, James G. R. Gilbert
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