James Hetherington

26 papers Journal 21Unranked 5
YearRankTypeTitle / Venue / Authors
2022 J jnl
J. Open Source Softw.
Frederik De Ceuster, Thomas Ceulemans, Atulit Srivastava, Ward Homan, Jan Bolte, Jeremy Yates, Leen Decin, Peter Boyle, James Hetherington
2020 conf
DH
Yann Ryan, Mariona Coll Ardanuy, Daniel van Strien, Kasra Hosseini, Kaspar Beelen, James Hetherington, Katherine McDonough, Barbara McGillivray, Mia Ridge, Olivia Vane, Daniel C. S. Wilson
2019 J jnl
CoRR
Diego Arenas, Jon Atkins, Clare Austin, David Beavan, Alvaro Cabrejas Egea, Stephen Carlysle-Davies, Ian Carter, Rob Clarke, James Cunningham, Tom Doel, Oliver Forrest, Evelina Gabasova, James Geddes, James Hetherington, Radka Jersakova, Franz J. Király, Catherine Lawrence, Jules Manser, Martin T. O'Reilly, James Robinson, Helen Sherwood-Taylor, Serena Tierney, Catalina A. Vallejos, Sebastian J. Vollmer, Kirstie J. Whitaker
2019 J jnl
CoRR
Jim Madge, Giovanni Colavizza, James Hetherington, Weisi Guo, Alan Wilson
2019 conf
eScience
Rosa Filgueira, Mariona Coll Ardanuy, Giovanni Colavizza, James Hetherington, Melissa Terras, Michael Jackson, Anna Roubícková, Amrey Krause, Ruth Ahnert, Tessa Hauswedell, Julianne Nyhan, David Beavan, Timothy Hobson
2018 J jnl
Digit. Scholarsh. Humanit.
Melissa Terras, James Baker, James Hetherington, David Beavan, Martin Zaltz Austwick, Anne Welsh, Helen O'Neill, Will Finley, Oliver Duke-Williams, Adam Farquhar
2017 J jnl
J. Open Source Softw.
Sinan Shi, David Pérez-Suárez, Steve K. Harris, Niall S. MacCallum, David Brealey, Mervyn Singer, James Hetherington
2016 conf
DH
Melissa Terras, James Baker, James Hetherington, David Beavan, Anne Welsh, Helen O'Neill, Will Finley, Oliver Duke-Williams, Adam Farquhar
2016 J jnl
Comput. Phys. Commun.
Derek Groen, Agastya Bhati, James J. Suter, James Hetherington, Stefan J. Zasada, Peter V. Coveney
2016 J jnl
CoRR
Daniel S. Katz, Sou-Cheng T. Choi, Kyle E. Niemeyer, James Hetherington, Frank Löffler, Dan Gunter, Ray Idaszak, Steven R. Brandt, Mark A. Miller, Sandra Gesing, Nick D. Jones, Nic Weber, Suresh Marru, Gabrielle Allen, Birgit Penzenstadler, Colin C. Venters, Ethan Davis, Lorraine J. Hwang, Ilian T. Todorov, Abani K. Patra, Miguel de Val-Borro
2015 J jnl
CoRR
Mohamed A. Itani, Ulf D. Schiller, Sebastian Schmieschek, James Hetherington, Miguel O. Bernabeu, Hoskote Chandrashekar, Fergus Robertson, Peter V. Coveney, Derek Groen
2015 J jnl
J. Comput. Sci.
Mohamed A. Itani, Ulf D. Schiller, Sebastian Schmieschek, James Hetherington, Miguel O. Bernabeu, Hoskote Chandrashekar, Fergus Robertson, Peter V. Coveney, Derek Groen
2015 J jnl
CoRR
Derek Groen, Agastya Bhati, James J. Suter, James Hetherington, Stefan J. Zasada, Peter V. Coveney
2014 J jnl
CoRR
Daniel S. Katz, Sou-Cheng T. Choi, Hilmar Lapp, Ketan Maheshwari, Frank Löffler, Matthew Turk, Marcus D. Hanwell, Nancy Wilkins-Diehr, James Hetherington, James Howison, Shel Swenson, Gabrielle Allen, Anne C. Elster, G. Bruce Berriman, Colin C. Venters
2013 J jnl
J. Comput. Sci.
Derek Groen, James Hetherington, Hywel B. Carver, Rupert W. Nash, Miguel O. Bernabeu, Peter V. Coveney
2013 J jnl
CoRR
Miguel O. Bernabeu, Claudio A. Franco, Martin Jones, Jens H. Nielsen, Timm Krüger, Rupert W. Nash, Derek Groen, James Hetherington, Holger Gerhardt, Peter V. Coveney
2012 J jnl
CoRR
Derek Groen, James Hetherington, Hywel B. Carver, Rupert W. Nash, Miguel O. Bernabeu, Peter V. Coveney
2012 J jnl
CoRR
Miguel O. Bernabeu, Rupert W. Nash, Derek Groen, Hywel B. Carver, James Hetherington, Timm Krüger, Peter V. Coveney
2012 J jnl
CoRR
Hywel B. Carver, Derek Groen, James Hetherington, Rupert W. Nash, Miguel O. Bernabeu, Peter V. Coveney
2012 conf
SC Companion
Fang Chen, Markus Flatken, Achim Basermann, Andreas Gerndt, James Hetherington, Timm Krüger, Gregor Matura, Rupert W. Nash
2012 J jnl
CoRR
Derek Groen, Joris Borgdorff, Carles Bona-Casas, James Hetherington, Rupert W. Nash, Stefan J. Zasada, Ilya Saverchenko, Mariusz Mamonski, Krzysztof Kurowski, Miguel O. Bernabeu, Alfons G. Hoekstra, Peter V. Coveney
2012 conf
PARA
J. A. Åström, Adam C. Carter, James Hetherington, K. Ioakimidis, Erik Lindahl, G. Mozdzynski, Rupert W. Nash, Philipp Schlatter, Artur Signell, Jan Westerholm
2007 J jnl
Comput. Chem. Eng.
James Hetherington, Ian David Lockhart Bogle, Peter Saffrey, Ofer Margoninski, Linzhong Li, Marta Varela-Rey, Sachie Yamaji, Stephen Baigent, Jonathan Ashmore, K. Page, Robert M. Seymour, Anthony Finkelstein, Anne Warner
2007 J jnl
Trans. Comp. Sys. Biology
Peter Saffrey, Ofer Margoninski, James Hetherington, Marta Varela-Rey, Sachie Yamaji, Anthony Finkelstein, Ian David Lockhart Bogle, Anne Warner
2006 J jnl
Trans. Comp. Sys. Biology
Ofer Margoninski, Peter Saffrey, James Hetherington, Anthony Finkelstein, Anne Warner
2004 J jnl
Computer
Anthony Finkelstein, James Hetherington, Linzhong Li, Ofer Margoninski, Peter Saffrey, Robert M. Seymour, Anne Warner
tests/integration/test_elf_extractor.py
← Index tests/integration/test_elf_extractor.py python
"""
Integration tests for the ELFExtractor base class.
"""
import pytest
from unittest.mock import Mock, patch, MagicMock

pytestmark = [pytest.mark.integration, pytest.mark.elf]


class TestELFExtractorInitialization:
    """Tests for ELFExtractor initialization."""

    def test_elf_extractor_with_valid_elf(self, elf_binary_path, mock_logger):
        """Test ELFExtractor initialization with valid ELF file."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

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

            assert extractor.filepath == elf_binary_path
            assert extractor._is_elf_file() is True

    def test_elf_extractor_with_invalid_file(self, pe_binary_path, mock_logger):
        """Test ELFExtractor initialization with non-ELF file."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(pe_binary_path, mock_logger)

            # Should not be a valid ELF
            assert extractor._is_elf_file() is False

    def test_elf_extractor_with_text_file(self, temp_text_file, mock_logger):
        """Test ELFExtractor initialization with text file."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(temp_text_file, mock_logger)

            # Should not be a valid ELF
            assert extractor._is_elf_file() is False


class TestELFExtractorMethods:
    """Tests for ELFExtractor helper methods."""

    def test_is_elf_file_true(self, elf_binary_path, mock_logger):
        """Test _is_elf_file returns True for valid ELF."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

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

            assert extractor._is_elf_file() is True

    def test_is_elf_file_cached(self, elf_binary_path, mock_logger):
        """Test _is_elf_file result is cached."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

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

            # First call
            result1 = extractor._is_elf_file()
            # Second call should use cached value
            result2 = extractor._is_elf_file()

            assert result1 == result2
            # Cache should be set
            assert extractor._elf_file_valid is not None

    def test_is_64bit(self, elf_binary_path, mock_logger):
        """Test _is_64bit method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

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

            result = extractor._is_64bit()
            # Result depends on the test binary
            assert isinstance(result, bool)

    def test_is_stripped(self, elf_binary_path, mock_logger):
        """Test _is_stripped method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

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

            result = extractor._is_stripped()
            assert isinstance(result, bool)

    def test_has_debug_info(self, elf_binary_path, mock_logger):
        """Test _has_debug_info method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

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

            result = extractor._has_debug_info()
            assert isinstance(result, bool)

    def test_get_architecture(self, elf_binary_path, mock_logger):
        """Test _get_architecture method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

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

            result = extractor._get_architecture()
            # Should return a string (architecture name)
            assert isinstance(result, str)
            assert result != ""

    def test_get_endianness(self, elf_binary_path, mock_logger):
        """Test _get_endianness method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

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

            result = extractor._get_endianness()
            # Should be one of: "little", "big", or "unknown"
            assert result in ["little", "big", "unknown"]

    def test_get_file_type(self, elf_binary_path, mock_logger):
        """Test _get_file_type method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

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

            result = extractor._get_file_type()
            # Should return a file type string
            assert isinstance(result, str)
            # Common values: "executable", "shared_object", "relocatable", etc.
            expected_types = ["none", "relocatable", "executable", "shared_object", "core_dump", "unknown"]
            assert result in expected_types or result.startswith("ET_")

    def test_is_pie(self, elf_binary_path, mock_logger):
        """Test _is_pie method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

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

            result = extractor._is_pie()
            assert isinstance(result, bool)

    def test_has_stack_protection(self, elf_binary_path, mock_logger):
        """Test _has_stack_protection method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

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

            result = extractor._has_stack_protection()
            assert isinstance(result, bool)

    def test_has_nx_bit(self, elf_binary_path, mock_logger):
        """Test _has_nx_bit method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

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

            result = extractor._has_nx_bit()
            assert isinstance(result, bool)

    def test_has_relro(self, elf_binary_path, mock_logger):
        """Test _has_relro method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

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

            result = extractor._has_relro()
            assert isinstance(result, bool)

    def test_get_build_id(self, elf_binary_path, mock_logger):
        """Test _get_build_id method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

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

            result = extractor._get_build_id()
            # Could be None if no build ID, or a hex string
            assert result is None or isinstance(result, str)

    def test_count_sections(self, elf_binary_path, mock_logger):
        """Test _count_sections method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

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

            result = extractor._count_sections()
            assert isinstance(result, int)
            assert result >= 0

    def test_count_segments(self, elf_binary_path, mock_logger):
        """Test _count_segments method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

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

            result = extractor._count_segments()
            assert isinstance(result, int)
            assert result >= 0

    def test_count_symbols(self, elf_binary_path, mock_logger):
        """Test _count_symbols method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

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

            result = extractor._count_symbols()
            assert isinstance(result, int)
            assert result >= 0

    def test_get_dependencies(self, elf_binary_path, mock_logger):
        """Test _get_dependencies method."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

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

            result = extractor._get_dependencies()
            assert isinstance(result, list)


class TestWithELFFile:
    """Tests for the _with_elf_file context manager method."""

    def test_with_elf_file_success(self, elf_binary_path, mock_logger):
        """Test _with_elf_file executes operation successfully."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

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

            # Define a simple operation
            def get_header(elf):
                return elf.header is not None

            result = extractor._with_elf_file(get_header)
            assert result is True

    def test_with_elf_file_error_handling(self, temp_text_file, mock_logger):
        """Test _with_elf_file handles errors gracefully."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(temp_text_file, mock_logger)

            # Define an operation that would fail
            def get_header(elf):
                return elf.header

            result = extractor._with_elf_file(get_header)
            # Should return None on error
            assert result is None


class TestELFExtractorTag:
    """Tests for tag method in ELF extractors."""

    def test_elf_features_tag(self, elf_binary_path, mock_logger):
        """Test that ELFFeaturesExtractor returns correct tag."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)
            tag = extractor.tag()
            # Should return the tag string
            assert isinstance(tag, str)
            assert "elf" in tag.lower() or "features" in tag.lower()


class TestELFExtractorClickHouseTable:
    """Tests for get_clickhouse_table method in ELF extractors."""

    def test_elf_features_clickhouse_table(self, elf_binary_path, mock_logger):
        """Test that ELFFeaturesExtractor returns correct ClickHouse table name."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_binary_path, mock_logger)
            assert extractor.get_clickhouse_table() == "redb_elf_features"


class TestELFExtractorExtract:
    """Tests for extract method in ELF extractors."""

    def test_elf_features_extract(self, elf_binary_path, mock_logger):
        """Test ELFFeaturesExtractor.extract() returns valid data."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor
        from redb.models.dataclasses import ELFFeatures

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

            result = extractor.extract()
            assert result is not None
            assert isinstance(result, ELFFeatures)

            # Check some expected fields
            assert isinstance(result.ei_class, int)
            assert isinstance(result.ei_data, int)
            assert isinstance(result.e_entry, int)
            assert isinstance(result.number_of_sections, int)
            assert isinstance(result.number_of_segments, int)

    def test_elf_features_extract_invalid_file(self, pe_binary_path, mock_logger):
        """Test ELFFeaturesExtractor.extract() handles invalid ELF."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(pe_binary_path, mock_logger)

            result = extractor.extract()
            # Should return None for invalid ELF
            assert result is None


class TestELFExtractorPrepareExportData:
    """Tests for prepare_export_data method in ELF extractors."""

    def test_elf_features_prepare_export_elasticsearch(self, elf_binary_path, mock_logger):
        """Test prepare_export_data for Elasticsearch."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

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

            # First extract
            extractor.extract()
            result = extractor.prepare_export_data("ElasticsearchExporter")
            # Should return the elf_features dataclass
            assert result is extractor.elf_features

    def test_elf_features_prepare_export_clickhouse(self, elf_binary_path, mock_logger):
        """Test prepare_export_data for ClickHouse."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

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

            # First extract
            extractor.extract()
            result = extractor.prepare_export_data("ClickHouseExporter")

            # Should return tuple of (data, column_names, column_type_names)
            assert isinstance(result, tuple)
            assert len(result) == 3
            data, column_names, column_type_names = result
            assert isinstance(data, list)
            assert isinstance(column_names, list)
            assert isinstance(column_type_names, list)
            # Column names and types should match in length
            assert len(column_names) == len(column_type_names)


class TestELFExtractorAdvanced:
    """Advanced tests for ELF extraction using hello_advanced binary."""

    def test_elf_advanced_features(self, elf_advanced_binary_path, mock_logger):
        """Test ELFFeaturesExtractor with more complex ELF binary."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_advanced_binary_path, mock_logger)

            result = extractor.extract()
            assert result is not None

            # Check that we can extract meaningful data
            assert result.number_of_sections > 0
            assert result.number_of_segments > 0

    def test_elf_advanced_architecture(self, elf_advanced_binary_path, mock_logger):
        """Test architecture detection for advanced ELF binary."""
        from redb.extractors.elf_extractors.elf_features import ELFFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = ELFFeaturesExtractor(elf_advanced_binary_path, mock_logger)

            arch = extractor._get_architecture()
            # Should detect a valid architecture
            assert arch != "unknown"
            assert arch != ""