Vassilios Ioannidis

11 papers Journal 11
YearRankTypeTitle / Venue / Authors
2022 J jnl
Bioinform.
Dimitri Höhler, Wayne Pfeiffer, Vassilios Ioannidis, Heinz Stockinger, Alexandros Stamatakis
2021 J jnl
Nucleic Acids Res.
Severine Duvaud, Chiara Gabella, Frédérique Lisacek, Heinz Stockinger, Vassilios Ioannidis, Christine Durinx
2020 J jnl
Data Sci. J.
Romain David, Laurence Mabile, Alison Specht, Sarah Stryeck, Mogens Thomsen, Mohamed Yahia, Clément Jonquet, Laurent Dollé, Daniel Jacob, Daniele Bailo, Elena Bravo, Sophie Gachet, Hannah Gunderman, Jean-Eudes Hollebecq, Vassilios Ioannidis, Yvan Le Bras, Emilie Lerigoleur, Anne Cambon-Thomsen
2017 J jnl
BMC Bioinform.
Cedric Simillion, Robin Liechti, Heidi E. L. Lischer, Vassilios Ioannidis, Rémy Bruggmann
2016 J jnl
Nucleic Acids Res.
Jon C. Ison, Kristoffer Rapacki, Hervé Ménager, Matús Kalas, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan M. Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn A. Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael C. Jiménez, Nick S. Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Micetic, Rune Møllegaard Friborg, Sébastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter M. Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vareková, Silvio C. E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen E. Parkinson, Peter Løngreen, Søren Brunak
2015 J jnl
BMC Bioinform.
Linda Dib, Xavier Meyer, Panu Artimo, Vassilios Ioannidis, Heinz Stockinger, Nicolas Salamin
2013 J jnl
Bioinform.
Rafael C. Jiménez, Juan P. Albar, Jong Bhak, Marie-Claude Blatter, Thomas Blicher, Michelle D. Brazas, Catherine Brooksbank, Aidan Budd, Javier De Las Rivas, Jacqueline Dreyer, Marc A. van Driel, Michael J. Dunn, Pedro L. Fernandes, Celia W. G. van Gelder, Henning Hermjakob, Vassilios Ioannidis, David Phillip Judge, Pascal Kahlem, Eija Korpelainen, Hans-Joachim Kraus, Jane E. Loveland, Christine Mayer, Jennifer McDowall, Federico Morán, Nicola J. Mulder, Tommi H. Nyrönen, Kristian Rother, Gustavo A. Salazar, Reinhard Schneider, Allegra Via, Jose M. Villaveces, Ping Yu, Maria Victoria Schneider, Teresa K. Attwood, Manuel Corpas
2012 J jnl
Nucleic Acids Res.
Panu Artimo, Manohar Jonnalagedda, Konstantin Arnold, Delphine Baratin, Gábor Csárdi, Edouard De Castro, Severine Duvaud, Volker Flegel, Arnaud Fortier, Elisabeth Gasteiger, Aurélien Grosdidier, Céline Hernandez, Vassilios Ioannidis, Dmitri Kuznetsov, Robin Liechti, Sébastien Moretti, Khaled Mostaguir, Nicole Redaschi, Grégoire Rossier, Ioannis Xenarios, Heinz Stockinger
2007 J jnl
Nucleic Acids Res.
Marco Pagni, Vassilios Ioannidis, Lorenzo Cerutti, Monique Zahn-Zabal, C. Victor Jongeneel, Jörg Hau, Olivier Martin, Dmitri Kuznetsov, Laurent Falquet
2004 J jnl
Nucleic Acids Res.
Marco Pagni, Vassilios Ioannidis, Lorenzo Cerutti, Monique Zahn-Zabal, C. Victor Jongeneel, Laurent Falquet
2003 J jnl
Nucleic Acids Res.
Laurent Falquet, Lorenza Bordoli, Vassilios Ioannidis, Marco Pagni, C. Victor Jongeneel
tests/integration/test_pe_extractor.py
← Index tests/integration/test_pe_extractor.py python
"""
Integration tests for the PEExtractor base class.
"""
import pytest
from unittest.mock import Mock, patch, MagicMock

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


class TestPEExtractorInitialization:
    """Tests for PEExtractor initialization."""

    def test_pe_extractor_with_valid_pe(self, pe_binary_path, mock_logger):
        """Test PEExtractor initialization with valid PE file."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor

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

            assert extractor.pe is not None
            assert extractor.filepath == pe_binary_path

    def test_pe_extractor_with_provided_pe_object(self, pe_binary_path, mock_logger, pe_object):
        """Test PEExtractor initialization with pre-existing PE object."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor

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

            # Should use the provided PE object, not create a new one
            assert extractor.pe is pe_object

    def test_pe_extractor_with_invalid_file(self, elf_binary_path, mock_logger):
        """Test PEExtractor initialization with non-PE file."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor

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

            # Should return None for pe when file is not a valid PE
            assert extractor.pe is None
            # Logger should have recorded an error
            assert mock_logger.error.called


class TestPEExtractorMethods:
    """Tests for PEExtractor helper methods."""

    def test_check_dotnet_true(self, pe_binary_path, mock_logger):
        """Test _check_dotnet returns True for .NET PE."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor

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

            # The test PE file is a .NET binary
            if extractor.pe is not None:
                result = extractor._check_dotnet()
                # d8637bdbcfc9112fcb1f0167b398e771 is a .NET binary
                assert result is True

    def test_check_dotnet_false(self, elf_binary_path, mock_logger):
        """Test _check_dotnet returns False for non-PE file."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor

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

            # Should return False when PE is None
            result = extractor._check_dotnet()
            assert result is False

    def test_is_signed_false(self, pe_binary_path, mock_logger):
        """Test _is_signed method."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor

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

            if extractor.pe is not None:
                result = extractor._is_signed()
                # Result depends on the actual binary
                assert isinstance(result, bool)

    def test_has_overlay(self, pe_binary_path, mock_logger):
        """Test _has_overlay method."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor

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

            if extractor.pe is not None:
                result = extractor._has_overlay()
                assert isinstance(result, bool)


class TestGeneratePEFileObject:
    """Tests for _generate_pefile_object method."""

    def test_generate_pefile_object_valid(self, pe_binary_path, mock_logger):
        """Test _generate_pefile_object with valid PE file."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor

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

            # The PE object should be created successfully
            assert extractor.pe is not None

    def test_generate_pefile_object_invalid(self, temp_text_file, mock_logger):
        """Test _generate_pefile_object with invalid file."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor

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

            # Should return None for invalid PE
            assert extractor.pe is None


class TestGenerateDotNetFileObject:
    """Tests for _generate_dotnetfile_object method."""

    def test_generate_dotnetfile_object_valid(self, pe_binary_path, mock_logger):
        """Test _generate_dotnetfile_object with .NET PE file."""
        from redb.extractors.pe_extractors.pe_dotnet import PEDotNetExtractor

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

            if extractor.pe is not None and extractor._check_dotnet():
                dotnet, error = extractor._generate_dotnetfile_object()
                # Should create dotnet object for .NET PE
                assert dotnet is not None
                assert error is None

    def test_generate_dotnetfile_object_invalid(self, elf_binary_path, mock_logger):
        """Test _generate_dotnetfile_object with non-.NET file."""
        from redb.extractors.pe_extractors.pe_dotnet import PEDotNetExtractor

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

            dotnet, error = extractor._generate_dotnetfile_object()
            # Should return error for non-.NET file
            assert dotnet is None
            assert error is not None


class TestPEExtractorTag:
    """Tests for tag method in PE extractors."""

    def test_pe_features_tag(self, pe_binary_path, mock_logger):
        """Test that PEFeaturesExtractor returns correct tag."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor
        from redb.extractors.enum import Tag

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = PEFeaturesExtractor(pe_binary_path, mock_logger)
            assert extractor.tag() == Tag.PE_FEATURES.value

    def test_pe_import_tag(self, pe_binary_path, mock_logger):
        """Test that PEImportExtractor returns correct tag."""
        from redb.extractors.pe_extractors.pe_imports import PEImportExtractor
        from redb.extractors.enum import Tag

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = PEImportExtractor(pe_binary_path, mock_logger)
            assert extractor.tag() == Tag.PE_IMPORT.value

    def test_pe_section_tag(self, pe_binary_path, mock_logger):
        """Test that PESectionExtractor returns correct tag."""
        from redb.extractors.pe_extractors.pe_sections import PESectionExtractor
        from redb.extractors.enum import Tag

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = PESectionExtractor(pe_binary_path, mock_logger)
            assert extractor.tag() == Tag.PE_SECTION.value


class TestPEExtractorClickHouseTable:
    """Tests for get_clickhouse_table method in PE extractors."""

    def test_pe_features_clickhouse_table(self, pe_binary_path, mock_logger):
        """Test that PEFeaturesExtractor returns correct ClickHouse table name."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = PEFeaturesExtractor(pe_binary_path, mock_logger)
            assert extractor.get_clickhouse_table() == "redb_pe_features"

    def test_pe_import_clickhouse_table(self, pe_binary_path, mock_logger):
        """Test that PEImportExtractor returns correct ClickHouse table name."""
        from redb.extractors.pe_extractors.pe_imports import PEImportExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = PEImportExtractor(pe_binary_path, mock_logger)
            assert extractor.get_clickhouse_table() == "redb_pe_imports"

    def test_pe_section_clickhouse_table(self, pe_binary_path, mock_logger):
        """Test that PESectionExtractor returns correct ClickHouse table name."""
        from redb.extractors.pe_extractors.pe_sections import PESectionExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = PESectionExtractor(pe_binary_path, mock_logger)
            assert extractor.get_clickhouse_table() == "redb_pe_sections"


class TestPEExtractorPrepareExportData:
    """Tests for prepare_export_data method in PE extractors."""

    def test_pe_features_prepare_export_elasticsearch(self, pe_binary_path, mock_logger):
        """Test prepare_export_data for Elasticsearch."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor

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

            if extractor.pe is not None:
                # First extract
                extractor.extract()
                result = extractor.prepare_export_data("ElasticsearchExporter")
                # Should return the pe_features dataclass
                assert result is extractor.pe_features

    def test_pe_features_prepare_export_clickhouse(self, pe_binary_path, mock_logger):
        """Test prepare_export_data for ClickHouse."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor

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

            if extractor.pe is not None:
                # 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)