Jan Fostier

33 papers B 2C 3Journal 22Unranked 6
YearRankTypeTitle / Venue / Authors
2025 J jnl
Bioinform.
Luca Renders, Lore Depuydt, Travis Gagie, Jan Fostier
2025 J jnl
Bioinform.
Marie Van Hecke, Niko Beerenwinkel, Thibault Lootens, Jan Fostier, Robrecht Raedt, Kathleen Marchal
2025 conf
The Expanding World of Compressed Data
Lore Depuydt, Jan Fostier, Simon Gottlieb, Gregory Kucherov, Knut Reinert, Luca Renders
2025 J jnl
Algorithms Mol. Biol.
Lore Depuydt, Luca Renders, Simon Van de Vyver, Lennart Veys, Travis Gagie, Jan Fostier
2024 B conf
RECOMB
Luca Renders, Lore Depuydt, Sven Rahmann, Jan Fostier
2024 B conf
DCC
Adrián Goga, Lore Depuydt, Nathaniel K. Brown, Jan Fostier, Travis Gagie, Gonzalo Navarro
2024 J jnl
J. Comput. Biol.
Luca Renders, Lore Depuydt, Sven Rahmann, Jan Fostier
2024 C conf
WABI
Lore Depuydt, Luca Renders, Simon Van de Vyver, Lennart Veys, Travis Gagie, Jan Fostier
2023 conf
EUSIPCO
Pratima Upretee, Sybren Santermans, Koen M. Martens, Juliette Gevers, Sanjin Marion, Wouter Van den Bosch, Jan Fostier, Nilesh Madhu
2023 J jnl
CoRR
Adrián Goga, Lore Depuydt, Nathaniel K. Brown, Jan Fostier, Travis Gagie, Gonzalo Navarro
2023 J jnl
IEEE ACM Trans. Comput. Biol. Bioinform.
Aranka Steyaert, Pieter Audenaert, Jan Fostier
2023 J jnl
BMC Bioinform.
Lore Depuydt, Luca Renders, Thomas Abeel, Jan Fostier
2022 conf
IWBBIO (2)
Luca Renders, Lore Depuydt, Jan Fostier
2020 J jnl
BMC Bioinform.
Aranka Steyaert, Pieter Audenaert, Jan Fostier
2020 J jnl
Bioinform.
Jan Voges, Tom Paridaens, Fabian Müntefering, Liudmila S. Mainzer, Brian Bliss, Mingyu Yang, Idoia Ochoa, Jan Fostier, Jörn Ostermann, Mikel Hernaez
2019 J jnl
BMC Bioinform.
Mahdi Heydari, Giles Miclotte, Yves Van de Peer, Jan Fostier
2018 conf
IWBBIO (1)
Jan Fostier
2018 J jnl
BMC Bioinform.
Mahdi Heydari, Giles Miclotte, Yves Van de Peer, Jan Fostier
2018 J jnl
PLoS Comput. Biol.
Nele Vandersickel, Masaya Watanabe, Qian Tao, Jan Fostier, Katja Zeppenfeld, Alexander V. Panfilov
2017 J jnl
BMC Bioinform.
Mahdi Heydari, Giles Miclotte, Piet Demeester, Yves Van de Peer, Jan Fostier
2017 J jnl
Bioinform.
Giles Miclotte, Stéphane Plaisance, Stephane Rombauts, Yves Van de Peer, Pieter Audenaert, Jan Fostier
2016 J jnl
Algorithms Mol. Biol.
Giles Miclotte, Mahdi Heydari, Piet Demeester, Stephane Rombauts, Yves Van de Peer, Pieter Audenaert, Jan Fostier
2015 J jnl
Bioinform.
Dieter De Witte, Jan Van de Velde, Dries Decap, Michiel Van Bel, Pieter Audenaert, Piet Demeester, Bart Dhoedt, Klaas Vandepoele, Jan Fostier
2015 J jnl
Bioinform.
Dries Decap, Joke Reumers, Charlotte Herzeel, Pascal Costanza, Jan Fostier
2015 C conf
WABI
Giles Miclotte, Mahdi Heydari, Piet Demeester, Pieter Audenaert, Jan Fostier
2015 conf
PPAM (2)
Dries Decap, Joke Reumers, Charlotte Herzeel, Pascal Costanza, Jan Fostier
2015 C conf
PDP
Arne De Coninck, Drosos Kourounis, Fabio Verbosio, Olaf Schenk, Bernard De Baets, Steven Maenhout, Jan Fostier
2014 J jnl
J. Intell. Inf. Syst.
Simon Dooms, Pieter Audenaert, Jan Fostier, Toon De Pessemier, Luc Martens
2013 conf
PPAM (2)
Dieter De Witte, Michiel Van Bel, Pieter Audenaert, Piet Demeester, Bart Dhoedt, Klaas Vandepoele, Jan Fostier
2013 J jnl
Bioinform.
Lieven P. C. Verbeke, Lore Cloots, Piet Demeester, Jan Fostier, Kathleen Marchal
2012 J jnl
J. Supercomput.
Maria Chtepen, Filip H. A. Claeys, Bart Dhoedt, Filip De Turck, Jan Fostier, Piet Demeester, Peter A. Vanrolleghem
2011 J jnl
Bioinform.
Jan Fostier, Sebastian Proost, Bart Dhoedt, Yvan Saeys, Piet Demeester, Yves Van de Peer, Klaas Vandepoele
2007 J jnl
IEICE Trans. Commun.
Jan Fostier, Femke Olyslager
redb/extractors/macho_extractors/macho_features.py
← Index redb/extractors/macho_extractors/macho_features.py python
import inspect
import json
from datetime import datetime, timezone
from typing import Any

from redb.extractors.enum import Tag
from redb.extractors.macho_extractor import MachOExtractor
from redb.models.dataclasses import MachO


class MachOFeaturesExtractor(MachOExtractor):

    def __init__(
        self,
        filepath,
        log,
        exporters=None,
        index_prefix=None,
        elastic_index=None,
        known_benign=False,
        known_malicious=False,
        macho=None,
    ):
        super().__init__(
            filepath,
            log,
            exporters,
            index_prefix,
            elastic_index,
            known_benign,
            known_malicious,
            macho,
        )
        self.elastic_index = self.index_prefix + "-macho_features"
        self.log.debug(inspect.currentframe().f_code.co_name)

    def tag(self):
        return Tag.MACHO_FEATURES.value

    def _extract_macho_features_for_arch(self, arch_name):
        """Extract basic MachO features for a specific architecture."""
        self.log.debug(inspect.currentframe().f_code.co_name)

        if not self.macho:
            return None

        try:
            # Get general info using new API
            general_info = self.macho.get_general_info()
            if not general_info:
                return None

            # Get header info for this specific architecture
            header_raw = self.macho.get_macho_header(arch=arch_name)
            header_formatted = self.macho.get_macho_header(arch=arch_name, formatted=True)

            if not header_raw or not header_formatted:
                return None

            # Get entry point using new API
            entry_point = None
            try:
                entry_point_info = self.macho.get_entry_point(arch=arch_name)
                if entry_point_info:
                    if isinstance(entry_point_info, dict):
                        entry_point = entry_point_info.get('entryoff') or entry_point_info.get('entry_address')
                    else:
                        entry_point = entry_point_info
            except Exception as e:
                self.log.debug(f"No entry point found: {e}")

            # Get UUID using new API
            uuid = None
            try:
                uuid_info = self.macho.get_uuid(arch=arch_name)
                if uuid_info:
                    uuid = str(uuid_info)
            except Exception as e:
                self.log.debug(f"No UUID found: {e}")

            # Get version info using new API with formatting
            version_info = None
            version_info_str = None
            try:
                version_info = self.macho.get_version_info(arch=arch_name)
                version_info_str = self.macho.get_version_info(arch=arch_name, formatted=True)
            except Exception as e:
                self.log.debug(f"No version info found: {e}")

            # Get segments using new API
            segments = self.macho.get_segments(arch=arch_name)
            number_of_segments = len(segments) if segments else 0

            # Get dylib info using new API
            dylib_names = self.macho.get_dylib_names(arch=arch_name)
            number_of_dylibs = len(dylib_names) if dylib_names else 0

            # Count imports using new API
            imported_functions = self.macho.get_imported_functions(arch=arch_name)
            number_of_imports = sum(len(funcs) for funcs in imported_functions.values()) if imported_functions else 0

            # Count exports using new API
            exported_symbols = self.macho.get_exported_symbols(arch=arch_name)
            number_of_exports = sum(len(symbols) for symbols in exported_symbols.values()) if exported_symbols else 0

            # Get unique load command types using new API
            load_commands_set = self.macho.get_load_commands_set(arch=arch_name, formatted=True)
            if isinstance(load_commands_set, set):
                load_commands_set = sorted(list(load_commands_set))

            # Get architectures for listing purposes
            architectures = self.macho.get_architectures()

            # Determine binary properties
            is_64bit = header_raw.get('magic') in [0xFEEDFACF, 0xCFFAEDFE]  # MH_MAGIC_64, MH_CIGAM_64
            is_signed = self._is_signed()
            
            # Create MachO dataclass
            macho_features = MachO(
                # Raw values from new API
                magic=header_raw.get('magic', 0),
                cputype=header_raw.get('cputype', 0),
                cpusubtype=header_raw.get('cpusubtype', 0),
                filetype=header_raw.get('filetype', 0),
                ncmds=header_raw.get('ncmds', 0),
                sizeofcmds=header_raw.get('sizeofcmds', 0),
                flags=header_raw.get('flags', 0),
                architecture=header_raw.get('cputype', 0),  # Use cputype as architecture
                architectures=[arch_info.get('cputype', 0) for arch_info in [self.macho.get_macho_header(arch=arch) for arch in architectures] if arch_info],
                # Human-readable values from formatted API
                magic_str=header_formatted.get('magic', ''),
                cputype_str=header_formatted.get('cputype', ''),
                cpusubtype_str=header_formatted.get('cpusubtype', ''),
                filetype_str=header_formatted.get('filetype', ''),
                flags_str=header_formatted.get('flags', '').split(', ') if header_formatted.get('flags') else [],
                architecture_str=header_formatted.get('cputype', ''),
                architectures_str=[arch_info.get('cputype', '') for arch_info in [self.macho.get_macho_header(arch=arch, formatted=True) for arch in architectures] if arch_info],
                # Additional properties
                is_64bit=is_64bit,
                is_signed=is_signed,
                number_of_load_commands=header_raw.get('ncmds', 0),
                load_commands_set=load_commands_set,
                number_of_segments=number_of_segments,
                number_of_dylibs=number_of_dylibs,
                number_of_imports=number_of_imports,
                number_of_exports=number_of_exports,
                entry_point=entry_point,
                uuid=uuid,
                version_info=version_info,
                version_info_str=version_info_str
            )
            
            return macho_features
            
        except Exception as e:
            self.log.error(f"Error extracting MachO features: {e}")
            return None

    def extract(self):
        self.log.debug(inspect.currentframe().f_code.co_name)
        try:
            if not self.macho:
                return None
            architectures = self.macho.get_architectures()
            if not architectures:
                return None

            # For FAT binaries, return features for all architectures
            # For single arch, return just the single result
            if len(architectures) > 1:
                # FAT binary - return list of features for each architecture
                results = []
                for arch_name in architectures:
                    features = self._extract_macho_features_for_arch(arch_name)
                    if features:
                        # Add architecture identifier to the result
                        if hasattr(features, '__dict__'):
                            # If it's a dataclass, we can access its dict
                            features.arch_identifier = arch_name
                        results.append(features)
                return results
            else:
                # Single architecture - return single result
                return self._extract_macho_features_for_arch(architectures[0])
        except Exception as e:
            self.log.error(f"Error extracting MachO features: {e}")
            return None

    def prepare_export_data(self, exporter_type: str) -> Any:
        if exporter_type == "ElasticsearchExporter":
            return self.extract()
        elif exporter_type == "ClickHouseExporter":
            if not self.macho:
                return None

            # Get architectures (macho is already parsed in __init__)
            try:
                architectures = self.macho.get_architectures()
            except Exception as e:
                self.log.error(f"Could not get architectures: {e}")
                return None

            data = []
            current_time = datetime.now(timezone.utc)

            # Loop through each architecture (1 for single, multiple for FAT)
            for arch_name in architectures:
                # Extract features for this specific architecture
                macho_features = self._extract_macho_features_for_arch(arch_name)
                if not macho_features:
                    continue

                # Get architecture-specific sha256
                try:
                    arch_general_info = self.macho.get_general_info(arch=arch_name)
                    arch_sha256 = arch_general_info.get('SHA256', self.sha256)
                except Exception as e:
                    self.log.warning(f"Could not get arch-specific hash for {arch_name}: {e}")
                    arch_sha256 = self.sha256

                # Architecture field (kept in features table for ORDER BY)
                architecture = macho_features.cputype    # Raw CPU type value

                data.append([
                    arch_sha256,                          # sha256 (architecture-specific)
                    architecture,                         # architecture (raw CPU type)
                    # Raw values
                    macho_features.magic,                 # magic
                    macho_features.cputype,               # cputype
                    macho_features.cpusubtype,            # cpusubtype
                    macho_features.filetype,              # filetype
                    macho_features.ncmds,                 # ncmds
                    macho_features.sizeofcmds,            # sizeofcmds
                    macho_features.flags,                 # flags
                    # Human-readable values
                    macho_features.magic_str,             # magic_str
                    macho_features.cputype_str,           # cputype_str
                    macho_features.cpusubtype_str,        # cpusubtype_str
                    macho_features.filetype_str,          # filetype_str
                    macho_features.flags_str,             # flags_str
                    # Other fields
                    macho_features.is_64bit,              # is_64bit
                    macho_features.is_signed,             # is_signed
                    macho_features.entry_point if macho_features.entry_point else None,           # entry_point
                    macho_features.uuid if macho_features.uuid else None,  # uuid
                    json.dumps(macho_features.version_info) if macho_features.version_info else "{}",  # version_info
                    json.dumps(macho_features.version_info_str) if macho_features.version_info_str else "{}",  # version_info_str
                    macho_features.load_commands_set,     # load_commands_set
                    macho_features.number_of_segments,    # number_of_segments
                    macho_features.number_of_dylibs,      # number_of_dylibs
                    macho_features.number_of_imports,     # number_of_imports
                    macho_features.number_of_exports,     # number_of_exports
                    current_time,                         # analysis_date
                ])

            column_names = [
                'sha256', 'architecture',
                # Raw values
                'magic', 'cputype', 'cpusubtype', 'filetype', 'ncmds', 'sizeofcmds', 'flags',
                # Human-readable values
                'magic_str', 'cputype_str', 'cpusubtype_str', 'filetype_str', 'flags_str',
                # Other fields
                'is_64bit', 'is_signed',
                'entry_point', 'uuid', 'version_info', 'version_info_str', 'load_commands_set',
                'number_of_segments', 'number_of_dylibs', 'number_of_imports', 'number_of_exports',
                'analysis_date'
            ]

            if not data:
                return None

            column_type_names = [
                'FixedString(64)', 'Nullable(UInt32)',
                # Raw values
                'UInt32', 'UInt32', 'UInt32', 'UInt32', 'UInt32', 'UInt32', 'UInt32',
                # Human-readable values
                'LowCardinality(String)', 'LowCardinality(String)', 'LowCardinality(String)', 'LowCardinality(String)', 'Array(LowCardinality(String))',
                # Other fields
                'UInt8', 'UInt8',
                'Nullable(UInt64)', 'Nullable(String)', 'JSON', 'JSON', 'Array(Nullable(String))',
                'UInt32', 'UInt32', 'UInt32', 'UInt32', 'DateTime64(3, \'UTC\')'
            ]

            return (data, column_names, column_type_names)
        
        return None

    def get_clickhouse_table(self) -> str:
        return "redb_macho_features"