Natalja Kurbatova

15 papers C 1Journal 12Unranked 2
YearRankTypeTitle / Venue / Authors
2024 J jnl
Comput. Biol. Medicine
Vladimir Makarov, Christophe Chabbert, Elina Koletou, Fotis E. Psomopoulos, Natalja Kurbatova, Samuel A. Ramirez, Chas Nelson, Prashant Natarajan, Bikalpa Neupane
2024 J jnl
J. Chem. Inf. Model.
Andrew J. Whitehouse, Melchor Sanchez-Martinez, Seyedeh Maryam Salehi, Natalja Kurbatova, Euan Dean
2021 J jnl
BMC Bioinform.
Natalja Kurbatova, Rowan Swiers
2015 J jnl
Nucleic Acids Res.
Nikolay Kolesnikov, Emma Hastings, Maria Keays, Olga Melnichuk, Y. Amy Tang, Eleanor Williams, Miroslaw Dylag, Natalja Kurbatova, Marco Brandizi, Tony Burdett, Karyn Megy, Ekaterina Pilicheva, Gabriella Rustici, Andrew Tikhonov, Helen E. Parkinson, Robert Petryszak, Ugis Sarkans, Alvis Brazma
2014 J jnl
Nucleic Acids Res.
Gautier Koscielny, Gagarine Yaikhom, Vivek Iyer, Terrence F. Meehan, Hugh Morgan, Julian Atienza-Herrero, Andrew Blake, Chao-Kung Chen, Richard Easty, Armida Di Fenza, Tanja Fiegel, Mark Grifiths, Alan Horne, Natasha A. Karp, Natalja Kurbatova, Jeremy C. Mason, Peter Matthews, Darren J. Oakley, Asfand Qazi, Jack Regnart, Ahmad Retha, Luis A. Santos, Duncan J. Sneddon, Jonathan Warren, Henrik Westerberg, Robert J. Wilson, David G. Melvin, Damian Smedley, Steve D. M. Brown, Paul Flicek, William C. Skarnes, Ann-Marie Mallon, Helen E. Parkinson
2013 J jnl
Nucleic Acids Res.
Gabriella Rustici, Nikolay Kolesnikov, Marco Brandizi, Tony Burdett, Miroslaw Dylag, Ibrahim Emam, Anna Farne, Emma Hastings, Jon C. Ison, Maria Keays, Natalja Kurbatova, James Malone, Roby Mani, Annalisa Mupo, Rui Pedro Pereira, Ekaterina Pilicheva, Johan Rung, Anjan Sharma, Y. Amy Tang, Tobias Ternent, Andrew Tikhonov, Danielle Welter, Eleanor Williams, Alvis Brazma, Helen E. Parkinson, Ugis Sarkans
2012 J jnl
Nucleic Acids Res.
Misha Kapushesky, Tomasz Adamusiak, Tony Burdett, Aedín C. Culhane, Anna Farne, Alexey Filippov, Ele Holloway, Andrey Klebanov, Nataliya Kryvych, Natalja Kurbatova, Pavel Kurnosov, James Malone, Olga Melnichuk, Robert Petryszak, Nikolay Pultsin, Gabriella Rustici, Andrew Tikhonov, Ravensara S. Travillian, Eleanor Williams, Andrey Zorin, Helen E. Parkinson, Alvis Brazma
2012 J jnl
Bioinform.
Marco Brandizi, Natalja Kurbatova, Ugis Sarkans, Philippe Rocca-Serra
2011 J jnl
Nucleic Acids Res.
Helen E. Parkinson, Ugis Sarkans, Nikolay Kolesnikov, Niran Abeygunawardena, Tony Burdett, Miroslaw Dylag, Ibrahim Emam, Anna Farne, Emma Hastings, Ele Holloway, Natalja Kurbatova, Margus Lukk, James Malone, Roby Mani, Ekaterina Pilicheva, Gabriella Rustici, Anjan Sharma, Eleanor Williams, Tomasz Adamusiak, Marco Brandizi, Nataliya Sklyar, Alvis Brazma
2011 J jnl
BMC Bioinform.
Tomasz Adamusiak, Tony Burdett, Natalja Kurbatova, K. Joeri van der Velde, Niran Abeygunawardena, Despoina Antonakaki, Misha Kapushesky, Helen E. Parkinson, Morris A. Swertz
2011 J jnl
Bioinform.
Natalja Kurbatova, Tomasz Adamusiak, Pavel Kurnosov, Morris A. Swertz, Misha Kapushesky
2009 J jnl
Bioinform.
Maria Krestyaninova, Andris Zarins, Juris Viksna, Natalja Kurbatova, Peteris Rucevskis, Sudeshna Guha Neogi, Mike Gostev, Teemu Perheentupa, Juha Knuuttila, Amy Barrett, Ilkka Lappalainen, Johan Rung, Karlis Podnieks, Ugis Sarkans, Mark I. McCarthy, Alvis Brazma
2008 C conf
ECCB
Rafael Najmanovich, Natalja Kurbatova, Janet M. Thornton
2008 conf
BIRD
Natalja Kurbatova, Juris Viksna
2007 conf
German Conference on Bioinformatics
Natalja Kurbatova, Laura Mancinska, Juris Viksna
redb/extractors/macho_extractor.py
← Index redb/extractors/macho_extractor.py python
import logging
from abc import ABCMeta, abstractmethod
import inspect
import sys
import os

import machofile

from redb.extractors.extractor import Extractor

logger = logging.getLogger(__name__)


@abstractmethod
class MachOExtractor(Extractor, metaclass=ABCMeta):

    def __init__(
        self,
        filepath,
        log,
        exporters=None,
        index_prefix=None,
        elastic_index=None,
        known_benign=False,
        known_malicious=False,
        macho=None,
    ):
        # Read binary and parse machofile BEFORE calling super().__init__
        # This avoids reading the file twice
        with open(filepath, "rb") as f:
            binary_data = f.read()

        # Parse machofile with binary data
        self.macho = macho if macho else self._generate_machofile_object(binary_data)

        # Extract hashes from machofile to pass to parent
        precomputed_hashes = None
        if self.macho:
            try:
                general_info = self.macho.get_general_info()
                if general_info:
                    # For FAT binaries, get_general_info() returns dict with 'fat' key
                    # For single-arch, it returns the info directly
                    if 'fat' in general_info:
                        fat_info = general_info['fat']
                        precomputed_hashes = {
                            'MD5': fat_info.get('MD5'),
                            'SHA1': fat_info.get('SHA1'),
                            'SHA256': fat_info.get('SHA256'),
                        }
                    else:
                        precomputed_hashes = {
                            'MD5': general_info.get('MD5'),
                            'SHA1': general_info.get('SHA1'),
                            'SHA256': general_info.get('SHA256'),
                        }
            except Exception as e:
                logger.debug(f"Could not get hashes from machofile: {e}")

        super().__init__(
            filepath,
            log,
            exporters,
            index_prefix,
            elastic_index,
            known_benign,
            known_malicious,
            precomputed_hashes=precomputed_hashes,
        )

        # Store binary data so base class doesn't re-read
        self._binary_data = binary_data

    @property
    def binary(self):
        """Override to use already-read binary data."""
        return self._binary_data

    def _generate_machofile_object(self, binary_data):
        """Generate and parse a machofile object from binary data."""
        macho = None
        try:
            macho = machofile.UniversalMachO(data=binary_data)
            if not macho:
                raise Exception("Empty file?")

            # Parse the MachO object once during initialization
            macho.parse()

        except Exception as e:
            logger.error(f"Format error parsing MachO: {e}")
        return macho

    # def _is_macho_file(self):
    #     """Check if the file is a valid Mach-O binary."""
    #     try:
    #         if not self.macho:
    #             return False
            
    #         # For Universal/FAT binaries, check if any architecture is valid
    #         if hasattr(self.macho, 'is_fat') and self.macho.is_fat:
    #             return len(self.macho.architectures) > 0
    #         else:
    #             # Single architecture binary
    #             return hasattr(self.macho, 'macho') and self.macho.macho is not None
    #     except Exception as e:
    #         self.log.error(f"Error checking Mach-O file: {e}")
    #         return False

    def _is_signed(self):
        """Check if the Mach-O binary is code signed using new API."""
        try:
            if not self.macho:
                return False

            # Get architectures using new API
            architectures = self.macho.get_architectures()

            # For each architecture, check if signed
            for arch in architectures:
                try:
                    signature_info = self.macho.get_code_signature_info(arch=arch)
                    if signature_info and signature_info.get('signed', False):
                        return True
                except Exception:
                    continue

            return False
        except Exception as e:
            self.log.error(f"Error checking Mach-O signature: {e}")
            return False

    def _get_architectures(self):
        """Get list of architectures in the Mach-O binary using new API."""
        try:
            if not self.macho:
                return []

            # Use new API method
            architectures = self.macho.get_architectures()
            return architectures if architectures else []
        except Exception as e:
            self.log.error(f"Error getting architectures: {e}")
            return []

    # def _get_macho_for_arch(self, arch_name=None):
    #     """Get MachO instance for specific architecture or default."""
    #     try:
    #         if not self.macho:
    #             return None
            
    #         if hasattr(self.macho, 'is_fat') and self.macho.is_fat:
    #             if arch_name:
    #                 return self.macho.architectures.get(arch_name)
    #             else:
    #                 # Return first available architecture
    #                 return next(iter(self.macho.architectures.values())) if self.macho.architectures else None
    #         else:
    #             # Single architecture binary
    #             return self.macho.macho if hasattr(self.macho, 'macho') else None
    #     except Exception as e:
    #         self.log.error(f"Error getting MachO for architecture: {e}")
    #         return None

    # def _get_formatted_header_values(self, header):
    #     """Get both raw and human-readable header values."""
    #     try:
    #         macho_instance = self._get_macho_for_arch()
    #         if not macho_instance:
    #             return None
            
    #         # Parse the MachO if not already parsed
    #         if not hasattr(macho_instance, 'header') or not macho_instance.header:
    #             macho_instance.parse()
            
    #         # Get human-readable values using machofile's formatting methods
    #         magic_str = macho_instance.format_magic_value(header.get('magic', 0))
            
    #         # Simple CPU type mapping since CPU_TYPE_MAP is not exposed
    #         cputype = header.get('cputype', 0)
    #         if cputype == 0x7:
    #             cputype_str = "x86"
    #         elif cputype == 0x1000007:
    #             cputype_str = "x86_64"
    #         elif cputype == 0xC:
    #             cputype_str = "ARM"
    #         elif cputype == 0x100000C:
    #             cputype_str = "ARM 64-bit"
    #         else:
    #             cputype_str = str(cputype)
            
    #         cpusubtype_str = macho_instance.decode_cpusubtype(header.get('cputype', 0), header.get('cpusubtype', 0))
    #         filetype_str = macho_instance.format_file_type(header.get('filetype', 0))
    #         flags_str = macho_instance.decode_flags(header.get('flags', 0))
            
    #         return {
    #             'raw': {
    #                 'magic': header.get('magic', 0),
    #                 'cputype': header.get('cputype', 0),
    #                 'cpusubtype': header.get('cpusubtype', 0),
    #                 'filetype': header.get('filetype', 0),
    #                 'flags': header.get('flags', 0),
    #             },
    #             'formatted': {
    #                 'magic_str': magic_str,
    #                 'cputype_str': cputype_str,
    #                 'cpusubtype_str': cpusubtype_str,
    #                 'filetype_str': filetype_str,
    #                 'flags_str': flags_str,
    #             }
    #         }
    #     except Exception as e:
    #         self.log.error(f"Error formatting header values: {e}")
    #         return None