Vadim Zalunin

11 papers Journal 11
YearRankTypeTitle / Venue / Authors
2018 J jnl
Nucleic Acids Res.
Nicole Silvester, Blaise T. F. Alako, Clara Amid, Ana Cerdeño-Tárraga, Laura Clarke, Iain Cleland, Peter W. Harrison, Suran Jayathilaka, Simon Kay, Thomas M. Keane, Rasko Leinonen, Xin Liu, Josué Martínez-Villacorta, Manuela Menchi, Kethi Reddy, Nima Pakseresht, Jeena Rajan, Marc Rossello, Dmitriy Smirnov, Ana Luisa Toribio, Daniel Vaughan, Vadim Zalunin, Guy Cochrane
2017 J jnl
Nucleic Acids Res.
Ana Luisa Toribio, Blaise T. F. Alako, Clara Amid, Ana Cerdeño-Tárraga, Laura Clarke, Iain Cleland, Susan Fairley, Richard Gibson, Neil Goodgame, Petra ten Hoopen, Suran Jayathilaka, Simon Kay, Rasko Leinonen, Xin Liu, Josué Martínez-Villacorta, Nima Pakseresht, Jeena Rajan, Kethi Reddy, Marc Rossello, Nicole Silvester, Dimitriy Smirnov, Daniel Vaughan, Vadim Zalunin, Guy Cochrane
2016 J jnl
Nucleic Acids Res.
Richard Gibson, Blaise T. F. Alako, Clara Amid, Ana Cerdeño-Tárraga, Iain Cleland, Neil Goodgame, Petra ten Hoopen, Suran Jayathilaka, Simon Kay, Rasko Leinonen, Xin Liu, Swapna Pallreddy, Nima Pakseresht, Jeena Rajan, Marc Rossello, Nicole Silvester, Dimitriy Smirnov, Ana Luisa Toribio, Daniel Vaughan, Vadim Zalunin, Guy Cochrane
2015 J jnl
Nucleic Acids Res.
Nicole Silvester, Blaise T. F. Alako, Clara Amid, Ana Cerdeño-Tárraga, Iain Cleland, Richard Gibson, Neil Goodgame, Petra ten Hoopen, Simon Kay, Rasko Leinonen, Weizhong Li, Xin Liu, Rodrigo Lopez, Nima Pakseresht, Swapna Pallreddy, Sheila Plaister, Rajesh Radhakrishnan, Marc Rossello, Alexander Senf, Dimitriy Smirnov, Ana Luisa Toribio, Daniel Vaughan, Vadim Zalunin, Guy Cochrane
2015 J jnl
F1000Research
Camilla L. C. Ip, Matthew Loose, John R. Tyson, Mariateresa de Cesare, Bonnie L. Brown, Miten Jain, Richard M. Leggett, David A. Eccles, Vadim Zalunin, John M. Urban, Paolo Piazza, Rory J. Bowden, Benedict Paten, Solomon Mwaigwisya, Elizabeth M. Batty, Jared T. Simpson, Terrance P. Snutch, Ewan Birney, David Buck, Sara Goodwin, Hans J. Jansen, Justin O'Grady, Hugh E. Olsen, MinION Analysis, Reference Consortium
2014 J jnl
Nucleic Acids Res.
Nima Pakseresht, Blaise T. F. Alako, Clara Amid, Ana Cerdeño-Tárraga, Iain Cleland, Richard Gibson, Neil Goodgame, Tamer Gur, Mikyung Jang, Simon Kay, Rasko Leinonen, Weizhong Li, Xin Liu, Rodrigo Lopez, Hamish McWilliam, Arnaud Oisel, Swapna Pallreddy, Sheila Plaister, Rajesh Radhakrishnan, Stéphane Rivière, Marc Rossello, Alexander Senf, Nicole Silvester, Dimitriy Smirnov, Silvano Squizzato, Petra ten Hoopen, Ana Luisa Toribio, Daniel Vaughan, Vadim Zalunin, Guy Cochrane
2013 J jnl
Nucleic Acids Res.
Guy Cochrane, Blaise T. F. Alako, Clara Amid, Lawrence Bower, Ana Cerdeño-Tárraga, Iain Cleland, Richard Gibson, Neil Goodgame, Mikyung Jang, Simon Kay, Rasko Leinonen, Xiu Lin, Rodrigo Lopez, Hamish McWilliam, Arnaud Oisel, Nima Pakseresht, Swapna Pallreddy, Young Mi Park, Sheila Plaister, Rajesh Radhakrishnan, Stéphane Rivière, Marc Rossello, Alexander Senf, Nicole Silvester, Dimitriy Smirnov, Petra ten Hoopen, Ana Luisa Toribio, Daniel Vaughan, Vadim Zalunin
2012 J jnl
Nucleic Acids Res.
Clara Amid, Ewan Birney, Lawrence Bower, Ana Cerdeño-Tárraga, Ying Cheng, Iain Cleland, Nadeem Faruque, Richard Gibson, Neil Goodgame, Christopher I. Hunter, Mikyung Jang, Rasko Leinonen, Xin Liu, Arnaud Oisel, Nima Pakseresht, Sheila Plaister, Rajesh Radhakrishnan, Kethi Reddy, Stéphane Rivière, Marc Rossello, Alexander Senf, Dimitriy Smirnov, Petra ten Hoopen, Daniel Vaughan, Robert Vaughan, Vadim Zalunin, Guy Cochrane
2011 J jnl
Nucleic Acids Res.
Rasko Leinonen, Ruth Akhtar, Ewan Birney, Lawrence Bower, Ana Cerdeño-Tárraga, Ying Cheng, Iain Cleland, Nadeem Faruque, Neil Goodgame, Richard Gibson, Gemma Hoad, Mikyung Jang, Nima Pakseresht, Sheila Plaister, Rajesh Radhakrishnan, Kethi Reddy, Siamak Sobhany, Petra ten Hoopen, Robert Vaughan, Vadim Zalunin, Guy Cochrane
2010 J jnl
Nucleic Acids Res.
Rasko Leinonen, Ruth Akhtar, Ewan Birney, James K. Bonfield, Lawrence Bower, Matthew Corbett, Ying Cheng, Fehmi Demiralp, Nadeem Faruque, Neil Goodgame, Richard Gibson, Gemma Hoad, Christopher I. Hunter, Mikyung Jang, Steven Leonard, Quan Lin, Rodrigo Lopez, Michael Maguire, Hamish McWilliam, Sheila Plaister, Rajesh Radhakrishnan, Siamak Sobhany, Guy Slater, Petra ten Hoopen, Franck Valentin, Robert Vaughan, Vadim Zalunin, Daniel R. Zerbino, Guy Cochrane
2009 J jnl
Nucleic Acids Res.
Guy Cochrane, Ruth Akhtar, James K. Bonfield, Lawrence Bower, Fehmi Demiralp, Nadeem Faruque, Richard Gibson, Gemma Hoad, Tim J. P. Hubbard, Christopher I. Hunter, Mikyung Jang, Szilveszter Juhos, Rasko Leinonen, Steven Leonard, Quan Lin, Rodrigo Lopez, Dariusz Lorenc, Hamish McWilliam, Gaurab Mukherjee, Sheila Plaister, Rajesh Radhakrishnan, Stephen Robinson, Siamak Sobhany, Petra ten Hoopen, Robert Vaughan, Vadim Zalunin, Ewan Birney
redb/extractors/macho_extractors/macho_segments.py
← Index redb/extractors/macho_extractors/macho_segments.py python
import hashlib
import inspect
import base64
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 MachOSegment


class MachOSegmentExtractor(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_segments"
        self.log.debug(inspect.currentframe().f_code.co_name)

    def _is_empty_result(self, extracted_data) -> bool:
        """
        Override: Empty segments is an ERROR, not a valid empty case.
        A valid MachO file must have segments (at minimum __PAGEZERO, __TEXT).
        """
        # Always return False - empty segments should be treated as an error
        return False

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

    def _extract_segments_for_arch(self, arch_name):
        """Extract segment information for a specific architecture."""
        self.log.debug(f"Extracting segments for architecture: {arch_name}")
        segments = []

        try:
            # Get segments using new API with architecture parameter
            segments_data = self.macho.get_segments(arch=arch_name)
            if not segments_data:
                return segments

            # Extract segments for this architecture
            for segment in segments_data:
                try:
                    segment_name = segment.get('segname', 'Unknown')

                    # Calculate segment hash
                    segment_data = self._get_segment_data(segment)
                    if segment_data:
                        seg_sha256 = hashlib.sha256(segment_data).hexdigest()
                    else:
                        seg_sha256 = ""

                    # Use entropy already calculated by machofile module, rounded to 3 decimal places
                    seg_entropy = round(segment.get('entropy', 0.0), 3)

                    # Create segment dataclass with architecture info
                    macho_segment = MachOSegment(
                        segment_name=segment_name,
                        segment_vaddr=segment.get('vaddr', 0),
                        segment_vsize=segment.get('vsize', 0),
                        segment_offset=segment.get('offset', 0),
                        segment_size=segment.get('size', 0),
                        segment_max_vm_protection=segment.get('max_vm_protection', 0),
                        segment_initial_vm_protection=segment.get('initial_vm_protection', 0),
                        segment_nsects=segment.get('nsects', 0),
                        segment_flags=segment.get('flags', 0),
                        segment_entropy=seg_entropy,
                        segment_sha256=seg_sha256,
                    )
                    # Add architecture info to the segment
                    macho_segment.architecture = arch_name
                    segments.append(macho_segment)

                except Exception as e:
                    self.log.warning(
                        f'Unable to process segment "{segment.get("segname", "Unknown")}" for architecture {arch_name} in {self.hash.sha256}: {e}'
                    )
                    continue

            return segments

        except Exception as e:
            self.log.error(f"Error extracting MachO segments for architecture {arch_name}: {e}")
            return segments

    def _extract_segments(self):
        """Extract segment information from all architectures in the MachO binary."""
        self.log.debug(inspect.currentframe().f_code.co_name)
        segments = []

        if not self.macho:
            return segments

        try:
            # Get architectures using new API (already parsed in base class)
            architectures = self.macho.get_architectures()
            if not architectures:
                return segments

            # Process each architecture
            for arch_name in architectures:
                arch_segments = self._extract_segments_for_arch(arch_name)
                segments.extend(arch_segments)

            return segments

        except Exception as e:
            self.log.error(f"Error extracting MachO segments: {e}")
            return segments

    def _get_segment_data(self, segment):
        """Get the raw data for a segment."""
        try:
            offset = segment.get('offset', 0)
            size = segment.get('size', 0)
            
            if size == 0:
                return None
            
            # Read segment data from file
            with open(self.filepath, 'rb') as f:
                f.seek(offset)
                return f.read(size)
                
        except Exception as e:
            self.log.warning(f"Error reading segment data: {e}")
            return None

    def extract(self):
        self.log.debug(inspect.currentframe().f_code.co_name)
        try:
            segments = self._extract_segments()
            return segments
        except Exception as e:
            self.log.error(f"Error extracting MachO segments: {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 base class)
            try:
                architectures = self.macho.get_architectures()
                is_fat = len(architectures) > 1
            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 segments for this specific architecture
                segments = self._extract_segments_for_arch(arch_name)
                if not segments:
                    continue

                # Get architecture-specific sha256 and header info
                try:
                    arch_general_info = self.macho.get_general_info(arch=arch_name)
                    arch_sha256 = arch_general_info.get('SHA256', self.sha256)

                    # Get raw architecture value
                    arch_header_raw = self.macho.get_macho_header(arch=arch_name)
                    arch_cputype_raw = arch_header_raw.get('cputype', 0) if arch_header_raw else 0
                except Exception as e:
                    self.log.warning(f"Could not get arch-specific data for {arch_name}: {e}")
                    arch_sha256 = self.sha256
                    arch_cputype_raw = 0

                for segment in segments:
                    data.append([
                        arch_sha256,                          # sha256 (architecture-specific)
                        segment.segment_name,                 # segment_name
                        segment.segment_vaddr,                # segment_vaddr
                        segment.segment_vsize,                # segment_vsize
                        segment.segment_offset,               # segment_offset
                        segment.segment_size,                 # segment_size
                        segment.segment_max_vm_protection,    # segment_max_vm_protection
                        segment.segment_initial_vm_protection, # segment_initial_vm_protection
                        segment.segment_nsects,               # segment_nsects
                        segment.segment_flags,                # segment_flags
                        segment.segment_entropy,              # segment_entropy
                        segment.segment_sha256,               # segment_sha256
                        current_time,                         # analysis_date
                    ])

            column_names = [
                'sha256',
                'segment_name', 'segment_vaddr', 'segment_vsize', 'segment_offset',
                'segment_size', 'segment_max_vm_protection', 'segment_initial_vm_protection',
                'segment_nsects', 'segment_flags', 'segment_entropy', 'segment_sha256',
                'analysis_date'
            ]

            if not data:
                return None

            column_type_names = [
                'FixedString(64)',
                'String', 'UInt64', 'UInt64', 'UInt64',
                'UInt64', 'UInt32', 'UInt32',
                'UInt32', 'UInt32', 'Float64', 'FixedString(64)',
                'DateTime64(3, \'UTC\')'
            ]

            return (data, column_names, column_type_names)

        return None

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