Nathaniel K. Brown

17 papers B 5C 2Journal 9Unranked 1
YearRankTypeTitle / Venue / Authors
2026 J jnl
CoRR
Nathaniel K. Brown, Ben Langmead
2026 J jnl
J. Comput. Biol.
Nathaniel K. Brown, Vikram Shivakumar, Ben Langmead
2026 J jnl
CoRR
Nathaniel K. Brown, Ahsan Sanaullah, Shaojie Zhang, Ben Langmead
2025 conf
From Strings to Graphs, and Back Again
Nathaniel K. Brown, Travis Gagie, Giovanni Manzini, Gonzalo Navarro, Marinella Sciortino
2025 B conf
RECOMB
Nathaniel K. Brown, Vikram Shivakumar, Ben Langmead
2025 J jnl
CoRR
Nathaniel K. Brown, Anas Alhadi, Nour Allam, Dove Begleiter, Nithin Bharathi Kabilan Karpagavalli, Suchith Sridhar Khajjayam, Hamza Wahed, Travis Gagie
2025 C conf
SPIRE
Nathaniel K. Brown, Lore Depuydt, Mohsen Zakeri, Anas Alhadi, Nour Allam, Dove Begleiter, Nithin Bharathi Kabilan Karpagavalli, Suchith Sridhar Khajjayam, Hamza Wahed, Travis Gagie, Ben Langmead
2025 J jnl
Algorithms Mol. Biol.
Stephen Hwang, Nathaniel K. Brown, Omar Y. Ahmed, Katharine M. Jenike, Sam Kovaka, Michael C. Schatz, Ben Langmead
2024 B conf
DCC
Adrián Goga, Lore Depuydt, Nathaniel K. Brown, Jan Fostier, Travis Gagie, Gonzalo Navarro
2024 C conf
WABI
Stephen Hwang, Nathaniel K. Brown, Omar Y. Ahmed, Katharine M. Jenike, Sam Kovaka, Michael C. Schatz, Ben Langmead
2024 J jnl
CoRR
Peter Peresíni, Nathaniel K. Brown, Travis Gagie, Ben Langmead
2023 B conf
DCC
César Martínez-Guardiola, Nathaniel K. Brown, Fernando Silva-Coira, Dominik Köppl, Travis Gagie, Susana Ladra
2023 J jnl
CoRR
Adrián Goga, Lore Depuydt, Nathaniel K. Brown, Jan Fostier, Travis Gagie, Gonzalo Navarro
2022 J jnl
CoRR
César Martínez-Guardiola, Nathaniel K. Brown, Fernando Silva-Coira, Dominik Köppl, Travis Gagie, Susana Ladra
2022 B conf
DCC
Nathaniel K. Brown, Travis Gagie, Massimiliano Rossi
2022 B conf
SEA
Nathaniel K. Brown, Travis Gagie, Massimiliano Rossi
2021 J jnl
CoRR
Nathaniel K. Brown, Travis Gagie, Massimiliano Rossi
redb/extractors/macho_extractors/macho_exports.py
← Index redb/extractors/macho_extractors/macho_exports.py python
import inspect
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 MachOExport


class MachOExportExtractor(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_exports"
        self.log.debug(inspect.currentframe().f_code.co_name)

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

    def _extract_exports(self, arch_name=None):
        """Extract export information from the MachO binary for a specific architecture."""
        self.log.debug(inspect.currentframe().f_code.co_name)

        if not self.macho:
            return None

        try:
            # Get exported symbols using new API for specific architecture
            exported_symbols = self.macho.get_exported_symbols(arch=arch_name)

            # Extract all exported symbols (may be empty for some binaries)
            # Handle None or empty dict
            if not exported_symbols:
                exported_symbols = {}
            all_symbols = []
            for dylib_name, symbols in exported_symbols.items():
                # Process symbol names
                for symbol in symbols:
                    if isinstance(symbol, bytes):
                        symbol = symbol.decode('utf-8', errors='replace')
                    all_symbols.append(symbol)

            # Create export dataclass
            macho_export = MachOExport(
                macho_exports_total=len(all_symbols),
                macho_export_symbols=all_symbols  # Empty list is fine, but None is not allowed for Array type
            )

            return macho_export

        except Exception as e:
            self.log.error(f"Error extracting MachO exports for arch {arch_name}: {e}")
            return None

    def extract(self):
        self.log.debug(inspect.currentframe().f_code.co_name)
        try:
            # Get architectures (macho is already parsed in base class)
            architectures = self.macho.get_architectures()
            if len(architectures) > 1:
                # FAT binary - return list of exports for each architecture
                results = []
                for arch_name in architectures:
                    exports = self._extract_exports(arch_name)
                    if exports:
                        exports.arch_identifier = arch_name
                        results.append(exports)
                return results
            else:
                # Single architecture - return single result
                return self._extract_exports(architectures[0] if architectures else None)
        except Exception as e:
            self.log.error(f"Error extracting MachO exports: {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:
                # Get architecture-specific sha256
                try:
                    arch_general_info = self.macho.get_general_info(arch=arch_name)
                    arch_header_raw = self.macho.get_macho_header(arch=arch_name)
                    arch_sha256 = arch_general_info.get('SHA256', self.sha256)
                    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

                # Get exports for this architecture
                macho_export = self._extract_exports(arch_name)
                if not macho_export:
                    continue

                data.append([
                    arch_sha256,                          # sha256 (arch-specific)
                    macho_export.macho_exports_total,     # macho_exports_total
                    macho_export.macho_export_symbols,    # macho_export_symbols (keep as array!)
                    current_time,                         # analysis_date
                ])

            column_names = [
                'sha256',
                'macho_exports_total', 'macho_export_symbols',
                'analysis_date'
            ]

            if not data:
                return None

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

            return (data, column_names, column_type_names)

        return None

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