Inimary T. Toby

11 papers Journal 11
YearRankTypeTitle / Venue / Authors
2025 J jnl
Frontiers Bioinform.
Sanskriti Baranwal, Ricardo Avila Sanchez, Clement-Andi Edet, Erick Chastain, Inimary T. Toby
2023 J jnl
Frontiers Bioinform.
Prajay Patel, Nisha Pillai, Inimary T. Toby
2022 J jnl
Frontiers Artif. Intell.
Ramin Homayouni, Huixiao Hong, Prashanti Manda, Bindu Nanduri, Inimary T. Toby
2021 J jnl
Comput. Biol. Medicine
Rolando García, Anas Hussain, Prasad Koduru, Murat Atis, Kathleen Wilson, Jason Y. Park, Inimary T. Toby, Kimberly Diwa, Lavang Vu, Samuel Ho, Fajar Adnan, Ashley Nguyen, Andrew Cox, Timothy Kirtek, Patricia García, Yanhui Li, Heather Jones, Guanglu Shi, Allen Green, David Rosenbaum
2019 J jnl
BMC Bioinform.
Jonathan D. Wren, Robert J. Doerksen, Inimary T. Toby, Bindu Nanduri, Ramin Homayouni, Prashanti Manda, Shraddha Thakkar
2017 J jnl
BMC Bioinform.
Jonathan D. Wren, Mikhail G. Dozmorov, Inimary T. Toby, Bindu Nanduri, Ramin Homayouni, Prashanti Manda, Shraddha Thakkar
2017 J jnl
BMC Bioinform.
Jared Ostmeyer, Scott Christley, William Rounds, Inimary T. Toby, Benjamin M. Greenberg, Nancy Monson, Lindsay G. Cowell
2017 J jnl
BMC Bioinform.
Scott Christley, Mikhail K. Levin, Inimary T. Toby, John M. Fonner, Nancy Monson, William Rounds, Florian Rubelt, Walter Scarborough, Richard H. Scheuermann, Lindsay G. Cowell
2016 J jnl
BMC Bioinform.
Jonathan D. Wren, Inimary T. Toby, Huxiao Hong, Bindu Nanduri, Rakesh Kaundal, Mikhail G. Dozmorov, Shraddha Thakkar
2016 J jnl
BMC Bioinform.
Inimary T. Toby, Mikhail K. Levin, Edward Salinas, Scott Christley, Sanchita Bhattacharya, Felix Breden, Adam Buntzman, Brian Corrie, John M. Fonner, Namita T. Gupta, Uri Hershberg, Nishanth Marthandan, Aaron M. Rosenfeld, William Rounds, Florian Rubelt, Walter Scarborough, Jamie K. Scott, Mohamed Uduman, Jason A. Vander Heiden, Richard H. Scheuermann, Nancy Monson, Steven H. Kleinstein, Lindsay G. Cowell
2014 J jnl
BMC Bioinform.
Inimary T. Toby, Jonah Widmer, David W. Dyer
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"