Nathan A. Dunn

14 papers B 2Journal 11Unranked 1
YearRankTypeTitle / Venue / Authors
2020 J jnl
Nucleic Acids Res.
Julie Agapite, Laurent-Philippe Albou, Suzi A. Aleksander, Joanna Argasinska, Valerio Arnaboldi, Helen Attrill, Susan M. Bello, Judith A. Blake, Olin Blodgett, Yvonne M. Bradford, Carol J. Bult, Scott Cain, Brian R. Calvi, Seth Carbon, Juancarlos Chan, Wen J. Chen, J. Michael Cherry, Jae-Hyoung Cho, Karen R. Christie, Madeline A. Crosby, Jeff de Pons, Mary E. Dolan, Gilberto dos Santos, Barbara Dunn, Nathan A. Dunn, Anne E. Eagle, Dustin Ebert, Stacia R. Engel, David Fashena, Ken Frazer, Sibyl Gao, Felix Gondwe, Joshua L. Goodman, L. Sian Gramates, Christian A. Grove, Todd W. Harris, Marie-Claire Harrison, Douglas G. Howe, Kevin L. Howe, Sagar Jha, James A. Kadin, Thomas C. Kaufman, Patrick Kalita, Kalpana Karra, Ranjana Kishore, Stanley J. F. Laulederkind, Raymond Y. N. Lee, Kevin A. MacPherson, Steven J. Marygold, Beverley Matthews, Gillian H. Millburn, Stuart R. Miyasato, Sierra A. T. Moxon, Hans-Michael Müller, Christopher J. Mungall, Anushya Muruganujan, Tremayne Mushayahama, Robert S. Nash, Patrick Ng, Michael Paulini, Norbert Perrimon, Christian Pich, Daniela Raciti, Joel E. Richardson, Matthew Russell, Susan Russo Gelbart, Leyla Ruzicka, Kevin Schaper, Mary Shimoyama, Matt Simison, Cynthia L. Smith, David R. Shaw, Ajay Shrivatsav, Marek S. Skrzypek, Jennifer R. Smith, Paul W. Sternberg, Christopher J. Tabone, Paul D. Thomas, Jyothi Thota, Sabrina Toro, Monika Tomczuk, Marek Tutaj, Monika Tutaj, Jose-Maria Urbano, Kimberly Van Auken, Ceri E. Van Slyke, Shur-Jen Wang, Shuai Weng, Monte Westerfield, Gary Williams, Edith D. Wong, Adam Wright, Karen Yook
2020 J jnl
Nucleic Acids Res.
Kent A. Shefchek, Nomi L. Harris, Michael A. Gargano, Nicolas Matentzoglu, Deepak R. Unni, Matthew H. Brush, Dan Keith, Tom Conlin, Nicole A. Vasilevsky, Xingmin Aaron Zhang, James P. Balhoff, Larry Babb, Susan M. Bello, Hannah Blau, Yvonne M. Bradford, Seth Carbon, Leigh Carmody, Lauren E. Chan, Valentina Cipriani, Alayne Cuzick, Maria G. Della Rocca, Nathan A. Dunn, Shahim Essaid, Petra Fey, Christian A. Grove, Jean-Philippe F. Gourdine, Ada Hamosh, Midori A. Harris, Ingo Helbig, Maureen E. Hoatlin, Marcin P. Joachimiak, Simon Jupp, Kenneth B. Lett, Suzanna E. Lewis, Craig McNamara, Zoë May Pendlington, Clare Pilgrim, Tim E. Putman, Vida Ravanmehr, Justin T. Reese, Erin Rooney Riggs, Sofia M. C. Robb, Paola Roncaglia, James Seager, Erik Segerdell, Morgan Similuk, Andrea L. Storm, Courtney Thaxon, Anne E. Thessen, Julius O. B. Jacobsen, Julie A. McMurry, Tudor Groza, Sebastian Köhler, Damian Smedley, Peter N. Robinson, Christopher J. Mungall, Melissa A. Haendel, Monica C. Munoz-Torres, David Osumi-Sutherland
2019 J jnl
PLoS Comput. Biol.
Nathan A. Dunn, Deepak R. Unni, Colin M. Diesh, Monica C. Munoz-Torres, Nomi L. Harris, Eric Yao, Helena Rasche, Ian H. Holmes, Christine G. Elsik, Suzanna E. Lewis
2018 J jnl
Database J. Biol. Databases Curation
Lisa C. Harper, Jacqueline D. Campbell, Ethalinda K. S. Cannon, Sook Jung, Monica Poelchau, Ramona L. Walls, Carson M. Andorf, Elizabeth Arnaud, Tanya Z. Berardini, Clayton L. Birkett, Steven B. Cannon, James D. Carson, Bradford Condon, Laurel Cooper, Nathan A. Dunn, Christine G. Elsik, Andrew D. Farmer, Stephen P. Ficklin, David M. Grant, Emily S. Grau, Nic Herndon, Zhi-Liang Hu, Jodi L. Humann, Pankaj Jaiswal, Clément Jonquet, Marie-Angélique Laporte, Pierre Larmande, Gerard R. Lazo, Fiona McCarthy, Naama Menda, Christopher J. Mungall, Monica C. Munoz-Torres, Sushma Naithani, Rex T. Nelson, Daureen Nesdill, Carissa A. Park, James M. Reecy, Leonore Reiser, Lacey-Anne Sanderson, Taner Z. Sen, Margaret Staton, Sabarinath Subramaniam, Marcela Karey Tello-Ruiz, Victor Unda, Deepak R. Unni, Liya Wang, Doreen Ware, Jill L. Wegrzyn, Jason Williams, Margaret Woodhouse, Jing Yu, Doreen Main
2018 J jnl
F1000Research
Evan Biederstedt, Jeffrey C. Oliver, Nancy F. Hansen, Aarti Jajoo, Nathan A. Dunn, Andrew Olson, Ben Busby, Alexander T. Dilthey
2018 J jnl
Nucleic Acids Res.
Laurel Cooper, Austin Meier, Marie-Angélique Laporte, Justin Elser, Chris Mungall, Brandon T. Sinn, Dario Cavaliere, Seth Carbon, Nathan A. Dunn, Barry Smith, Botong Qu, Justin Preece, Eugene Zhang, Sinisa Todorovic, Georgios V. Gkoutos, John H. Doonan, Dennis W. Stevenson, Elizabeth Arnaud, Pankaj Jaiswal
2017 J jnl
Nucleic Acids Res.
Christopher J. Mungall, Julie A. McMurry, Sebastian Köhler, James P. Balhoff, Charles D. Borromeo, Matthew H. Brush, Seth Carbon, Tom Conlin, Nathan A. Dunn, Mark Engelstad, Erin Foster, Jean-Philippe F. Gourdine, Julius O. B. Jacobsen, Dan Keith, Bryan Laraway, Suzanna E. Lewis, Jeremy NguyenXuan, Kent A. Shefchek, Nicole A. Vasilevsky, Zhou Yuan, Nicole L. Washington, Harry Hochheiser, Tudor Groza, Damian Smedley, Peter N. Robinson, Melissa A. Haendel
2017 J jnl
Database J. Biol. Databases Curation
Tim E. Putman, Sebastien Lelong, Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Colin M. Diesh, Nathan A. Dunn, Monica C. Munoz-Torres, Gregory S. Stupp, Chunlei Wu, Andrew I. Su, Benjamin M. Good
2011 J jnl
Nucleic Acids Res.
Yvonne M. Bradford, Tom Conlin, Nathan A. Dunn, David Fashena, Ken Frazer, Douglas G. Howe, Jonathan Knight, Prita Mani, Ryan Martin, Sierra A. T. Moxon, Holly Paddock, Christian Pich, Sridhar Ramachandran, Barbara J. Ruef, Leyla Ruzicka, Holle Bauer Schaper, Kevin Schaper, Xiang Shao, Amy Singer, Judy Sprague, Brock Sprunger, Ceri E. Van Slyke, Monte Westerfield
2008 J jnl
Nucleic Acids Res.
Judy Sprague, Leyla Bayraktaroglu, Yvonne M. Bradford, Tom Conlin, Nathan A. Dunn, David Fashena, Ken Frazer, Melissa A. Haendel, Douglas G. Howe, Jonathan Knight, Prita Mani, Sierra A. T. Moxon, Christian Pich, Sridhar Ramachandran, Kevin Schaper, Erik Segerdell, Xiang Shao, Amy Singer, Peiran Song, Brock Sprunger, Ceri E. Van Slyke, Monte Westerfield
2006 B conf
IJCNN
Nathan A. Dunn, Jonathan T. Pierce-Shimomura, John S. Conery, Shawn R. Lockery
2004 J jnl
J. Comput. Neurosci.
Nathan A. Dunn, Shawn R. Lockery, Jonathan T. Pierce-Shimomura, John S. Conery
2003 B conf
IJCNN
Nathan A. Dunn, John S. Conery, Shawn R. Lockery
2003 conf
NIPS
Nathan A. Dunn, John S. Conery, Shawn R. Lockery
redb/extractors/elf_extractors/elf_imports.py
← Index redb/extractors/elf_extractors/elf_imports.py python
import inspect
from datetime import datetime, timezone
from typing import Any, List, Set

from elftools.elf.elffile import ELFFile
from elftools.common.exceptions import ELFError

from redb.extractors.enum import Tag
from redb.extractors.elf_extractor import ELFExtractor
from redb.models.dataclasses import ELFImport


class ELFImportExtractor(ELFExtractor):

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

    def _get_import_libraries(self, elf) -> List[str]:
        """Extract imported libraries from dynamic section."""
        libraries = []

        try:
            # Get the dynamic section
            dynamic_section = elf.get_section_by_name('.dynamic')
            if not dynamic_section:
                return libraries

            # Extract DT_NEEDED entries (required libraries)
            for tag in dynamic_section.iter_tags():
                if tag.entry.d_tag == 'DT_NEEDED':
                    libraries.append(tag.needed)

        except Exception as e:
            self.log.error(f"Error extracting import libraries: {e}")

        return libraries

    def _get_imported_functions_from_symbols(self, elf) -> Set[str]:
        """Extract imported functions from dynamic symbol table."""
        imported_functions = set()

        try:
            # Get the dynamic symbol table
            dynsym_section = elf.get_section_by_name('.dynsym')
            if not dynsym_section or not hasattr(dynsym_section, 'iter_symbols'):
                return imported_functions

            # Look for undefined symbols (imports)
            for symbol in dynsym_section.iter_symbols():
                # Check if symbol is undefined (imported)
                if (symbol.entry.get('st_shndx', 0) == 'SHN_UNDEF' and
                    symbol.name and
                    symbol.entry.get('st_info', {}).get('bind') in ['STB_GLOBAL', 'STB_WEAK']):
                    imported_functions.add(symbol.name)

        except Exception as e:
            self.log.error(f"Error extracting imported functions from symbols: {e}")

        return imported_functions

    def _get_imported_functions_from_relocations(self, elf) -> Set[str]:
        """Extract imported functions from relocation sections."""
        imported_functions = set()

        try:
            # Look through relocation sections
            for section in elf.iter_sections():
                if hasattr(section, 'iter_relocations'):
                    try:
                        for relocation in section.iter_relocations():
                            # Get symbol associated with relocation
                            if hasattr(relocation, 'symbol') and relocation.symbol:
                                symbol_name = relocation.symbol.name
                                if symbol_name:
                                    imported_functions.add(symbol_name)
                    except Exception as e:
                        self.log.debug(f"Could not process relocations in section {section.name}: {e}")

        except Exception as e:
            self.log.error(f"Error extracting imported functions from relocations: {e}")

        return imported_functions

    def _get_plt_functions(self, elf) -> Set[str]:
        """Extract functions from PLT (Procedure Linkage Table) sections."""
        plt_functions = set()

        try:
            # Look for PLT-related sections
            plt_sections = ['.plt', '.plt.got', '.plt.sec']

            for section_name in plt_sections:
                section = elf.get_section_by_name(section_name)
                if section:
                    # PLT functions are typically associated with relocations
                    # We'll get them from the relocation analysis
                    pass

        except Exception as e:
            self.log.error(f"Error extracting PLT functions: {e}")

        return plt_functions

    def tag(self):
        return Tag.ELF_IMPORTS.value if hasattr(Tag, 'ELF_IMPORTS') else "elf_imports"

    def extract(self):
        try:
            self.log.debug(inspect.currentframe().f_code.co_name)

            def extract_data(elf):
                # Extract import libraries
                import_libraries = self._get_import_libraries(elf)

                # Extract imported functions from multiple sources
                imported_functions = set()

                # From dynamic symbols
                symbol_imports = self._get_imported_functions_from_symbols(elf)
                imported_functions.update(symbol_imports)

                # From relocations
                relocation_imports = self._get_imported_functions_from_relocations(elf)
                imported_functions.update(relocation_imports)

                # From PLT
                plt_imports = self._get_plt_functions(elf)
                imported_functions.update(plt_imports)

                # Convert to sorted lists for consistent output
                import_libraries_list = sorted(list(set(import_libraries)))
                import_functions_list = sorted(list(imported_functions))

                # Return ELFImport dataclass
                return ELFImport(
                    elf_imports_total=len(import_functions_list),
                    elf_import_libraries=import_libraries_list,
                    elf_import_functions=import_functions_list,
                )

            if not self._is_elf_file():
                return None

            result = self._with_elf_file(extract_data)
            if result is None:
                return None

            self.elf_imports = result
            return self.elf_imports

        except Exception as e:
            self.log.error(f"Error extracting ELF imports {self.hash.sha256}: {e}")
            return None

    def prepare_export_data(self, exporter_type: str) -> Any:
        self.log.debug(inspect.currentframe().f_code.co_name)

        if exporter_type == "ElasticsearchExporter":
            return self.elf_imports
        elif exporter_type == "ClickHouseExporter":
            try:
                if not self.elf_imports:
                    return None

                # Prepare data array
                data = [[
                    self.sha256,
                    self.md5,
                    self.sha1,
                    self.elf_imports.elf_imports_total,
                    self.elf_imports.elf_import_libraries,
                    self.elf_imports.elf_import_functions,
                    datetime.now(timezone.utc)
                ]]

                column_names = [
                    'sha256', 'md5', 'sha1',
                    'elf_imports_total',
                    'elf_import_libraries',
                    'elf_import_functions',
                    'analysis_date'
                ]

                column_type_names = [
                    'FixedString(64)', 'FixedString(32)', 'FixedString(40)',
                    'UInt32',
                    'Array(LowCardinality(String))',
                    'Array(LowCardinality(String))',
                    'DateTime64(3, \'UTC\')'
                ]

                if not data:
                    return None

                return (data, column_names, column_type_names)

            except Exception as e:
                self.log.error(f"Error preparing export data: {e}")
                raise

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