Katerina J. Kechris

27 papers B 1Journal 24Unranked 2
YearRankTypeTitle / Venue / Authors
2025 J jnl
PLoS Comput. Biol.
Weixuan Liu, Katherine A. Pratte, Peter J. Castaldi, Craig P. Hersh, Russell P. Bowler, Farnoush Banaei Kashani, Katerina J. Kechris
2025 J jnl
CoRR
Vicente Ramos, Sundous Hussein, Mohamed Abdel-Hafiz, Arunangshu Sarkar, Weixuan Liu, Katerina J. Kechris, Russell P. Bowler, Leslie Lange, Farnoush Banaei Kashani
2024 J jnl
PLoS Comput. Biol.
Alexandria M. Jensen, Peter Dewitt, Brianne M. Bettcher, Julia Wrobel, Katerina J. Kechris, Debashis Ghosh
2024 conf
BIBM
Sundous Hussein, Vicente Ramos, Weixuan Liu, Katerina J. Kechris, Leslie Lange, Russell P. Bowler, Farnoush Banaei Kashani
2024 J jnl
PLoS Comput. Biol.
Cecilia Wieder, Juliette Cooke, Clément Frainay, Nathalie Poupin, Russell Bowler, Fabien Jourdan, Katerina J. Kechris, Rachel P. J. Lai, Timothy M. D. Ebbels
2024 J jnl
BMC Bioinform.
Weixuan Liu, Thao Vu, Iain R. Konigsberg, Katherine A. Pratte, Yonghua Zhuang, Katerina J. Kechris
2023 J jnl
Bioinform.
Thao Vu, Elizabeth Litkowski, Weixuan Liu, Katherine A. Pratte, Leslie Lange, Russell Bowler, Farnoush Banaei Kashani, Katerina J. Kechris
2023 J jnl
PLoS Comput. Biol.
Souvik Seal, Qunhua Li, Elle Butler Basner, Laura M. Saba, Katerina J. Kechris
2023 J jnl
BMC Bioinform.
Charlie M. Carpenter, Lucas A. Gillenwater, Russell Bowler, Katerina J. Kechris, Debashis Ghosh
2022 conf
BIBM
Sundous Hussein, Thao Vu, Leslie Lange, Russell Bowler, Katerina J. Kechris, Farnoush Banaei Kashani
2022 J jnl
BMC Bioinform.
Jonathan P. Dekermanjian, Elin Shaddox, Debmalya Nandy, Debashis Ghosh, Katerina J. Kechris
2022 B conf
IEEE Big Data
Andrew Hill, Russell Bowler, Katerina J. Kechris, Farnoush Banaei Kashani
2022 J jnl
Frontiers Big Data
Mohamed Abdel-Hafiz, Mesbah Najafi, Shahab Helmi, Katherine A. Pratte, Yonghua Zhuang, Weixuan Liu, Katerina J. Kechris, Russell Bowler, Leslie Lange, Farnoush Banaei Kashani
2021 J jnl
PLoS Comput. Biol.
Charlie M. Carpenter, Weiming Zhang, Lucas A. Gillenwater, Cameron Severn, Tusharkanti Ghosh, Russell Bowler, Katerina J. Kechris, Debashis Ghosh
2021 J jnl
BMC Bioinform.
Tusharkanti Ghosh, Daisy Philtron, Weiming Zhang, Katerina J. Kechris, Debashis Ghosh
2021 J jnl
BMC Bioinform.
Charlie M. Carpenter, Daniel N. Frank, Kayla Williamson, Jaron Arbet, Brandie D. Wagner, Katerina J. Kechris, Miranda Kroehl
2020 J jnl
BMC Bioinform.
Brian Vestal, Camille M. Moore, Elizabeth Wynn, Laura M. Saba, Tasha Fingerlin, Katerina J. Kechris
2019 J jnl
Bioinform.
W. Jenny Shi, Yonghua Zhuang, Pamela H. Russell, Brian D. Hobbs, Margaret M. Parker, Peter J. Castaldi, Pratyaydipta Rudra, Brian Vestal, Craig P. Hersh, Laura M. Saba, Katerina J. Kechris
2018 J jnl
PLoS Comput. Biol.
Yafei Lyu, Lingzhou Xue, Feipeng Zhang, Hillary Koch, Laura M. Saba, Katerina J. Kechris, Qunhua Li
2017 J jnl
BMC Bioinform.
Pratyaydipta Rudra, W. Jenny Shi, Brian Vestal, Pamela H. Russell, Aaron Odell, Robin D. Dowell, Richard Radcliffe, Laura M. Saba, Katerina J. Kechris
2017 J jnl
Bioinform.
Charlotte Siska, Russell Bowler, Katerina J. Kechris
2016 J jnl
Bioinform.
Charlotte Siska, Russell Bowler, Katerina J. Kechris
2014 J jnl
Bioinform.
Grant Hughes, Charmion Cruickshank-Quinn, Richard Reisdorph, Sharon Lutz, Irina Petrache, Nichole Reisdorph, Russell Bowler, Katerina J. Kechris
2014 J jnl
Briefings Bioinform.
Subhajyoti De, Brent S. Pedersen, Katerina J. Kechris
2013 J jnl
Genom. Proteom. Bioinform.
Nichole Reisdorph, Robert Stearman, Katerina J. Kechris, Tzu Lip Phang, Richard Reisdorph, Jessica E. Prenni, David J. Erle, Christopher Coldren, Kevin L. Schey, Alexey I. Nesvizhskii, Marc Geraci
2012 J jnl
Bioinform.
Brent S. Pedersen, David A. Schwartz, Ivana V. Yang, Katerina J. Kechris
2008 J jnl
BMC Bioinform.
Katerina J. Kechris, Hao Li
redb/extractors/elf_extractors/elf_dependencies.py
← Index redb/extractors/elf_extractors/elf_dependencies.py python
import inspect
from datetime import datetime, timezone
from typing import Any, List, Dict

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 ELFDependency


class ELFDependencyExtractor(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_dependencies = []
        self.elastic_index = self.index_prefix + "-elf_dependencies"
        self.log.debug(inspect.currentframe().f_code.co_name)

    def _map_dependency_type(self, dt_tag_str: str) -> int:
        """Map dynamic tag string to enum value."""
        type_map = {
            'DT_NEEDED': 1,
            'DT_SONAME': 14,
            'DT_RPATH': 15,
            'DT_RUNPATH': 29
        }
        return type_map.get(dt_tag_str, 0)

    def _extract_dynamic_dependencies(self, elf) -> List[Dict]:
        """Extract dependencies from the dynamic section."""
        dependencies = []

        try:
            # Get the dynamic section
            dynamic_section = elf.get_section_by_name('.dynamic')
            if not dynamic_section:
                self.log.debug("No .dynamic section found")
                return dependencies

            # Iterate through dynamic tags
            for tag in dynamic_section.iter_tags():
                dt_tag = tag.entry.d_tag

                # Handle different dependency types
                if dt_tag == 'DT_NEEDED':
                    # Required library
                    dependency_name = tag.needed
                    dependencies.append(ELFDependency(
                        dependency_name=dependency_name,
                        dependency_type=self._map_dependency_type('DT_NEEDED'),
                        dependency_type_str='NEEDED'
                    ))

                elif dt_tag == 'DT_SONAME':
                    # Shared object name
                    dependency_name = tag.soname
                    dependencies.append(ELFDependency(
                        dependency_name=dependency_name,
                        dependency_type=self._map_dependency_type('DT_SONAME'),
                        dependency_type_str='SONAME'
                    ))

                elif dt_tag == 'DT_RPATH':
                    # Runtime library search path
                    dependency_name = tag.rpath
                    dependencies.append(ELFDependency(
                        dependency_name=dependency_name,
                        dependency_type=self._map_dependency_type('DT_RPATH'),
                        dependency_type_str='RPATH'
                    ))

                elif dt_tag == 'DT_RUNPATH':
                    # Runtime library search path (newer)
                    dependency_name = tag.runpath
                    dependencies.append(ELFDependency(
                        dependency_name=dependency_name,
                        dependency_type=self._map_dependency_type('DT_RUNPATH'),
                        dependency_type_str='RUNPATH'
                    ))

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

        return dependencies

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

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

            def extract_data(elf):
                # Extract dependencies - returns list of ELFDependency dataclasses
                dependencies = self._extract_dynamic_dependencies(elf)
                return dependencies

            if not self._is_elf_file():
                return None

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

            self.elf_dependencies = result
            return self.elf_dependencies

        except Exception as e:
            self.log.error(f"Error extracting ELF dependencies {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_dependencies
        elif exporter_type == "ClickHouseExporter":
            try:
                # Return valid empty structure if no dependencies (e.g., statically linked binary)
                # None is reserved for actual errors

                # Prepare data arrays for all dependencies
                data = []
                current_time = datetime.now(timezone.utc)
                for dep in self.elf_dependencies:
                    row = [
                        self.sha256,
                        self.md5,
                        self.sha1,
                        dep.dependency_name,
                        dep.dependency_type,
                        dep.dependency_type_str,
                        current_time
                    ]
                    data.append(row)

                column_names = [
                    'sha256', 'md5', 'sha1',
                    'dependency_name', 'dependency_type', 'dependency_type_str',
                    'analysis_date'
                ]

                if not data:
                    return None

                column_type_names = [
                    'FixedString(64)', 'FixedString(32)', 'FixedString(40)',
                    'LowCardinality(String)',
                    "Enum8('NEEDED'=1, 'SONAME'=14, 'RPATH'=15, 'RUNPATH'=29)",
                    'LowCardinality(String)',
                    'DateTime64(3, \'UTC\')'
                ]

                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_dependencies"