James C. Costello

15 papers A 1C 1Misc 2Journal 8Unranked 3
YearRankTypeTitle / Venue / Authors
2025 J jnl
Bioinform.
Lucas A. Gillenwater, Lawrence E. Hunter, James C. Costello
2025 J jnl
J. Data-centric Mach. Learn. Res.
Gustavo Stolovitzky, Julio Saez-Rodriguez, Julie Bletz, Jake Albrecht, Gaia Andreoletti, James C. Costello, Paul C. Boutros
2023 J jnl
CoRR
Gustavo Stolovitzky, Julio Saez-Rodriguez, Julie Bletz, Jacob Albrecht, Gaia Andreoletti, James C. Costello, Paul C. Boutros
2022 J jnl
Genom. Proteom. Bioinform.
Alexandra J. Lee, Dallas L. Mould, Jake Crawford, Dongbo Hu, Rani K. Powers, Georgia Doing, James C. Costello, Deborah A. Hogan, Casey S. Greene
2018 J jnl
Bioinform.
Rani K. Powers, Andrew Goodspeed, Harrison Pielke-Lombardo, Aik Choon Tan, James C. Costello
2018 J jnl
BMC Syst. Biol.
Brian C. Ross, Mayla Boguslav, Holly Weeks, James C. Costello
2017 Misc conf
PSB
Kimberly R. Kanigel Winner, James C. Costello
2015 J jnl
F1000Research
Thomas Cokelaer, Mukesh Bansal, Christopher Bare, Erhan Bilal, Brian M. Bot, Elias Chaibub Neto, Federica Eduati, Mehmet Gönen, Steven M. Hill, Bruce R. Hoff, Jonathan R. Karr, Robert Küffner, Michael P. Menden, Pablo Meyer, Raquel Norel, Abhishek Pratap, Robert J. Prill, Matthew T. Weirauch, James C. Costello, Gustavo Stolovitzky, Julio Saez-Rodriguez
2009 J jnl
J. Comput. Biol.
Daniel R. Schrider, James C. Costello, Matthew W. Hahn
2009 Misc conf
Pacific Symposium on Biocomputing
James C. Costello, Daniel R. Schrider, Jeff Gehlhausen, Mehmet M. Dalkilic
2008 conf
RECOMB-CG
James C. Costello, Mira V. Han, Matthew W. Hahn
2007 C conf
CIBCB
James C. Costello, Jade E. Buchanan-Carter, Mehmet M. Dalkilic, Justen Andrews
2006 A conf
SDM
Mehmet M. Dalkilic, Wyatt T. Clark, James C. Costello, Predrag Radivojac
2004 conf
SIGDOC
Arijit Sengupta, Mehmet M. Dalkilic, James C. Costello
2004 conf
TREC
Kazuhiro Seki, James C. Costello, Vasanth R. Singan, Javed Mostafa
redb/extractors/pe_extractors/pe_imports.py
← Index redb/extractors/pe_extractors/pe_imports.py python
import inspect
from typing import Any, List, Tuple
from datetime import datetime, timezone

from redb.extractors.enum import Tag
from redb.extractors.pe_extractor import PEExtractor
from redb.models.dataclasses import PEImport


class PEImportExtractor(PEExtractor):

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

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

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

        imports_symbols = []
        imports_lib = []
        imports_total = 0
        # pe_import = None
        try:
            directory_entry_import = getattr(self.pe, "DIRECTORY_ENTRY_IMPORT", [])
            imports_total = len(directory_entry_import)
            for entry in directory_entry_import:
                symbols = []
                tmp_import = {}
                libname = entry.dll.decode() if entry.dll else ""
                imports_lib.append(libname)
                # replace . with _ to avoid issues with elastic
                # entryname = entryname.replace(".", "_")
                for symbol in entry.imports:
                    if symbol.name:
                        symbols.append(symbol.name.decode())
                # imports_symbols[entryname] = symbols
                tmp_import[libname] = symbols
                imports_symbols.append(tmp_import)
            return PEImport(
                pe_imports_total=imports_total,
                pe_import_libraryName=imports_lib if imports_lib else None,
                pe_import_functions=imports_symbols if imports_symbols else None,
            )
        except Exception as e:
            self.log.error(f"Extract imports error {self.hash.sha256} Exception: {e}")
        return pe_import

    def extract(self):
        try:
            self.log.debug(inspect.currentframe().f_code.co_name)
            return self._extract_imports()
        except Exception as e:
            self.log.error(f"Extract imports error {self.hash.sha256} Exception: {e}")
            return None

    def prepare_export_data(self, exporter_type: str) -> Any:
        if exporter_type == "ElasticsearchExporter":
            return self.extract()
        elif exporter_type == "ClickHouseExporter":
            imports = self.extract()
            if (
                imports is None
                or imports.pe_imports_total == 0
                or (
                    imports.pe_import_libraryName is None
                    and imports.pe_import_functions is None
                )
            ):
                return None

            # Flatten the data - one row per function import
            data = []
            current_time = datetime.now(timezone.utc)

            for lib_funcs in imports.pe_import_functions:
                for lib, funcs in lib_funcs.items():
                    for func in funcs:
                        data.append(
                            [
                                self.sha256,  # sha256
                                self.md5,  # md5
                                self.sha1,  # sha1
                                lib,  # library_name
                                func,  # function_name
                                current_time,  # analysis_date
                            ]
                        )

            column_names = [
                "sha256",
                "md5",
                "sha1",
                "library_name",
                "function_name",
                "analysis_date",
            ]

            column_type_names = [
                "FixedString(64)",
                "FixedString(32)",
                "FixedString(40)",
                "LowCardinality(Nullable(String))",
                "LowCardinality(Nullable(String))",
                "DateTime64(3, 'UTC')",
            ]

            if not data:
                return None

            return (data, column_names, column_type_names)

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