Oliver Beckstein

24 papers B 1Journal 16Unranked 7
YearRankTypeTitle / Venue / Authors
2024 J jnl
J. Open Source Softw.
Zhiyi Wu, David L. Dotson, Irfan Alibay, Bryce K. Allen, Mohammad Soroush Barhaghi, Jérôme Hénin, Thomas T. Joseph, Ian M. Kenney, Hyungro Lee, Haoxi Li, Victoria T. Lim, Shuai Liu, Domenico Marson, Pascal T. Merz, Alexander Schlaich, David L. Mobley, Michael R. Shirts, Oliver Beckstein
2023 conf
SciPy
Irfan Alibay, Lily Wang, Fiona Naughton, Ian M. Kenney, Jonathan Barnoud, Richard J. Gowers, Oliver Beckstein
2021 conf
SciPy
Edis Jakupovic, Oliver Beckstein
2021 J jnl
J. Comput. Aided Mol. Des.
Shujie Fan, Hristo Nedev, Ranjit Vijayan, Bogdan I. Iorga, Oliver Beckstein
2020 J jnl
Concurr. Comput. Pract. Exp.
Mahzad Khoshlessan, Ioannis Paraskevakos, Geoffrey C. Fox, Shantenu Jha, Oliver Beckstein
2020 J jnl
J. Comput. Aided Mol. Des.
Shujie Fan, Bogdan I. Iorga, Oliver Beckstein
2019 J jnl
PLoS Comput. Biol.
Sean L. Seyler, Avishek Kumar, M. F. Thorpe, Oliver Beckstein
2019 conf
IPDPS Workshops
Geoffrey C. Fox, James A. Glazier, J. C. S. Kadupitiya, Vikram Jadhao, Minje Kim, Judy Qiu, James P. Sluka, Endre T. Somogyi, Madhav V. Marathe, Abhijin Adiga, Jiangzhuo Chen, Oliver Beckstein, Shantenu Jha
2019 J jnl
CoRR
Geoffrey C. Fox, James A. Glazier, J. C. S. Kadupitiya, Vikram Jadhao, Minje Kim, Judy Qiu, James P. Sluka, Endre T. Somogyi, Madhav V. Marathe, Abhijin Adiga, Jiangzhuo Chen, Oliver Beckstein, Shantenu Jha
2019 conf
SciPy
Shujie Fan, Max Linke, Ioannis Paraskevakos, Richard J. Gowers, Michael Gecht, Oliver Beckstein
2019 J jnl
CoRR
Mahzad Khoshlessan, Ioannis Paraskevakos, Geoffrey C. Fox, Shantenu Jha, Oliver Beckstein
2018 J jnl
J. Comput. Aided Mol. Des.
Edithe Selwa, Ian M. Kenney, Oliver Beckstein, Bogdan I. Iorga
2018 B conf
ICPP
Ioannis Paraskevakos, André Luckow, Mahzad Khoshlessan, George Chantzialexiou, Thomas E. Cheatham, Oliver Beckstein, Geoffrey C. Fox, Shantenu Jha
2018 J jnl
CoRR
Ioannis Paraskevakos, André Luckow, George Chantzialexiou, Mahzad Khoshlessan, Oliver Beckstein, Geoffrey C. Fox, Shantenu Jha
2017 J jnl
Bioinform.
Jan J. Domanski, Oliver Beckstein, Bogdan I. Iorga
2017 conf
SciPy
Mahzad Khoshlessan, Ioannis Paraskevakos, Shantenu Jha, Oliver Beckstein
2016 conf
SciPy
Richard J. Gowers, Max Linke, Jonathan Barnoud, Tyler J. E. Reddy, Manuel N. Melo, Sean L. Seyler, Jan J. Domanski, David L. Dotson, Sébastien Buchoux, Ian M. Kenney, Oliver Beckstein
2016 J jnl
J. Comput. Aided Mol. Des.
Ian M. Kenney, Oliver Beckstein, Bogdan I. Iorga
2016 conf
SciPy
David L. Dotson, Sean L. Seyler, Max Linke, Richard J. Gowers, Oliver Beckstein
2015 J jnl
PLoS Comput. Biol.
Sean L. Seyler, Avishek Kumar, M. F. Thorpe, Oliver Beckstein
2014 J jnl
J. Comput. Aided Mol. Des.
Oliver Beckstein, Anaïs Fourrier, Bogdan I. Iorga
2012 J jnl
J. Comput. Aided Mol. Des.
Oliver Beckstein, Bogdan I. Iorga
2011 J jnl
J. Comput. Chem.
Juan R. Perilla, Oliver Beckstein, Elizabeth J. Denning, Thomas B. Woolf
2011 J jnl
J. Comput. Chem.
Naveen Michaud-Agrawal, Elizabeth J. Denning, Thomas B. Woolf, Oliver Beckstein
redb/extractors/pe_extractors/pe_signature_old.py
← Index redb/extractors/pe_extractors/pe_signature_old.py python
import inspect
import pefile

from hashlib import md5, sha1, sha256

from asn1crypto import cms, pem, x509, core

from redb.extractors.enum import Tag
from redb.extractors.pe_extractor import PEExtractor
from redb.models.dataclasses import PECertificate, PESigner


class PESignatureExtractor(PEExtractor):
    """
    RFC 3161 - Internet X.509 Public Key Infrastructure Time-Stamp Protocol (TSP)
    Section 2.4.2 defines the TSTInfo structure.
    https://tools.ietf.org/html/rfc3161#section-2.4.2

    Microsoft Authenticode Time Stamping Specification
    https://download.microsoft.com/download/9/c/5/9c5b2167-8017-4bae-9fde-d599bac8184a/Authenticode_PE.docx
    """

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

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

    @staticmethod
    def _extract_certificate_info(cert_data):
        # self.log.debug(inspect.currentframe().f_code.co_name)

        certificate = x509.Certificate.load(cert_data)
        certificate_serial_number = format(certificate.serial_number, "x").upper()
        grouped_serial_number = ":".join(
            [
                certificate_serial_number[i : i + 2]
                for i in range(0, len(certificate_serial_number), 2)
            ]
        )
        return PECertificate(
            _id=format(certificate.serial_number, "x").upper(),
            certificate_serial_number=grouped_serial_number,
            certificate_issuer=certificate.issuer.human_friendly,
            certificate_subject=certificate.subject.human_friendly,
            certificate_valid_from=certificate["tbs_certificate"]["validity"][
                "not_before"
            ].native.strftime("%Y-%m-%d %H:%M:%S"),
            certificate_valid_to=certificate["tbs_certificate"]["validity"][
                "not_after"
            ].native.strftime("%Y-%m-%d %H:%M:%S"),
            certificate_thumbprint=sha1(cert_data).hexdigest().upper(),
            certificate_md5=md5(cert_data).hexdigest().upper(),
            certificate_sha256=sha256(cert_data).hexdigest().upper(),
        )

    @staticmethod
    def _parse_microsoft_time_stamp(ts_token):
        class TSTInfo(core.Sequence):
            _fields = [
                ("version", core.Integer),
                ("policy_id", core.ObjectIdentifier),
                ("message_imprint", core.Sequence),
                ("serial_number", core.Integer),
                ("gen_time", core.GeneralizedTime),
                ("accuracy", core.Sequence, {"optional": True}),
                ("ordering", core.Boolean, {"optional": True}),
                ("nonce", core.Integer, {"optional": True}),
                ("tsa", core.Sequence, {"optional": True}),
                ("extensions", core.Sequence, {"optional": True}),
            ]

        # The content should be SignedData
        signed_data = ts_token["content"]

        # The actual timestamp should be in the encapContentInfo
        encap_content_info = signed_data["encap_content_info"]
        tst_info = TSTInfo.load(encap_content_info["content"])

        # Extract the genTime field from TSTInfo, type(genTime): <class 'datetime.datetime'>
        gen_time = tst_info["gen_time"].native

        return gen_time

    def _extract_signer_info(self, signer):
        self.log.debug(inspect.currentframe().f_code.co_name)
        signing_time = None

        for attr_set in [signer["signed_attrs"], signer["unsigned_attrs"]]:
            if attr_set:
                for attribute in attr_set:
                    attr_type = attribute["type"].dotted
                    if attr_type == "1.2.840.113549.1.9.5":  # signingTime
                        signing_time = attribute["values"][0].native
                        break
                    elif (
                        attr_type == "1.3.6.1.4.1.311.3.2.1"
                        or attr_type == "1.3.6.1.4.1.311.3.3.1"
                    ):  # microsoft_time_stamp_token
                        try:
                            ts_token = attribute["values"][0].native
                            signing_time = self._parse_microsoft_time_stamp(ts_token)
                            self.log.debug(
                                f"Signing Time from Microsoft Time Stamp Token: {signing_time}"
                            )
                        except Exception as e:
                            self.log.error(
                                f"Error parsing Microsoft Time Stamp Token: {e}"
                            )
                            self.log.error("Token structure:", attribute["values"][0])
                    elif attr_type == "1.2.840.113549.1.9.6":  # counterSignature
                        counter_sig_values = attribute["values"]
                        for counter_sig_value in counter_sig_values:
                            try:
                                counter_sig_info = cms.SignerInfo.load(
                                    counter_sig_value.native
                                )
                                cs_signed_attrs = counter_sig_info["signed_attrs"]
                                for cs_attr in cs_signed_attrs:
                                    cs_attr_type = cs_attr["type"].dotted
                                    if (
                                        cs_attr_type == "1.2.840.113549.1.9.5"
                                    ):  # signingTime
                                        signing_time = cs_attr["values"][0].native
                                        self.log.debug(
                                            "Signing Time (from countersignature):",
                                            signing_time,
                                        )
                                        break
                                if signing_time:
                                    break
                            except Exception as e:
                                self.log.error(
                                    f"Error processing countersignature: {e}"
                                )
                    if signing_time:
                        break
            if signing_time:
                break
        signer_serial_number = format(
            signer["sid"].native["serial_number"], "x"
        ).upper()
        grouped_serial_number = " ".join(
            [
                signer_serial_number[i : i + 2]
                for i in range(0, len(signer_serial_number), 2)
            ]
        )
        return PESigner(
            # this is to avoid duplicate _id with the Signer certificate used to sign as they are in the same ES index
            _id=format(signer["sid"].native["serial_number"], "x").upper()
            + signer["digest_algorithm"]["algorithm"].native,
            signer_serial_number=grouped_serial_number,
            signer_digest_algorithm=signer["digest_algorithm"]["algorithm"].native,
            signer_signature_algorithm=signer["signature_algorithm"][
                "algorithm"
            ].native,
            signing_time=(
                signing_time.strftime("%Y-%m-%d %H:%M:%S") if signing_time else None
            ),
            # "countersigners": extract_countersigners(signer), # TODO: Implement this
        )

    def _extract_signature_info(self):
        self.log.debug(inspect.currentframe().f_code.co_name)
        address = self.pe.OPTIONAL_HEADER.DATA_DIRECTORY[
            pefile.DIRECTORY_ENTRY["IMAGE_DIRECTORY_ENTRY_SECURITY"]
        ].VirtualAddress
        size = self.pe.OPTIONAL_HEADER.DATA_DIRECTORY[
            pefile.DIRECTORY_ENTRY["IMAGE_DIRECTORY_ENTRY_SECURITY"]
        ].Size

        addr_8 = address + 8
        signature_data = bytes(
            self.pe.write()[addr_8 : addr_8 + size]  # noqa E203
        )  # Ensure this is a bytes object
        if pem.detect(signature_data):
            signature_data = pem.unarmor(signature_data)

        content_info = cms.ContentInfo.load(signature_data)
        signed_data = content_info["content"]

        certificates = signed_data["certificates"]
        signers = signed_data["signer_infos"]

        certificates_list = []
        for cert in certificates:
            cert_info = self._extract_certificate_info(cert.chosen.dump())
            certificates_list.append(cert_info)

        signer_info_list = []
        for signer in signers:
            signer_info = self._extract_signer_info(signer)
            signer_info_list.append(signer_info)

        return certificates_list, signer_info_list

    def extract(self):
        try:
            self.log.debug(inspect.currentframe().f_code.co_name)
            if self._is_signed():
                certificates_list, signers_list = self._extract_signature_info()
                # self.export_to_elastic([PECodeSigning(certificates_list, signers_list)])
                self.export_to_elastic(certificates_list, Tag.PE_CERTIFICATE.value)
                self.export_to_elastic(signers_list, Tag.PE_SIGNER.value)
            return True
        except Exception as e:
            self.log.error(f"Error extracting PE Signature: {e}")
            return None