Rajesh Chowdhary

13 papers B 1Journal 11Unranked 1
YearRankTypeTitle / Venue / Authors
2013 J jnl
Bioinform.
Manal Kalkatawi, Farania Rangkuti, Michael Schramm, Boris R. Jankovic, Allan Kamau, Rajesh Chowdhary, John A. C. Archer, Vladimir B. Bajic
2013 J jnl
Bioinform.
Arturo Magana-Mora, Haitham Ashoor, Boris R. Jankovic, Allan Kamau, Karim Awara, Rajesh Chowdhary, John A. C. Archer, Vladimir B. Bajic
2013 J jnl
Int. J. Data Min. Bioinform.
Rajesh Chowdhary, Jinfeng Zhang, Sin Lam Tan, Daniel E. Osborne, Vladimir B. Bajic, Jun S. Liu
2012 J jnl
Bioinform.
Manal Kalkatawi, Farania Rangkuti, Michael Schramm, Boris R. Jankovic, Allan Kamau, Rajesh Chowdhary, John A. C. Archer, Vladimir B. Bajic
2012 J jnl
Bioinform.
Sentil Balaji, Charles Mcclendon, Rajesh Chowdhary, Jun S. Liu, Jinfeng Zhang
2012 conf
EMBC
Shreyas Karnik, Sin Lam Tan, Bess Berg, Ingrid Glurich, Jinfeng Zhang, Humberto J. Vidaillet, C. David Page, Rajesh Chowdhary
2010 J jnl
BMC Syst. Biol.
Rajesh Chowdhary, Vladimir B. Bajic, Difeng Dong, Limsoon Wong, Jun S. Liu
2009 J jnl
Bioinform.
Rajesh Chowdhary, Jinfeng Zhang, Jun S. Liu
2006 J jnl
BMC Bioinform.
Manisha Brahmachary, Christian Schönbach, Liang Yang, Enli Huang, Sin Lam Tan, Rajesh Chowdhary, S. P. T. Krishnan, Chin-Yo Lin, David A. Hume, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Vladimir B. Bajic
2006 J jnl
Bioinform.
Rajesh Chowdhary, Sin Lam Tan, R. Ayesha Ali, Brent Boerlage, Limsoon Wong, Vladimir B. Bajic
2006 J jnl
Int. J. Bioinform. Res. Appl.
Rajesh Chowdhary, Limsoon Wong, Vladimir B. Bajic
2005 B conf
APBC
Rajesh Chowdhary, R. Ayesha Ali, Vladimir B. Bajic
2005 J jnl
Bioinform.
Rajesh Chowdhary, R. Ayesha Ali, Werner Albig, Detlef Doenecke, Vladimir B. Bajic
redb/extractors/pe_extractors/pe_extra_findings.py
← Index redb/extractors/pe_extractors/pe_extra_findings.py python
from hashlib import md5, sha1, sha256
import inspect
import pefile
from magika import Magika
import json
from datetime import datetime, timezone
from typing import List, Optional, Any
from asn1crypto import cms, pem, x509, core
from dataclasses import asdict

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


class PEExtraFindings(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_extrafindings"
        self.log.debug(inspect.currentframe().f_code.co_name)
        self.has_binary_overlay = False
        self.has_binary_resource = False
        self.findings = []

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

    """
    The section below triggers in case of a binary which is not signed.
    It trigger the scan for Certificates inside the binary, for example
    inside a resource or an overlay.
    """

    def _scan_for_certificates(self):
        """
        Comprehensive scan for certificate data in PE file.
        Returns list of tuples (location_description, certificate_data)
        """
        self.log.debug(inspect.currentframe().f_code.co_name)

        # 1. Scan resources for embedded PE files
        self._scan_resources_for_certificates()

        # 3. Scan overlay
        overlay_data = self.pe.get_overlay()
        if overlay_data:
            self._scan_overlay_for_certificates(overlay_data)


    def _extract_certificate_info(self, 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(
            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_algorithm=None,
        )

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

        addr_8 = address + 8
        signature_data = bytes(
            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"]

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

        return certificates_list

    def _is_signed(self, pedata):
        address = pedata.OPTIONAL_HEADER.DATA_DIRECTORY[
            pefile.DIRECTORY_ENTRY["IMAGE_DIRECTORY_ENTRY_SECURITY"]
        ].VirtualAddress
        if address == 0:
            return False
        return True

    def _scan_resources_for_certificates(self):
        """Scan resources for embedded PE files and their certificates"""
        self.log.debug(inspect.currentframe().f_code.co_name)

        try:
            if hasattr(self.pe, "DIRECTORY_ENTRY_RESOURCE"):
                for entry in self.pe.DIRECTORY_ENTRY_RESOURCE.entries:
                    for resource in self._get_resource_data(entry):
                        # Check if resource data might be a PE file
                        resource_magika = Magika().identify_bytes(resource).output.label
                        if resource.startswith(b"MZ") or resource_magika == "pebin":
                            try:
                                embedded_pe = pefile.PE(data=resource)
                                if self._is_signed(embedded_pe):
                                    cert_data = self._extract_standard_certificates(
                                        embedded_pe
                                    )
                                    if cert_data:
                                        # certificates.append(
                                        #     (f"Resource_{entry.id}", cert_data)
                                        # )
                                        self.findings.append(
                                            PEExtraFinding(
                                                context=f"Resource ({sha256(resource).hexdigest()}) is a PE file. Found Code Signing Certificates information inside.",
                                                finding=cert_data,
                                            )
                                        )
                            except Exception as e:
                                self.log.warning(
                                    f"Resource {sha256(resource).hexdigest()} is not a valid PE: {e}"
                                )

                        # Direct certificate pattern matching in resource
                        cert_data = self._find_certificate_patterns(resource)
                        if cert_data:
                            # certificates.append((f"Resource_{entry.id}", cert_data))
                            self.findings.append(
                                PEExtraFinding(
                                    context=f"Resource ({sha256(resource).hexdigest()}) is a PE file.\
                                    Found Code Signing Certificates information inside.",
                                    finding=cert_data,
                                )
                            )

        except Exception as e:
            self.log.error(f"Failed to scan resources: {e}")


    def _scan_overlay_for_certificates(self, overlay_data) -> List[bytes]:
        """Scan PE overlay for certificate data"""
        self.log.debug(inspect.currentframe().f_code.co_name)
        try:
            # Check if overlay is a PE file
            overlay_magika = Magika().identify_bytes(overlay_data).output.ct_label
            if overlay_data.startswith(b"MZ") or overlay_magika == "pebin":
                try:
                    overlay_pe = pefile.PE(data=overlay_data)
                    if self._is_signed(overlay_pe):
                        cert_data = self._extract_standard_certificates(overlay_data)
                        if cert_data:
                            self.findings.append(
                                PEExtraFinding(
                                    context=f"Overlay data ({sha256(overlay_data).hexdigest()}) is a PE file.\
                                    Found Code Signing Certificates information inside.",
                                    finding=cert_data,
                                )
                            )
                except Exception as e:
                    self.log.warning(f"Error looking for certificates in Overlay: {e}")
                    pass

            # Direct certificate pattern matching in overlay
            cert_data = self._find_certificate_patterns(overlay_data)
            if cert_data:
                self.findings.append(
                    PEExtraFinding(
                        context=f"Overlay data ({sha256(overlay_data).hexdigest()}) is a PE file.\
                        Found Code Signing Certificates information inside.",
                        finding=cert_data,
                    )
                )
        except Exception as e:
            self.log.error(f"Failed to scan overlay: {e}")


    def _get_resource_data(self, entry) -> List[bytes]:
        """Recursively get resource data"""
        resources = []
        try:
            if hasattr(entry, "directory"):
                for subentry in entry.directory.entries:
                    resources.extend(self._get_resource_data(subentry))
            else:
                data = self.pe.get_data(
                    entry.data.struct.OffsetToData, entry.data.struct.Size
                )
                resources.append(data)
        except Exception as e:
            self.log.error(f"Failed to get resource data: {e}")
        return resources

    def _find_certificate_patterns(self, data: bytes) -> Optional[bytes]:
        """Find certificate patterns in binary data"""
        # PKCS#7 SignedData OID pattern
        PKCS7_PATTERN = b"\x06\x09\x2A\x86\x48\x86\xF7\x0D\x01\x07\x02"

        try:
            idx = data.find(PKCS7_PATTERN)
            if idx != -1:
                # Search backwards for ASN.1 sequence marker
                for i in range(idx, max(0, idx - 50), -1):
                    if data[i] == 0x30:  # ASN.1 SEQUENCE
                        try:
                            # Try to parse as X.509 certificate
                            cert = x509.load_der_x509_certificate(
                                data[i:], default_backend()
                            )
                            return data[i:]
                        except Exception:
                            continue
        except Exception as e:
            self.log.error(f"Failed to find certificate patterns: {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.findings
        elif exporter_type == "ClickHouseExporter":
            current_time = datetime.now(timezone.utc)
            
            data = [
                [
                    self.sha256,
                    self.md5,
                    self.sha1,
                    finding.context,
                    [asdict(cert) for cert in finding.finding] if finding.finding else None,
                    current_time
                ]
                for finding in self.findings
            ]
            
            column_names = [
                'sha256', 'md5', 'sha1', 'context', 'finding', 'analysis_date'
            ]
            
            if not data:
                return None

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

            return (data, column_names, column_type_names)

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

    def extract(self):
        try:
            self.log.debug(inspect.currentframe().f_code.co_name)
            self._scan_for_certificates()
            if len(self.findings) > 0:
                return self.findings
            return None
        except Exception as e:
            self.log.error(f"Error extracting PE Extras: {e}")
            return None