Karsten Suhre

25 papers Misc 1Journal 22Unranked 2
YearRankTypeTitle / Venue / Authors
2022 J jnl
Bioinform.
Mustafa Buyukozkan, Karsten Suhre, Jan Krumsiek
2022 J jnl
Briefings Bioinform.
Siyu Han, Jialing Huang, Francesco Foppiano, Cornelia Prehn, Jerzy Adamski, Karsten Suhre, Ying Li, Giuseppe Matullo, Freimut Schliess, Christian Gieger, Annette Peters, Rui Wang-Sattler
2022 J jnl
Bioinform.
Kelsey Chetnik, Elisa Benedetti, Daniel P. Gomari, Annalise Schweickart, Richa Batra, Mustafa Buyukozkan, Zeyu Wang, Matthias Arnold, Jonas Zierer, Karsten Suhre, Jan Krumsiek
2021 J jnl
Briefings Bioinform.
Heike Deutelmoser, Dominique Scherer, Hermann Brenner, Melanie Waldenberger, Karsten Suhre, Gabi Kastenmüller, Justo Lorenzo Bermejo
2019 J jnl
Bioinform.
Kieu Trinh Do, David J. N. P. Rasp, Gabi Kastenmüller, Karsten Suhre, Jan Krumsiek
2018 J jnl
Nat.
Benjamin B. Sun, Joseph C. Maranville, James E. Peters, David Stacey, James R. Staley, James A. Blackshaw, Stephen Burgess, Tao Jiang, Ellie Paige, Praveen Surendran, Clare Oliver-Williams, Mihir A. Kamat, Bram P. Prins, Sheri K. Wilcox, Erik S. Zimmerman, An Chi, Narinder Bansal, Sarah L. Spain, Angela M. Wood, Nicholas W. Morrell, John R. Bradley, Nebojsa Janjic, David J. Roberts, Willem H. Ouwehand, John A. Todd, Nicole Soranzo, Karsten Suhre, Dirk S. Paul, Caroline S. Fox, Robert M. Plenge, John Danesh, Heiko Runz, Adam S. Butterworth
2017 J jnl
BMC Bioinform.
Sophie Molnos, Clemens Baumbach, Simone Wahl, Martina Müller-Nurasyid, Konstantin Strauch, Rui Wang-Sattler, Melanie Waldenberger, Thomas Meitinger, Jerzy Adamski, Gabi Kastenmüller, Karsten Suhre, Annette Peters, Harald Grallert, Fabian J. Theis, Christian Gieger
2016 J jnl
J. Comput. Sci.
Gaurav Thareja, Ziad Kronfol, Karsten Suhre, Pankaj Kumar
2014 J jnl
BMC Bioinform.
Simone Wahl, Nora Fenske, Sonja Zeilinger, Karsten Suhre, Christian Gieger, Melanie Waldenberger, Harald Grallert, Matthias Schmid
2013 Misc conf
ICCS
Zeinab Atieh, Karsten Suhre, Halima Bensmail
2012 J jnl
BMC Bioinform.
Ann-Kristin Petersen, Jan Krumsiek, Brigitte Wägele, Fabian J. Theis, Heinz-Erich Wichmann, Christian Gieger, Karsten Suhre
2011 J jnl
BMC Syst. Biol.
Jan Krumsiek, Karsten Suhre, Thomas Illig, Jerzy Adamski, Fabian J. Theis
2011 J jnl
Nucleic Acids Res.
Hans-Werner Mewes, Andreas Ruepp, Fabian J. Theis, Thomas Rattei, Mathias C. Walter, Dmitrij Frishman, Karsten Suhre, Manuel Spannagl, Klaus F. X. Mayer, Volker Stümpflen, Alexey V. Antonov
2008 J jnl
Nucleic Acids Res.
Karsten Suhre, Philippe Schmitt-Kopplin
2006 J jnl
BMC Bioinform.
Ghislain Bidaut, Karsten Suhre, Jean-Michel Claverie, Michael F. Ochs
2006 J jnl
J. Chem. Inf. Model.
Stéphane Betzi, Karsten Suhre, Bernard Chétrit, Françoise Guerlesquin, Xavier Morelli
2005 J jnl
BMC Bioinform.
François Enault, Karsten Suhre, Jean-Michel Claverie
2004 J jnl
Nucleic Acids Res.
Olivier Poirot, Karsten Suhre, Chantal Abergel, Eamonn O'Toole, Cédric Notredame
2004 J jnl
Nucleic Acids Res.
Jean-Baptiste Claude, Karsten Suhre, Cédric Notredame, Jean-Michel Claverie, Chantal Abergel
2004 J jnl
Nucleic Acids Res.
Karsten Suhre, Yves-Henri Sanejouand
2004 J jnl
Nucleic Acids Res.
Karsten Suhre, Jean-Michel Claverie
2004 J jnl
Nucleic Acids Res.
François Enault, Karsten Suhre, Olivier Poirot, Chantal Abergel, Jean-Michel Claverie
2003 conf
CSB
Ghislain Bidaut, Karsten Suhre, Jean-Michel Claverie, Michael F. Ochs
2003 conf
ISMB (Supplement of Bioinformatics)
François Enault, Karsten Suhre, Chantal Abergel, Olivier Poirot, Jean-Michel Claverie
2003 J jnl
Nucleic Acids Res.
François Enault, Karsten Suhre, Olivier Poirot, Chantal Abergel, Jean-Michel Claverie
redb/extractors/js_extractors/js_strings.py
← Index redb/extractors/js_extractors/js_strings.py python
import base64
import bisect
import inspect
import re
from datetime import datetime, timezone
from typing import Any

from redb.extractors.enum import Tag
from redb.extractors.js_extractor import JSExtractor
from redb.extractors.js_extractors.js_patterns import STRING_PATTERNS, line_offsets

# Local aliases for the compiled patterns this extractor uses. Defined and
# compiled exactly once in js_patterns.STRING_PATTERNS.
_HEX_STRING_RE = STRING_PATTERNS["hex_escape_seq"]
_UNICODE_STRING_RE = STRING_PATTERNS["unicode_escape_seq"]
_CHARCODE_RE = STRING_PATTERNS["charcode_call"]
_BASE64_STRING_RE = STRING_PATTERNS["base64_quoted"]
_CONCAT_STRING_RE = STRING_PATTERNS["concat_chain"]

# Tokeniser used inside _reconstruct_concat to pull each quoted part out of a
# matched concat chain. Compiled once at module load (was recompiled on every
# concat match before).
_CONCAT_TOKEN_RE = re.compile(r'["\']([^"\']*)["\']')


class JSStringsExtractor(JSExtractor):

    def __init__(
        self, filepath, log, exporters=None, index_prefix=None,
        known_benign=False, known_malicious=False, source=None, context=None,
    ):
        super().__init__(
            filepath, log, exporters, index_prefix,
            known_benign, known_malicious, source, context=context,
        )
        self.string_findings = None
        self.log.debug(inspect.currentframe().f_code.co_name)

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

    def _decode_hex_string(self, hex_str):
        """Decode \\x41\\x42 style hex strings."""
        try:
            # Remove \\x prefix and decode
            clean = hex_str.replace('\\x', '')
            return bytes.fromhex(clean).decode('utf-8', errors='replace')
        except Exception:
            return None

    def _decode_unicode_string(self, uni_str):
        """Decode \\u0041\\u0042 style unicode strings."""
        try:
            return uni_str.encode('utf-8').decode('unicode_escape')
        except Exception:
            return None

    def _decode_charcode(self, charcode_str):
        """Decode String.fromCharCode(72, 101, 108, ...) sequences."""
        try:
            codes = [int(c.strip()) for c in charcode_str.split(',') if c.strip().isdigit()]
            return ''.join(chr(c) for c in codes if 0 <= c <= 0x10FFFF)
        except Exception:
            return None

    def _decode_base64(self, b64_str):
        """Attempt to decode base64 string."""
        try:
            decoded = base64.b64decode(b64_str)
            # Check if result is printable text
            text = decoded.decode('utf-8', errors='strict')
            # Only return if it looks like text (>80% printable)
            printable = sum(1 for c in text if c.isprintable() or c in '\n\r\t')
            if printable / len(text) > 0.8:
                return text
        except Exception:
            pass
        return None

    def _reconstruct_concat(self, concat_match):
        """Reconstruct concatenated string parts."""
        try:
            parts = _CONCAT_TOKEN_RE.findall(concat_match)
            return ''.join(parts)
        except Exception:
            return None

    def _find_line_number(self, match_start):
        """1-indexed line number for `match_start`, looked up in O(log L) via
        bisect over `self._line_offsets` (built once per extract() call).

        Replaces the historical `self.js_source[:match_start].count('\\n') + 1`
        which was O(N) per call and quadratic across all matches in a sample.
        """
        return bisect.bisect_right(self._line_offsets, match_start)

    def _scan_text(self, text):
        """Run every encoded-string pattern over `text` and return a list of
        finding dicts. Stateless apart from the per-call `_line_offsets` cache,
        which `_find_line_number` reads — callers must reset it before invoking
        this so line numbers reference the text being scanned, not the previous
        one.
        """
        findings = []

        # Hex-encoded strings
        for m in _HEX_STRING_RE.finditer(text):
            raw = m.group()
            decoded = self._decode_hex_string(raw)
            if decoded and len(decoded) >= 4:
                findings.append({
                    'string': decoded[:4000],
                    'string_raw': raw[:4000],
                    'string_encoding': 'hex',
                    'string_offset': self._find_line_number(m.start()),
                    'string_length': len(decoded),
                    'string_raw_length': len(raw),
                    'string_entropy': self._calculate_text_entropy(decoded),
                })

        # Unicode-encoded strings
        for m in _UNICODE_STRING_RE.finditer(text):
            raw = m.group()
            decoded = self._decode_unicode_string(raw)
            if decoded and len(decoded) >= 3:
                findings.append({
                    'string': decoded[:4000],
                    'string_raw': raw[:4000],
                    'string_encoding': 'unicode',
                    'string_offset': self._find_line_number(m.start()),
                    'string_length': len(decoded),
                    'string_raw_length': len(raw),
                    'string_entropy': self._calculate_text_entropy(decoded),
                })

        # String.fromCharCode sequences
        for m in _CHARCODE_RE.finditer(text):
            raw = m.group()
            decoded = self._decode_charcode(m.group(1))
            if decoded and len(decoded) >= 4:
                findings.append({
                    'string': decoded[:4000],
                    'string_raw': raw[:4000],
                    'string_encoding': 'charcode',
                    'string_offset': self._find_line_number(m.start()),
                    'string_length': len(decoded),
                    'string_raw_length': len(raw),
                    'string_entropy': self._calculate_text_entropy(decoded),
                })

        # Base64-encoded strings
        for m in _BASE64_STRING_RE.finditer(text):
            raw = m.group(0)
            b64_val = m.group(1)
            decoded = self._decode_base64(b64_val)
            if decoded and len(decoded) >= 10:
                findings.append({
                    'string': decoded[:4000],
                    'string_raw': raw[:4000],
                    'string_encoding': 'base64',
                    'string_offset': self._find_line_number(m.start()),
                    'string_length': len(decoded),
                    'string_raw_length': len(raw),
                    'string_entropy': self._calculate_text_entropy(decoded),
                })

        # Concatenated strings (reassembled)
        for m in _CONCAT_STRING_RE.finditer(text):
            raw = m.group()
            reconstructed = self._reconstruct_concat(raw)
            if reconstructed and len(reconstructed) >= 20:
                findings.append({
                    'string': reconstructed[:4000],
                    'string_raw': raw[:4000],
                    'string_encoding': 'concat',
                    'string_offset': self._find_line_number(m.start()),
                    'string_length': len(reconstructed),
                    'string_raw_length': len(raw),
                    'string_entropy': self._calculate_text_entropy(reconstructed),
                })

        return findings

    def extract(self):
        src = self.js_source
        if not src:
            return None

        # Pass 1: raw source. _line_offsets is keyed off whichever text is
        # currently being scanned so _find_line_number resolves to that text.
        self._line_offsets = line_offsets(src)
        findings = self._scan_text(src)

        # Pass 2: deobfuscated text, when the deobfuscator produced something
        # meaningfully different. Same patterns, but a different surface — for
        # samples where the encoded payload is hidden behind an outer wrapper
        # (e.g. array.join() + eval in Vjw0rm/WSH-RAT) only this pass yields
        # any rows at all.
        deobf_text, _ = self._context.deobfuscated
        if deobf_text and deobf_text != src:
            self._line_offsets = line_offsets(deobf_text)
            findings.extend(self._scan_text(deobf_text))

        if not findings:
            return None

        # Deduplicate by decoded string value (raw pass wins on collision: it
        # comes first in `findings`). A string that surfaces only in the
        # deobfuscated text still gets persisted, which is the whole point of
        # the second pass.
        seen_values = set()
        deduped = []
        for f in findings:
            val_key = f['string'][:100]
            if val_key not in seen_values:
                seen_values.add(val_key)
                deduped.append(f)

        self.string_findings = deduped[:500]  # Limit per file
        # Publish to the shared context so post-loop consumers (notably the IOC
        # plumbing in workers.py) can scrape the decoded strings without
        # holding a reference to this extractor instance.
        self._context.decoded_strings = self.string_findings
        return self.string_findings

    def prepare_export_data(self, exporter_type: str) -> Any:
        if exporter_type == "ClickHouseExporter":
            if not self.string_findings:
                return None

            data = []
            for f in self.string_findings:
                data.append([
                    self.sha256,
                    f['string'],
                    f['string_raw'],
                    f['string_encoding'],
                    f['string_offset'],
                    f['string_length'],
                    f['string_raw_length'],
                    f['string_entropy'],
                ])

            column_names = [
                "sha256",
                "string",
                "string_raw",
                "string_encoding",
                "string_offset",
                "string_length",
                "string_raw_length",
                "string_entropy",
            ]

            column_type_names = [
                "FixedString(64)",
                "String",
                "String",
                "LowCardinality(String)",
                "UInt64",
                "UInt32",
                "UInt32",
                "Float32",
            ]

            return (data, column_names, column_type_names)

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