Neil D. Rawlings

22 papers Journal 22
YearRankTypeTitle / Venue / Authors
2019 J jnl
Nucleic Acids Res.
Lorna J. Richardson, Neil D. Rawlings, Gustavo A. Salazar, Alexandre Almeida, David Haft, Gregory Ducq, Granger G. Sutton, Robert D. Finn
2019 J jnl
Nucleic Acids Res.
Alex L. Mitchell, Teresa K. Attwood, Patricia C. Babbitt, Matthias Blum, Peer Bork, Alan J. Bridge, Shoshana D. Brown, Hsin-Yu Chang, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft, Hongzhan Huang, Ivica Letunic, Rodrigo Lopez, Aurelien Luciani, Fábio Madeira, Aron Marchler-Bauer, Huaiyu Mi, Darren A. Natale, Marco Necci, Gift Nuka, Christine A. Orengo, Arun Prasad Pandurangan, Typhaine Paysan-Lafosse, Sebastien Pesseat, Simon C. Potter, Matloob Qureshi, Neil D. Rawlings, Nicole Redaschi, Lorna J. Richardson, Catherine Rivoire, Gustavo A. Salazar, Amaia Sangrador-Vegas, Christian J. A. Sigrist, Ian Sillitoe, Granger G. Sutton, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Siew-Yit Yong, Robert D. Finn
2019 J jnl
Briefings Bioinform.
Fuyi Li, Yanan Wang, Chen Li, Tatiana T. Marquez-Lago, André Leier, Neil D. Rawlings, Gholamreza Haffari, Jerico Nico De Leon Revote, Tatsuya Akutsu, Kuo-Chen Chou, Anthony W. Purcell, Robert N. Pike, Geoffrey I. Webb, Alexander Ian Smith, Trevor Lithgow, Roger J. Daly, James C. Whisstock, Jiangning Song
2019 J jnl
Briefings Bioinform.
Jiangning Song, Yanan Wang, Fuyi Li, Tatsuya Akutsu, Neil D. Rawlings, Geoffrey I. Webb, Kuo-Chen Chou
2018 J jnl
Nucleic Acids Res.
Neil D. Rawlings, Alan J. Barrett, Paul D. Thomas, Xiaosong Huang, Alex Bateman, Robert D. Finn
2017 J jnl
Nucleic Acids Res.
Robert D. Finn, Teresa K. Attwood, Patricia C. Babbitt, Alex Bateman, Peer Bork, Alan J. Bridge, Hsin-Yu Chang, Zsuzsanna Dosztányi, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft, Gemma L. Holliday, Hongzhan Huang, Xiaosong Huang, Ivica Letunic, Rodrigo Lopez, Shennan Lu, Aron Marchler-Bauer, Huaiyu Mi, Jaina Mistry, Darren A. Natale, Marco Necci, Gift Nuka, Christine A. Orengo, Young Mi Park, Sebastien Pesseat, Damiano Piovesan, Simon C. Potter, Neil D. Rawlings, Nicole Redaschi, Lorna J. Richardson, Catherine Rivoire, Amaia Sangrador-Vegas, Christian J. A. Sigrist, Ian Sillitoe, Ben Smithers, Silvano Squizzato, Granger G. Sutton, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Ioannis Xenarios, Lai-Su L. Yeh, Siew-Yit Yong, Alex L. Mitchell
2016 J jnl
Nucleic Acids Res.
Neil D. Rawlings, Alan J. Barrett, Robert D. Finn
2015 J jnl
Database J. Biol. Databases Curation
Patricia C. Babbitt, Pantelis G. Bagos, Amos Bairoch, Alex Bateman, Arnaud Chatonnet, Mark Jinan Chen, David J. Craik, Robert D. Finn, David E. Gloriam, Daniel H. Haft, Bernard Henrissat, Gemma L. Holliday, Vignir Ísberg, Quentin Kaas, David Landsman, Nicolas Lenfant, Gerard Manning, Nozomi Nagano, Narayanaswamy Srinivasan, Claire O'Donovan, Kim D. Pruitt, Ramanathan Sowdhamini, Neil D. Rawlings, Milton H. Saier Jr., Joanna L. Sharman, Michael Spedding, Konstantinos D. Tsirigos, Åke Västermark, Gerrit Vriend
2014 J jnl
BMC Bioinform.
Christine B. Trame, Yuanyuan Chang, Herbert L. Axelrod, Ruth Y. Eberhardt, Penelope Coggill, Marco Punta, Neil D. Rawlings
2014 J jnl
BMC Bioinform.
Debanu Das, Alexey G. Murzin, Neil D. Rawlings, Robert D. Finn, Penelope Coggill, Alex Bateman, Adam Godzik, L. Aravind
2013 J jnl
Database J. Biol. Databases Curation
Neil D. Rawlings
2013 J jnl
BMC Bioinform.
William C. Hwang, Constantina Bakolitsa, Marco Punta, Penelope Coggill, Alex Bateman, Herbert L. Axelrod, Neil D. Rawlings, Mayya Sedova, Scott N. Peterson, Ruth Y. Eberhardt, L. Aravind, Jaime Pascual, Adam Godzik
2010 J jnl
Nucleic Acids Res.
Neil D. Rawlings, Alan J. Barrett, Alex Bateman
2009 J jnl
Database J. Biol. Databases Curation
Neil D. Rawlings
2008 J jnl
Nucleic Acids Res.
Neil D. Rawlings, Fraser R. Morton, Chai Yin Kok, Jun Kong, Alan J. Barrett
2006 J jnl
Nucleic Acids Res.
Neil D. Rawlings, Fraser R. Morton, Alan J. Barrett
2004 J jnl
Nucleic Acids Res.
Neil D. Rawlings, Dominic P. Tolle, Alan J. Barrett
2003 J jnl
BMC Bioinform.
David J. Studholme, Neil D. Rawlings, Alan J. Barrett, Alex Bateman
2002 J jnl
Nucleic Acids Res.
Neil D. Rawlings, Emmet A. O'Brien, Alan J. Barrett
2000 J jnl
Nucleic Acids Res.
Neil D. Rawlings, Alan J. Barrett
1999 J jnl
Nucleic Acids Res.
Neil D. Rawlings, Alan J. Barrett
1990 J jnl
Comput. Appl. Biosci.
Neil D. Rawlings, Alan J. Barrett
redb/extractors/js_extractors/js_deobfuscator.py
← Index redb/extractors/js_extractors/js_deobfuscator.py python
"""Subprocess-driven JavaScript deobfuscator with jsbeautifier fallback.

Owns the heavy lifting that was previously embedded inside
`JSDeobfuscationExtractor` (`_run_deobfuscator` + `_try_jsbeautifier`). Exposed
as a single module-level entry point `deobfuscate(source, log)` so it can be
called from `JSContext.deobfuscated` (cached per sample) without dragging
extractor state through the call.

Configuration (env vars):
    JS_DEOBFUSCATOR_PATH    Path or name of the external tool (default: webcrack).
    JS_DEOBFUSCATE_TIMEOUT  Seconds before the external tool is killed
                            (process-group SIGTERM, then SIGKILL). Default: 60.

If the external tool produces non-empty output and exits 0, that wins. Otherwise
the source is run through jsbeautifier (which only normalises formatting, but
already exposes strings hidden by minification). If neither path produces
output, returns (None, None).

`FileNotFoundError` for the external tool is treated as routine — the analysis
server is either provisioned with the tool or it isn't — and demoted to a
debug-level log.
"""

import os
import signal
import subprocess
import tempfile
from typing import Optional, Tuple

DEFAULT_DEOBFUSCATOR = "webcrack"
DEFAULT_TIMEOUT_SECS = 60


def _run_external(
    source: str, deobfuscator_path: str, timeout: int, log
) -> Tuple[Optional[str], int]:
    """Run the configured external deobfuscator over `source` and capture stdout.

    Returns (text, returncode). `text` is `None` and `returncode` is `-1` when
    the binary is missing, the run timed out, or any other unexpected failure
    occurred. Missing-binary is logged at debug; timeouts and unexpected errors
    surface at warning/error.
    """
    try:
        with tempfile.NamedTemporaryFile(
            suffix=".js", mode="w", delete=False, encoding="utf-8"
        ) as tmp:
            tmp.write(source)
            tmp_path = tmp.name

        try:
            process = subprocess.Popen(
                [deobfuscator_path, tmp_path],
                stdout=subprocess.PIPE,
                stderr=subprocess.PIPE,
                preexec_fn=os.setsid,
            )

            try:
                stdout, _ = process.communicate(timeout=timeout)
                return stdout.decode("utf-8", errors="replace"), process.returncode
            except subprocess.TimeoutExpired:
                # Kill the entire process group so spawned helpers (e.g. node
                # subprocesses webcrack itself launches) get cleaned up too.
                try:
                    os.killpg(os.getpgid(process.pid), signal.SIGTERM)
                    process.wait(timeout=5)
                except Exception:
                    try:
                        os.killpg(os.getpgid(process.pid), signal.SIGKILL)
                    except Exception:
                        pass
                log.warning(f"Deobfuscation timed out after {timeout}s")
                return None, -1
        finally:
            try:
                os.unlink(tmp_path)
            except Exception:
                pass
    except FileNotFoundError:
        log.debug(f"Deobfuscator binary not found at {deobfuscator_path}")
        return None, -1
    except Exception as e:
        log.error(f"Error running deobfuscator: {e}")
        return None, -1


def _try_jsbeautifier(source: str, log) -> Tuple[Optional[str], Optional[str]]:
    """Fallback path: format the source with jsbeautifier. Returns
    `(text, "jsbeautifier")` or `(None, None)` if jsbeautifier isn't installed
    or the call raised."""
    try:
        import jsbeautifier
        opts = jsbeautifier.default_options()
        opts.indent_size = 2
        return jsbeautifier.beautify(source, opts), "jsbeautifier"
    except ImportError:
        log.debug("jsbeautifier not available")
        return None, None
    except Exception as e:
        log.warning(f"jsbeautifier failed: {e}")
        return None, None


def deobfuscate(source: str, log) -> Tuple[Optional[str], Optional[str]]:
    """Run the configured external deobfuscator, falling back to jsbeautifier.

    Returns `(text, normalizer_used)` on success, or `(None, None)` when neither
    path produced non-empty output. `normalizer_used` is the basename of the
    external tool (e.g. `"webcrack"`) or the literal `"jsbeautifier"`.
    """
    if not source:
        return None, None

    deobfuscator_path = os.getenv("JS_DEOBFUSCATOR_PATH", DEFAULT_DEOBFUSCATOR)
    timeout = int(os.getenv("JS_DEOBFUSCATE_TIMEOUT", str(DEFAULT_TIMEOUT_SECS)))

    text, returncode = _run_external(source, deobfuscator_path, timeout, log)
    if text and returncode == 0 and text.strip():
        return text, os.path.basename(deobfuscator_path)

    return _try_jsbeautifier(source, log)