Olivier Sallou

12 papers C 1Journal 10Unranked 1
YearRankTypeTitle / Venue / Authors
2018 J jnl
F1000Research
Björn A. Grüning, Olivier Sallou, Pablo A. Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes L. Röst, Timo Sachsenberg, Brian O'Connor, Fábio Madeira, Victoria Dominguez Del Angel, Michael R. Crusoe, Susheel Varma, Daniel J. Blankenberg, Rafael C. Jiménez, Daniel Blankenberg, Yasset Pérez-Riverol
2018 J jnl
Bioinform.
Thomas A. Darde, Pierre Gaudriault, Rémi Beranger, Clément Lancien, Annaëlle Caillarec-Joly, Olivier Sallou, Nathalie Bonvallot, Cécile Chevrier, Séverine Mazaud-Guittot, Bernard Jégou, Olivier Collin, Emmanuelle Becker, Antoine D. Rolland, Frédéric Chalmel
2016 J jnl
Database J. Biol. Databases Curation
Olivier Sallou, Paula Duek Roggli, Thomas A. Darde, Olivier Collin, Lydie Lane, Frédéric Chalmel
2015 J jnl
F1000Research
François Moreews, Olivier Sallou, Hervé Ménager, Yvan Le Bras, Cyril Monjeaud, Christophe Blanchet, Olivier Collin
2015 C conf
CLUSTER
Olivier Sallou, Cyril Monjeaud
2015 J jnl
Nucleic Acids Res.
Damian Smedley, Syed Haider, Steffen Durinck, Luca Pandini, Paolo Provero, James E. Allen, Olivier Arnaiz, Mohammad Hamza Awedh, Richard A. Baldock, Giulia Barbiera, Philippe Bardou, Tim Beck, Andrew Blake, Merideth Bonierbale, Anthony J. Brookes, Gabriele Bucci, Iwan Buetti, Sarah W. Burge, Cédric Cabau, Joseph W. Carlson, Claude Chelala, Charalambos Chrysostomou, Davide Cittaro, Olivier Collin, Raul Cordova, Rosalind J. Cutts, Erik Dassi, Alex Di Génova, Anis Djari, Anthony Esposito, Heather Estrella, Eduardo Eyras, Julio Fernandez-Banet, Simon A. Forbes, Robert C. Free, Takatomo Fujisawa, Emanuela Gadaleta, Jose M. Garcia-Manteiga, David M. Goodstein, Kristian A. Gray, José Afonso Guerra-Assunção, Bernard Haggarty, Dongjin Han, Byungwoo Han, Todd W. Harris, Jayson Harshbarger, Robert K. Hastings, Richard D. Hayes, Claire Hoede, Shen Hu, Zhi-Liang Hu, Lucie N. Hutchins, Zhengyan Kan, Hideya Kawaji, Aminah-Olivia Keliet, Arnaud Kerhornou, Sunghoon Kim, Rhoda Kinsella, Christophe Klopp, Lei Kong, Daniel Lawson, Dejan Lazarevic, Ji-Hyun Lee, Thomas Letellier, Chuan-Yun Li, Pietro Liò, Chu-Jun Liu, Jie Luo, Alejandro Maass, Jérôme Mariette, Thomas Maurel, Stefania Merella, Azza Mostafa Mohamed, François Moreews, Nabihoudine Ibouniyamine, Nelson Ndegwa, Céline Noirot, Christian Perez-Llamas, Michael Primig, Alessandro Quattrone, Hadi Quesneville, Davide Rambaldi, James M. Reecy, Michela Riba, Steven Rosanoff, Amna Ali Saddiq, Elisa Salas, Olivier Sallou, Rebecca Shepherd, Reinhard Simon, Linda Sperling, William Spooner, Daniel M. Staines, Delphine Steinbach, Kevin R. Stone, Elia Stupka, Jon W. Teague, Abu Z. Dayem Ullah, Jun Wang, Doreen Ware, Marie Wong-Erasmus, Ken Youens-Clark, Amonida Zadissa, Shi-Jian Zhang, Arek Kasprzyk
2015 J jnl
Nucleic Acids Res.
Thomas A. Darde, Olivier Sallou, Emmanuelle Becker, Bertrand Evrard, Cyril Monjeaud, Yvan Le Bras, Bernard Jégou, Olivier Collin, Antoine D. Rolland, Frédéric Chalmel
2014 J jnl
BMC Bioinform.
Steffen Möller, Enis Afgan, Michael Banck, Raoul Jean Pierre Bonnal, Timothy Booth, John Chilton, Peter J. A. Cock, Markus Gumbel, Nomi L. Harris, Richard C. G. Holland, Matús Kalas, László Kaján, Eri Kibukawa, David R. Powell, Pjotr Prins, Jacqueline Quinn, Olivier Sallou, Francesco Strozzi, Torsten Seemann, Clare Sloggett, Stian Soiland-Reyes, William Spooner, Sascha Steinbiss, Andreas Tille, Anthony J. Travis, Roman Guimera, Toshiaki Katayama, Brad A. Chapman
2014 conf
PRIB
Catherine Belleannée, Olivier Sallou, Jacques Nicolas
2012 J jnl
Nucleic Acids Res.
Ramona Britto, Olivier Sallou, Olivier Collin, Grégoire Michaux, Michael Primig, Frédéric Chalmel
2012 J jnl
BMC Bioinform.
Olivier Sallou, Anthony Bretaudeau, Aurelien Roult
2011 J jnl
Nucleic Acids Res.
Frédéric Lecerf, Anthony Bretaudeau, Olivier Sallou, Colette Désert, Yuna Blum, Sandrine Lagarrigue, Oliver Demeure
redb/extractors/js_extractors/js_xray.py
← Index redb/extractors/js_extractors/js_xray.py python
"""Subprocess wrapper for the bundled js-x-ray Node bridge.

Mirrors `js_deobfuscator.py`: shell out to a Node script with a per-sample
timeout, kill the process group on hang, demote `FileNotFoundError` to debug
(missing tool is routine — the host either has Node + the bundled package
installed or it doesn't), and return a structured result on success.

The bridge lives at `redb/extractors/js_extractors/scripts/js-xray-runner.js`.
Operators install the JS dependency once with `npm install` in that directory
(or override the path with `JS_XRAY_RUNNER_PATH`).

Configuration (env vars):
    JS_XRAY_RUNNER_PATH   Path to the Node bridge script (default: bundled).
    JS_XRAY_TIMEOUT       Seconds before the subprocess is killed. Default: 30.

`run(source, log)` returns `XRayResult(obfuscator, warnings)` on a successful
analysis, or `XRayResult(None, [])` for any non-success path (binary missing,
timeout, parse failure, etc.). The two unsuccessful states are
indistinguishable to the caller on purpose — they all collapse to "no
js-x-ray verdict, fall back to heuristic".
"""

from __future__ import annotations

import json
import os
import signal
import subprocess
import tempfile
from dataclasses import dataclass, field
from typing import List, Optional

# Bundled bridge: redb/extractors/js_extractors/scripts/js-xray-runner.js
_DEFAULT_RUNNER = os.path.join(
    os.path.dirname(__file__), "scripts", "js-xray-runner.js"
)
_DEFAULT_NODE = "node"
_DEFAULT_TIMEOUT_SECS = 30


@dataclass
class XRayResult:
    """Parsed js-x-ray output. `obfuscator` is the recognised family name
    (e.g. "jsfuck", "obfuscator.io") or None when js-x-ray did not flag the
    code. `warnings` carries every {kind, value} pair the analyser produced;
    the heuristic uses it as a corroborating signal. `avg_identifier_length`
    is js-x-ray's own AST-derived figure — used as a fallback for the
    heuristic's `avg_identifier_length<2` strong signal when pyjsparser
    can't parse the source (anything ES2015+ trips it)."""

    obfuscator: Optional[str] = None
    warnings: List[dict] = field(default_factory=list)
    avg_identifier_length: Optional[float] = None

    @property
    def flagged(self) -> bool:
        return self.obfuscator is not None


def _empty() -> XRayResult:
    return XRayResult(obfuscator=None, warnings=[])


def run(source: str, log) -> XRayResult:
    if not source:
        return _empty()

    runner = os.getenv("JS_XRAY_RUNNER_PATH", _DEFAULT_RUNNER)
    node_bin = os.getenv("JS_XRAY_NODE_BIN", _DEFAULT_NODE)
    timeout = int(os.getenv("JS_XRAY_TIMEOUT", str(_DEFAULT_TIMEOUT_SECS)))

    if not os.path.exists(runner):
        log.debug(f"js-x-ray runner not found at {runner}")
        return _empty()

    # Skip the subprocess entirely when the JS dependency isn't installed.
    # Without this, every call to a host that has `node` but never ran
    # `npm install` next to the runner would still fork node, get a require
    # error, and exit nonzero — wasted ~50–200ms per JS sample (and per test).
    runner_dir = os.path.dirname(runner)
    if not os.path.isdir(os.path.join(runner_dir, "node_modules", "@nodesecure", "js-x-ray")):
        log.debug(f"@nodesecure/js-x-ray not installed in {runner_dir}")
        return _empty()

    tmp_path = None
    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(
                [node_bin, runner, tmp_path],
                stdout=subprocess.PIPE,
                stderr=subprocess.PIPE,
                preexec_fn=os.setsid,
            )
            try:
                stdout, stderr = process.communicate(timeout=timeout)
            except subprocess.TimeoutExpired:
                # Kill the whole process group so any node helpers die 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"js-x-ray timed out after {timeout}s")
                return _empty()

            if process.returncode != 0:
                err = stderr.decode("utf-8", errors="replace").strip()
                log.debug(f"js-x-ray exited {process.returncode}: {err}")
                return _empty()

            text = stdout.decode("utf-8", errors="replace").strip()
            if not text:
                return _empty()

            try:
                payload = json.loads(text)
            except json.JSONDecodeError as e:
                log.warning(f"js-x-ray emitted non-JSON output: {e}")
                return _empty()

            obfuscator = payload.get("obfuscator")
            warnings = payload.get("warnings") or []
            if not isinstance(warnings, list):
                warnings = []

            ids_avg = payload.get("idsLengthAvg")
            if not isinstance(ids_avg, (int, float)):
                ids_avg = None

            return XRayResult(
                obfuscator=obfuscator,
                warnings=warnings,
                avg_identifier_length=ids_avg,
            )
        finally:
            if tmp_path:
                try:
                    os.unlink(tmp_path)
                except Exception:
                    pass
    except FileNotFoundError:
        log.debug(f"node binary not found at {node_bin}")
        return _empty()
    except Exception as e:
        log.error(f"js-x-ray subprocess error: {e}")
        return _empty()