R. Gonzalo Parra

15 papers Journal 15
YearRankTypeTitle / Venue / Authors
2025 J jnl
PLoS Comput. Biol.
Pradeep Eranti, Megha Hegde, Syed Muktadir Al Sium, R. Gonzalo Parra, Alastair M. Kilpatrick, Sayane Shome, Farzana Rahman
2022 J jnl
Nucleic Acids Res.
Mihaly Varadi, Stephen Anyango, David R. Armstrong, John M. Berrisford, Preeti Choudhary, Mandar S. Deshpande, Nurul Nadzirin, Sreenath Nair, Lukás Pravda, Ahsan Tanweer, Bissan Al-Lazikani, Claudia Andreini, Geoffrey J. Barton, David Bednar, Karel Berka, Tom L. Blundell, Kelly Brock, José María Carazo, Jirí Damborský, Alessia David, Sucharita Dey, Roland L. Dunbrack Jr., Juan Fernández-Recio, Franca Fraternali, Toby J. Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas A. Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivák, Manjeet Kumar, Emmanuel D. Levy, Nir London, José Ramón Macías, Mallur Srivatsan Madhusudhan, Debora S. Marks, Lennart Martens, Stuart A McGowan, Jake E. McGreig, Vivek Modi, R. Gonzalo Parra, Gerardo Pepe, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro G. Radusky, Pathmanaban Ramasamy, Atilio O. Rausch, Nathalie Reuter, Luis A. Rodriguez, Nathan J. Rollins, Antonio Rosato, Pawel Rubach, Luis Serrano, Gulzar Singh, Petr Skoda, Carlos Oscar Sánchez Sorzano, Jan Stourac, Joanna I. Sulkowska, Radka Svobodová Vareková, Natalia Tichshenko, Silvio C. E. Tosatto, Wim F. Vranken, Mark N. Wass, Dandan Xue, Daniel Zaidman, Janet M. Thornton, Michael J. E. Sternberg, Christine A. Orengo, Sameer Velankar
2021 J jnl
Bioinform.
Atilio O. Rausch, Maria I. Freiberger, Cesar O. Leonetti, Diego M. Luna, Leandro G. Radusky, Peter G. Wolynes, Diego U. Ferreiro, R. Gonzalo Parra
2019 J jnl
Bioinform.
Nikolaos Papadopoulos, R. Gonzalo Parra, Johannes Söding
2018 J jnl
BMC Bioinform.
Mehedi Hassan, Aishwarya Alex Namasivayam, Dan F. DeBlasio, Nazeefa Fatima, Benjamin Siranosian, R. Gonzalo Parra, Bart Cuypers, Sayane Shome, Alexander Miguel Monzon, Julien Fumey, Farzana Rahman
2017 J jnl
PLoS Comput. Biol.
Rocío Espada, R. Gonzalo Parra, Thierry Mora, Aleksandra M. Walczak, Diego U. Ferreiro
2016 J jnl
BMC Bioinform.
Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob B. Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan F. DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman, Griet Laenen, Sander Willems, Lieven Thorrez, Yves Moreau, Raju Nagarajan, Sonia P. Chothani, C. Ramakrishnan, Masakazu Sekijima, M. Michael Gromiha, Paddy J. Slator, Nigel J. Burroughs, Przemyslaw Szalaj, Zhonghui Tang, Paul J. Michalski, Oskar Luo, Xingwang Li, Yijun Ruan, Dariusz Plewczynski, Giulia Fiscon, Emanuel Weitschek, Massimo Ciccozzi, Paola Bertolazzi, Giovanni Felici, Pieter Meysman, Manu Vanaerschot, Maya Berg, Hideo Imamura, Jean-Claude Dujardin, Kris Laukens, Westa Domanova, James R. Krycer, Rima Chaudhuri, Pengyi Yang, Fatemeh Vafaee, Daniel J. Fazakerley, Sean J. Humphrey, David E. James, Zdenka Kuncic
2016 J jnl
Bioinform.
R. Gonzalo Parra, Cristian Oscar Rohr, Daniel Koile, Carolina Perez-Castro, Patricio Yankilevich
2016 J jnl
Nucleic Acids Res.
R. Gonzalo Parra, Nicholas P. Schafer, Leandro G. Radusky, Min-Yeh Tsai, A. Brenda Guzovsky, Peter G. Wolynes, Diego U. Ferreiro
2015 J jnl
BMC Bioinform.
Rocío Espada, R. Gonzalo Parra, Thierry Mora, Aleksandra M. Walczak, Diego U. Ferreiro
2015 J jnl
PLoS Comput. Biol.
R. Gonzalo Parra, Rocío Espada, Nina Verstraete, Diego U. Ferreiro
2014 J jnl
Nucleic Acids Res.
Tomás Di Domenico, Emilio Potenza, Ian Walsh, R. Gonzalo Parra, Manuel Giollo, Giovanni Minervini, Damiano Piovesan, Awais Ihsan, Carlo Ferrari, Andrey V. Kajava, Silvio C. E. Tosatto
2014 J jnl
PLoS Comput. Biol.
Tarun Mishra, R. Gonzalo Parra, Thomas Abeel
2013 J jnl
Bioinform.
Cristian Oscar Rohr, R. Gonzalo Parra, Patricio Yankilevich, Carolina Perez-Castro
2012 J jnl
Nucleic Acids Res.
Michael Jenik, R. Gonzalo Parra, Leandro G. Radusky, Adrian Gustavo Turjanski, Peter G. Wolynes, Diego U. Ferreiro
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"