Nadav Rappoport

30 papers A* 1B 2Journal 22Unranked 4
YearRankTypeTitle / Venue / Authors
2025 J jnl
J. Biomed. Informatics
Hadasa Kaufman, Nadav Rappoport, Amir Gilad, Michal Linial
2025 A* conf
AAAI
Oriel Perets, Ofir Ben Shoham, Nir Grinberg, Nadav Rappoport
2025 J jnl
CoRR
Oriel Perets, Ofir Ben Shoham, Nir Grinberg, Nadav Rappoport
2025 J jnl
CoRR
Tomer Lavi, Bracha Shapira, Nadav Rappoport
2025 conf
AIME (2)
Shira Sadot Shaharabani, Tal Shavit, Nadav Rappoport
2024 J jnl
CoRR
Oriel Perets, Nadav Rappoport
2024 conf
Tiny Papers @ ICLR
Oriel Perets, Nadav Rappoport
2024 J jnl
J. Am. Medical Informatics Assoc.
Nephi A. Walton, Radhakrishnan Nagarajan, Chen Wang, Murat Sincan, Robert R. Freimuth, David B. Everman, Derek C. Walton, Scott P. McGrath, Dominick J. Lemas, Panayiotis V. Benos, Alexander V. Alekseyenko, Qianqian Song, Ece D. Gamsiz Uzun, Casey Overby Taylor, Alper Uzun, Thomas N. Person, Nadav Rappoport, Zhongming Zhao, Marc S. Williams
2024 J jnl
CoRR
Ofir Ben Shoham, Nadav Rappoport
2024 J jnl
Comput. Biol. Medicine
Ofir Ben Shoham, Nadav Rappoport
2024 J jnl
IEEE J. Biomed. Health Informatics
David Azriel, Yosef Rinott, Orna Tal, Benyamine Abbou, Nadav Rappoport
2023 J jnl
CoRR
Ofir Ben Shoham, Nadav Rappoport
2023 J jnl
CoRR
Oriel Perets, Nadav Rappoport
2023 J jnl
CoRR
Ofir Ben Shoham, Nadav Rappoport
2023 J jnl
J. Am. Medical Informatics Assoc.
Anna Ostropolets, Yasser Albogami, Mitchell Conover, Juan M. Banda, William A. Baumgartner Jr., Clair Blacketer, Priyamvada Desai, Scott L. DuVall, Stephen P. Fortin, James P. Gilbert, Asieh Golozar, Joshua Ide, Andrew S. Kanter, David M. Kern, Chungsoo Kim, Lana Y. H. Lai, Chenyu Li, Feifan Liu, Kristine E. Lynch, Evan Minty, Maria Inês Neves, Ding Quan Ng, Tontel Obene, Victor Pera, Nicole Pratt, Gowtham Rao, Nadav Rappoport, Ines Reinecke, Paola Saroufim, Azza Shoaibi, Katherine Simon, Marc A. Suchard, Joel N. Swerdel, Erica A. Voss, James Weaver, Linying Zhang, George Hripcsak, Patrick B. Ryan
2022 B conf
AIME
Gerta Salillari, Nadav Rappoport
2022 conf
MIE
Lin Peretz, Nadav Rappoport
2022 B conf
AIME
Tomer Hermelin, Pierre Singer, Nadav Rappoport
2022 conf
MIE
Bar H. Ezra, Shreyas Havaldar, Benjamin S. Glicksberg, Nadav Rappoport
2022 J jnl
Big Data Cogn. Comput.
Benyamine Abbou, Orna Tal, Gil Frenkel, Robyn Rubin, Nadav Rappoport
2022 J jnl
Bioinform.
Nadav Brandes, Dan Ofer, Yam Peleg, Nadav Rappoport, Michal Linial
2019 J jnl
Bioinform.
Benjamin S. Glicksberg, Boris Oskotsky, Phyllis M. Thangaraj, Nicholas Giangreco, Marcus A. Badgeley, Kipp W. Johnson, Debajyoti Datta, Vivek A. Rudrapatna, Nadav Rappoport, Mark M. Shervey, Riccardo Miotto, Theodore C. Goldstein, Eugenia Rutenberg, Remi Frazier, Nelson Lee, Sharat Israni, Rick Larsen, Bethany Percha, Li Li, Joel T. Dudley, Nicholas P. Tatonetti, Atul J. Butte
2015
Nadav Rappoport
2015 J jnl
Database J. Biol. Databases Curation
Nadav Rappoport, Michal Linial
2014 J jnl
Bioinform.
Nadav Rappoport, Amos Stern, Nathan Linial, Michal Linial
2014 J jnl
Nucleic Acids Res.
Solange Karsenty, Nadav Rappoport, Dan Ofer, Adva Zair, Michal Linial
2013 J jnl
BMC Bioinform.
Nadav Rappoport, Michal Linial
2012 J jnl
Nucleic Acids Res.
Nadav Rappoport, Solange Karsenty, Amos Stern, Nathan Linial, Michal Linial
2012 J jnl
PLoS Comput. Biol.
Nadav Rappoport, Michal Linial
2010 J jnl
Nucleic Acids Res.
Nadav Rappoport, Menachem Fromer, Regev Schweiger, Michal Linial
redb/extractors/decompiler/apk/jadx_wrapper.py
← Index redb/extractors/decompiler/apk/jadx_wrapper.py python
"""JADX decompiler subprocess wrapper.

Manages JADX subprocess execution for Java decompilation,
following the CAPA extractor subprocess pattern.
"""

import os
import re
import signal
import subprocess
from typing import Dict, Optional


class JADXDecompiler:
    """Subprocess wrapper for JADX Java decompilation."""

    def __init__(self, jadx_path: str = None, timeout: int = None, log=None):
        self.jadx_path = jadx_path or os.getenv("JADX_PATH", "jadx")
        self.timeout = timeout or int(os.getenv("JADX_TIMEOUT", "300"))
        self.log = log

    def decompile(self, apk_path: str, output_dir: str) -> bool:
        """Run JADX decompilation on an APK file.

        Returns True on success, False on failure.
        """
        cmd = [
            self.jadx_path,
            "--no-res",
            "--no-imports",
            "--threads-count", "2",
            "--output-dir", output_dir,
            apk_path,
        ]

        try:
            process = subprocess.Popen(
                cmd,
                stdout=subprocess.PIPE,
                stderr=subprocess.PIPE,
                text=True,
                preexec_fn=os.setsid,
            )

            try:
                stdout, stderr = process.communicate(timeout=self.timeout)
                if process.returncode != 0:
                    if self.log:
                        self.log.warning(
                            f"JADX returned non-zero exit code {process.returncode}: "
                            f"{stderr[:500] if stderr else 'no stderr'}"
                        )
                    # JADX may still produce partial output on non-zero exit
                    return os.path.isdir(os.path.join(output_dir, "sources"))
                return True

            except subprocess.TimeoutExpired:
                if self.log:
                    self.log.error(
                        f"JADX timed out after {self.timeout}s"
                    )
                # Kill the process group
                try:
                    os.killpg(os.getpgid(process.pid), signal.SIGTERM)
                    process.wait(timeout=3)
                except (ProcessLookupError, subprocess.TimeoutExpired):
                    try:
                        os.killpg(os.getpgid(process.pid), signal.SIGKILL)
                    except ProcessLookupError:
                        pass
                return False

        except FileNotFoundError:
            if self.log:
                self.log.error(
                    f"JADX not found at '{self.jadx_path}'. "
                    "Install JADX or set JADX_PATH env var."
                )
            return False
        except Exception as e:
            if self.log:
                self.log.error(f"JADX execution error: {e}")
            return False

    def parse_java_methods(self, output_dir: str) -> Dict[str, str]:
        """Parse JADX output into per-method Java source.

        Returns dict keyed by 'package.ClassName.methodName(ParamType1, ParamType2)'.
        """
        sources_dir = os.path.join(output_dir, "sources")
        if not os.path.isdir(sources_dir):
            return {}

        methods = {}
        for root, _dirs, files in os.walk(sources_dir):
            for fname in files:
                if not fname.endswith(".java"):
                    continue
                fpath = os.path.join(root, fname)
                try:
                    with open(fpath, "r", encoding="utf-8", errors="replace") as f:
                        content = f.read()

                    # Derive the fully qualified class name from file path
                    rel_path = os.path.relpath(fpath, sources_dir)
                    class_fqn = rel_path.replace(os.sep, ".").replace("/", ".")
                    if class_fqn.endswith(".java"):
                        class_fqn = class_fqn[:-5]

                    file_methods = self._extract_methods_from_java(
                        content, class_fqn
                    )
                    methods.update(file_methods)

                except Exception:
                    continue

        return methods

    def _extract_methods_from_java(
        self, source: str, class_fqn: str
    ) -> Dict[str, str]:
        """Extract individual methods from a Java source file.

        Uses brace-depth tracking to find method boundaries.
        """
        methods = {}
        lines = source.split("\n")
        i = 0

        while i < len(lines):
            line = lines[i]
            match = self._is_method_declaration(line)
            if match:
                method_name, param_types = match
                # Track brace depth to find method end
                start_line = i
                brace_depth = 0
                found_open = False

                for j in range(i, len(lines)):
                    for ch in lines[j]:
                        if ch == "{":
                            brace_depth += 1
                            found_open = True
                        elif ch == "}":
                            brace_depth -= 1

                    if found_open and brace_depth == 0:
                        method_body = "\n".join(lines[start_line : j + 1])
                        key = f"{class_fqn}.{method_name}({param_types})"
                        methods[key] = method_body
                        i = j + 1
                        break
                else:
                    i += 1
            else:
                i += 1

        return methods

    # Regex for method declarations (not constructors, not class/interface decl)
    _METHOD_DECL_RE = re.compile(
        r"^\s*(?:(?:public|private|protected|static|final|synchronized|"
        r"native|abstract|strictfp)\s+)*"
        r"(?:[\w<>\[\]?.]+\s+)"  # return type
        r"(\w+)"  # method name
        r"\s*\(([^)]*)\)"  # parameters
        r"(?:\s*throws\s+[\w.,\s]+)?"
        r"\s*\{"
    )

    def _is_method_declaration(self, line: str) -> Optional[tuple]:
        """Check if a line is a method declaration.

        Returns (method_name, param_types_str) or None.
        """
        m = self._METHOD_DECL_RE.match(line)
        if not m:
            return None

        method_name = m.group(1)
        params_raw = m.group(2).strip()

        # Skip class-level blocks
        if method_name in ("if", "for", "while", "switch", "try", "catch"):
            return None

        # Extract just the type names from parameters
        if not params_raw:
            return (method_name, "")

        param_types = []
        for param in params_raw.split(","):
            param = param.strip()
            if not param:
                continue
            parts = param.split()
            # Last non-annotation token before the variable name is the type
            # Simple heuristic: type is second-to-last, name is last
            if len(parts) >= 2:
                param_types.append(parts[-2])
            elif len(parts) == 1:
                param_types.append(parts[0])

        return (method_name, ", ".join(param_types))