Katharina Jahn

22 papers B 4C 2Journal 11Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
Bioinform.
Jack Kuipers, Mustafa Anil Tuncel, Pedro F. Ferreira, Katharina Jahn, Niko Beerenwinkel
2023 ed.
RECOMB-CG
Katharina Jahn, Tomás Vinar
2021 J jnl
PLoS Comput. Biol.
Jack Kuipers, Ariane L. Moore, Katharina Jahn, Peter Schraml, Feng Wang, Kiyomi Morita, P. Andrew Futreal, Koichi Takahashi, Christian Beisel, Holger Moch, Niko Beerenwinkel
2021 J jnl
Algorithms Mol. Biol.
Katharina Jahn, Niko Beerenwinkel, Louxin Zhang
2020 C conf
WABI
Katharina Jahn, Niko Beerenwinkel, Louxin Zhang
2019 J jnl
PeerJ Prepr.
David Laehnemann, Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie C. Hicks, Mark D. Robinson, Catalina A. Vallejos, Niko Beerenwinkel, Kieran R. Campbell, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn A. Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M. Keizer, Indu Khatri, Szymon M. Kielbasa, Jan O. Korbel, Alexey M. Kozlov, Tzu-Hao Kuo, Boudewijn P. F. Lelieveldt, Ion I. Mandoiu, John C. Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Lukasz Raczkowski, Marcel J. T. Reinders, Jeroen de Ridder, Antoine-Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alex Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth
2019 ed.
ISMCO
George Bebis, Takis Benos, Ken Chen, Katharina Jahn, Ernesto Lima
2018 B conf
RECOMB
Salem Malikic, Katharina Jahn, Jack Kuipers, Süleyman Cenk Sahinalp, Niko Beerenwinkel
2018 B conf
RECOMB
Jochen Singer, Jack Kuipers, Katharina Jahn, Niko Beerenwinkel
2016 B conf
RECOMB
Katharina Jahn, Jack Kuipers, Niko Beerenwinkel
2013 J jnl
BMC Bioinform.
Katharina Jahn, Sascha Winter, Jens Stoye, Sebastian Böcker
2013 ch.
Models and Algorithms for Genome Evolution
Marília D. V. Braga, Cédric Chauve, Daniel Doerr, Katharina Jahn, Jens Stoye, Annelyse Thévenin, Roland Wittler
2012 J jnl
BMC Bioinform.
Katharina Jahn, Chunfang Zheng, Jakub Kovác, David Sankoff
2012 J jnl
BMC Bioinform.
Katharina Jahn, Henner Sudek, Jens Stoye
2011
Katharina Jahn
2011 J jnl
J. Comput. Biol.
Katharina Jahn
2011 J jnl
BMC Bioinform.
Franziska Hufsky, Léon Kuchenbecker, Katharina Jahn, Jens Stoye, Sebastian Böcker
2010 conf
RECOMB-CG
Katharina Jahn
2010 C conf
WABI
Franziska Hufsky, Léon Kuchenbecker, Katharina Jahn, Jens Stoye, Sebastian Böcker
2009 J jnl
Inform. Spektrum
Katharina Jahn, Jens Stoye
2009 J jnl
J. Comput. Biol.
Sebastian Böcker, Katharina Jahn, Julia Mixtacki, Jens Stoye
2008 B conf
RECOMB
Sebastian Böcker, Katharina Jahn, Julia Mixtacki, Jens Stoye
redb/extractors/apk_extractors/apk_inconsistency_tests.py
← Index redb/extractors/apk_extractors/apk_inconsistency_tests.py python
import inspect
import re
from datetime import datetime, timezone
from typing import Any

from redb.extractors.enum import Tag
from redb.extractors.apk_extractor import APKExtractor
from redb.models.dataclasses import APKInconsistencyTests

# Emulator detection indicator strings
EMULATOR_INDICATORS = {
    "generic", "sdk", "google_sdk", "Emulator",
    "goldfish", "ranchu", "Andy", "Genymotion",
    "BlueStacks", "nox", "ttVM_Hdragon",
}

# Root detection indicator strings
ROOT_INDICATORS = {
    "/system/app/Superuser.apk",
    "/system/xbin/su",
    "/system/bin/su",
    "com.noshufou.android.su",
    "com.thirdparty.superuser",
    "eu.chainfire.supersu",
    "com.koushikdutta.superuser",
    "com.topjohnwu.magisk",
}

# Standard DEX filename pattern
STANDARD_DEX_PATTERN = re.compile(r"^classes\d*\.dex$")


class APKInconsistencyTestsExtractor(APKExtractor):

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

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

    def _test_zip_bomb(self):
        """Check if any ZIP entry has compression ratio > 100:1."""
        try:
            zf = self._get_zip_file()
            if not zf:
                return None
            with zf:
                for info in zf.infolist():
                    if info.compress_size > 0:
                        ratio = info.file_size / info.compress_size
                        if ratio > 100:
                            return True
            return False
        except Exception as e:
            self.log.warning(f"Error in zip bomb test: {e}")
            return None

    def _test_zip_duplicate_entries(self):
        """Check for duplicate filenames in ZIP directory."""
        try:
            zf = self._get_zip_file()
            if not zf:
                return None
            with zf:
                names = [info.filename for info in zf.infolist()]
                return len(names) != len(set(names))
        except Exception as e:
            self.log.warning(f"Error in duplicate entries test: {e}")
            return None

    def _test_zip_path_traversal(self):
        """Check for path traversal (../) in ZIP entry names."""
        try:
            for f in self._list_files():
                if ".." in f or f.startswith("/"):
                    return True
            return False
        except Exception as e:
            self.log.warning(f"Error in path traversal test: {e}")
            return None

    def _test_zip_suspicious_timestamps(self):
        """Check for timestamps at epoch (1980) or in the future."""
        try:
            zf = self._get_zip_file()
            if not zf:
                return None
            now = datetime.now()
            with zf:
                for info in zf.infolist():
                    try:
                        dt = datetime(*info.date_time)
                        if dt.year <= 1980 or dt > now:
                            return True
                    except (ValueError, TypeError):
                        continue
            return False
        except Exception as e:
            self.log.warning(f"Error in suspicious timestamps test: {e}")
            return None

    def _test_hidden_dex_files(self):
        """Check for DEX files not matching classes*.dex pattern."""
        try:
            for f in self._list_files():
                if f.endswith(".dex"):
                    basename = f.split("/")[-1]
                    if not STANDARD_DEX_PATTERN.match(basename):
                        return True
            return False
        except Exception as e:
            self.log.warning(f"Error in hidden DEX files test: {e}")
            return None

    def _test_manifest_component_mismatch(self):
        """Check for declared components that don't exist in DEX."""
        try:
            if not self._is_valid_apk():
                return None

            # Get all class names from DEX
            dex_classes = set()
            try:
                from androguard.core.dex import DEX
                for dex_data in (self.apk.get_all_dex() or []):
                    try:
                        d = DEX(dex_data)
                        for cls in d.get_classes():
                            name = cls.get_name()
                            if name:
                                # Convert "Lcom/example/Foo;" to "com.example.Foo"
                                dex_classes.add(
                                    name[1:-1].replace("/", ".") if name.startswith("L") else name
                                )
                    except Exception:
                        continue
            except Exception:
                return None

            if not dex_classes:
                return None

            # Check manifest components against DEX classes
            components = []
            try:
                components.extend(self.apk.get_activities() or [])
                components.extend(self.apk.get_services() or [])
                components.extend(self.apk.get_receivers() or [])
                components.extend(self.apk.get_providers() or [])
            except Exception:
                return None

            for comp in components:
                if comp and comp not in dex_classes:
                    # Component might use a shorthand; check with package prefix
                    package = self.apk.get_package() or ""
                    full_name = package + comp if comp.startswith(".") else comp
                    if full_name not in dex_classes:
                        return True

            return False
        except Exception as e:
            self.log.warning(f"Error in manifest component mismatch test: {e}")
            return None

    def _test_debuggable_release(self):
        """Check android:debuggable=true combined with a release signature."""
        try:
            if not self._is_valid_apk():
                return None

            is_debuggable = self.apk.get_attribute_value(
                "application", "debuggable"
            ) == "true"

            if not is_debuggable:
                return False

            # Check if it has a signing certificate (release builds have certs)
            try:
                certs = self.apk.get_certificates()
                if certs and len(certs) > 0:
                    return True
            except Exception:
                pass

            return False
        except Exception as e:
            self.log.warning(f"Error in debuggable release test: {e}")
            return None

    def _get_dex_strings(self):
        """Get all string constants from DEX files."""
        all_strings = set()
        try:
            from androguard.core.dex import DEX
            for dex_data in (self.apk.get_all_dex() or []):
                try:
                    d = DEX(dex_data)
                    for s in d.get_strings():
                        if s:
                            all_strings.add(s)
                except Exception:
                    continue
        except Exception:
            pass
        return all_strings

    def _test_emulator_detection_strings(self):
        """Check for emulator detection patterns in DEX strings."""
        try:
            if not self._is_valid_apk():
                return None

            dex_strings = self._get_dex_strings()
            for indicator in EMULATOR_INDICATORS:
                for s in dex_strings:
                    if indicator in s:
                        return True
            return False
        except Exception as e:
            self.log.warning(f"Error in emulator detection test: {e}")
            return None

    def _test_debugger_detection(self):
        """Check for debugger detection API calls in DEX."""
        try:
            if not self._is_valid_apk():
                return None

            dex_strings = self._get_dex_strings()
            debugger_patterns = {
                "isDebuggerConnected",
                "waitingForDebugger",
                "Debug.isDebuggerConnected",
            }
            for pattern in debugger_patterns:
                for s in dex_strings:
                    if pattern in s:
                        return True
            return False
        except Exception as e:
            self.log.warning(f"Error in debugger detection test: {e}")
            return None

    def _test_root_detection(self):
        """Check for root detection patterns in DEX."""
        try:
            if not self._is_valid_apk():
                return None

            dex_strings = self._get_dex_strings()
            for indicator in ROOT_INDICATORS:
                for s in dex_strings:
                    if indicator in s:
                        return True
            return False
        except Exception as e:
            self.log.warning(f"Error in root detection test: {e}")
            return None

    def extract(self):
        if not self._is_valid_apk():
            self.log.error(f"Invalid APK for {self.hash.sha256}")
            return None

        self.test_results = APKInconsistencyTests(
            test_zip_bomb=self._test_zip_bomb(),
            test_zip_duplicate_entries=self._test_zip_duplicate_entries(),
            test_zip_path_traversal=self._test_zip_path_traversal(),
            test_zip_suspicious_timestamps=self._test_zip_suspicious_timestamps(),
            test_hidden_dex_files=self._test_hidden_dex_files(),
            test_manifest_component_mismatch=self._test_manifest_component_mismatch(),
            test_debuggable_release=self._test_debuggable_release(),
            test_emulator_detection_strings=self._test_emulator_detection_strings(),
            test_debugger_detection=self._test_debugger_detection(),
            test_root_detection=self._test_root_detection(),
        )
        return self.test_results

    def _bool_to_nullable(self, val):
        """Convert bool/None to ClickHouse Nullable(UInt8)."""
        if val is None:
            return None
        return int(val)

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

            current_time = datetime.now(timezone.utc)
            t = self.test_results

            data = [[
                self.sha256,
                self._bool_to_nullable(t.test_zip_bomb),
                self._bool_to_nullable(t.test_zip_duplicate_entries),
                self._bool_to_nullable(t.test_zip_path_traversal),
                self._bool_to_nullable(t.test_zip_suspicious_timestamps),
                self._bool_to_nullable(t.test_hidden_dex_files),
                self._bool_to_nullable(t.test_manifest_component_mismatch),
                self._bool_to_nullable(t.test_debuggable_release),
                self._bool_to_nullable(t.test_emulator_detection_strings),
                self._bool_to_nullable(t.test_debugger_detection),
                self._bool_to_nullable(t.test_root_detection),
                current_time,
            ]]

            column_names = [
                'sha256',
                'test_zip_bomb', 'test_zip_duplicate_entries',
                'test_zip_path_traversal', 'test_zip_suspicious_timestamps',
                'test_hidden_dex_files', 'test_manifest_component_mismatch',
                'test_debuggable_release', 'test_emulator_detection_strings',
                'test_debugger_detection', 'test_root_detection',
                'analysis_date',
            ]

            column_type_names = [
                'FixedString(64)',
                'Nullable(UInt8)', 'Nullable(UInt8)',
                'Nullable(UInt8)', 'Nullable(UInt8)',
                'Nullable(UInt8)', 'Nullable(UInt8)',
                'Nullable(UInt8)', 'Nullable(UInt8)',
                'Nullable(UInt8)', 'Nullable(UInt8)',
                "DateTime64(3, 'UTC')",
            ]

            return (data, column_names, column_type_names)

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