Ole Lund

40 papers A 1Journal 33Unranked 5
YearRankTypeTitle / Venue / Authors
2021 J jnl
Bioinform.
Rosa L. Allesøe, Camilla K. Lemvigh, My V. T. Phan, Philip T. L. C. Clausen, Alfred F. Florensa, Marion Koopmans, Ole Lund, Matthew Cotten
2019 J jnl
Database J. Biol. Databases Curation
Clara Amid, Nima Pakseresht, Nicole Silvester, Suran Jayathilaka, Ole Lund, Lukasz D. Dynovski, Bálint Á Pataki, Dávid Visontai, Basil Britto Xavier, Blaise T. F. Alako, Ariane Belka, Jose L. B. Cisneros, Matthew Cotten, George B. Haringhuizen, Peter W. Harrison, Dirk Höper, Sam Holt, Camilla Hundahl, Abdulrahman Hussein, Rolf S. Kaas, Xin Liu, Rasko Leinonen, Surbhi Malhotra-Kumar, David F. Nieuwenhuijse, Nadim Rahman, Carolina dos S. Ribeiro, Jeffrey E. Skiby, Dennis Schmitz, József Stéger, János M. Szalai-Gindl, Martin Christen Frølund Thomsen, Simone M. Cacciò, István Csabai, Annelies Kroneman, Marion Koopmans, Frank Aarestrup, Guy Cochrane
2018 J jnl
BMC Bioinform.
Maria Luisa Matey-Hernandez, Lasse Maretty, Jacob Malte Jensen, Bent Petersen, Jonas Andreas Sibbesen, Siyang Liu, Palle Villesen, Laurits Skov, Kirstine Belling, Christian Theil Have, José M. G. Izarzugaza, Marie Grosjean, Jette Bork-Jensen, Jakob Grove, Thomas D. Als, Shujia Huang, Yuqi Chang, Ruiqi Xu, Weijian Ye, Junhua Rao, Xiaosen Guo, Jihua Sun, Hongzhi Cao, Chen Ye, John van Beusekom, Thomas Espeseth, Esben N. Flindt, Rune M. Friborg, Anders E. Halager, Stephanie Le Hellard, Christina M. Hultman, Francesco Lescai, Shengting Li, Ole Lund, Peter Løngreen, Thomas Mailund, Ole Mors, Christian N. S. Pedersen, Thomas Sicheritz-Pontén, Patrick F. Sullivan, Ali Syed, David Westergaard, Rachita Yadav, Ning Li, Xun Xu, Torben Hansen, Anders Krogh, Lars Bolund, Thorkild I. A. Sørensen, Oluf Pedersen, Ramneek Gupta, Simon Rasmussen, Søren Besenbacher, Anders D. Børglum, Jun Wang, Hans Eiberg, Karsten Kristiansen, Mikkel Heide Schierup, Søren Brunak
2018 J jnl
BMC Bioinform.
Philip T. L. C. Clausen, Frank Aarestrup, Ole Lund
2017 J jnl
Bioinform.
Martin Christen Frølund Thomsen, Henrik Hasman, Henrik Westh, Hülya Kaya, Ole Lund
2017 J jnl
Nat.
Lasse Maretty, Jacob Malte Jensen, Bent Petersen, Jonas Andreas Sibbesen, Siyang Liu, Palle Villesen, Laurits Skov, Kirstine Belling, Christian Theil Have, José M. G. Izarzugaza, Marie Grosjean, Jette Bork-Jensen, Jakob Grove, Thomas D. Als, Shujia Huang, Yuqi Chang, Ruiqi Xu, Weijian Ye, Junhua Rao, Xiaosen Guo, Jihua Sun, Hongzhi Cao, Chen Ye, John van Beusekom, Thomas Espeseth, Esben N. Flindt, Rune M. Friborg, Anders E. Halager, Stephanie Le Hellard, Christina M. Hultman, Francesco Lescai, Shengting Li, Ole Lund, Peter Løngreen, Thomas Mailund, Maria Luisa Matey-Hernandez, Ole Mors, Christian N. S. Pedersen, Thomas Sicheritz-Pontén, Patrick F. Sullivan, Ali Syed, David Westergaard, Rachita Yadav, Ning Li, Xun Xu, Torben Hansen, Anders Krogh, Lars Bolund, Thorkild I. A. Sørensen, Oluf Pedersen, Ramneek Gupta, Simon Rasmussen, Søren Besenbacher, Anders D. Børglum, Jun Wang, Hans Eiberg, Karsten Kristiansen, Søren Brunak, Mikkel Heide Schierup
2016 J jnl
Database J. Biol. Databases Curation
Jens Kringelum, Sonny Kim Kjærulff, Søren Brunak, Ole Lund, Tudor I. Oprea, Olivier Taboureau
2015 J jnl
Bioinform.
Thomas Trolle, Imir G. Metushi, Jason A. Greenbaum, Yohan Kim, John Sidney, Ole Lund, Alessandro Sette, Bjoern Peters, Morten Nielsen
2015 J jnl
BMC Bioinform.
Dhany Saputra, Simon Rasmussen, Mette V. Larsen, Nizar Haddad, Maria Sperotto, Frank Aarestrup, Ole Lund, Thomas Sicheritz-Pontén
2013 J jnl
Nucleic Acids Res.
Sonny Kim Kjærulff, Louis Wich, Jens Kringelum, Ulrik Plesner Jacobsen, Irene Kouskoumvekaki, Karine Audouze, Ole Lund, Søren Brunak, Tudor I. Oprea, Olivier Taboureau
2013 J jnl
Bioinform.
Massimo Andreatta, Ole Lund, Morten Nielsen
2012 J jnl
Nucleic Acids Res.
Yohan Kim, Julia V. Ponomarenko, Zhanyang Zhu, Dorjee Tamang, Peng Wang, Jason Greenbaum, Claus Lundegaard, Alessandro Sette, Ole Lund, Philip E. Bourne, Morten Nielsen, Bjoern Peters
2012 J jnl
PLoS Comput. Biol.
Jens Vindahl Kringelum, Claus Lundegaard, Ole Lund, Morten Nielsen
2011 J jnl
Bioinform.
Nicolas Rapin, Ole Lund, Filippo Castiglione
2010 J jnl
Nucleic Acids Res.
Morten Nielsen, Claus Lundegaard, Ole Lund, Thomas Nordahl Petersen
2010 J jnl
BMC Bioinform.
Peng Wang, John Sidney, Yohan Kim, Alessandro Sette, Ole Lund, Morten Nielsen, Björn Peters
2010 conf
BCB
Claus Lundegaard, M. Buggert, A. C. Karlsson, Ole Lund, Carina Perez, Morten Nielsen
2009 J jnl
Bioinform.
Hao Zhang, Ole Lund, Morten Nielsen
2008 J jnl
Bioinform.
Claus Lundegaard, Ole Lund, Morten Nielsen
2008 J jnl
Nucleic Acids Res.
Qing Zhang, Peng Wang, Yohan Kim, Pernille Haste-Andersen, John E. Beaver, Philip E. Bourne, Huynh-Hoa Bui, Søren Buus, Sune Frankild, Jason Greenbaum, Ole Lund, Claus Lundegaard, Morten Nielsen, Julia V. Ponomarenko, Alessandro Sette, Zhanyang Zhu, Björn Peters
2008 J jnl
Nucleic Acids Res.
Claus Lundegaard, Kasper Lamberth, Mikkel Harndahl, Søren Buus, Ole Lund, Morten Nielsen
2008 J jnl
PLoS Comput. Biol.
Morten Nielsen, Claus Lundegaard, Thomas Blicher, Bjoern Peters, Alessandro Sette, Sune Justesen, Søren Buus, Ole Lund
2007 J jnl
BMC Bioinform.
Mette V. Larsen, Claus Lundegaard, Kasper Lamberth, Søren Buus, Ole Lund, Morten Nielsen
2007 J jnl
Bioinform.
Claus Lundegaard, Ole Lund, Can Kesmir, Søren Brunak, Morten Nielsen
2007 J jnl
BMC Bioinform.
Morten Nielsen, Claus Lundegaard, Ole Lund
2006 J jnl
PLoS Comput. Biol.
Bjoern Peters, Huynh-Hoa Bui, Sune Frankild, Morten Nielsen, Claus Lundegaard, Emrah Kostem, Derek Basch, Kasper Lamberth, Mikkel Harndahl, Ward Fleri, Stephen S. Wilson, John Sidney, Ole Lund, Søren Buus, Alessandro Sette
2006 conf
PRIB
Alessandro Sette, Huynh-Hoa Bui, John Sidney, Philip E. Bourne, Søren Buus, Ward Fleri, R. Kubo, Ole Lund, D. Nemazee, Julia V. Ponomarenko, Muthu Sathiamurthy, Scott Stewart, Scott Way, Stephen S. Wilson, Björn Peters
2005 book
Immunological bioinformatics.
Ole Lund, Morten Nielsen, Claus Lundegaard, Can Kesmir, Søren Brunak
2004 J jnl
BMC Bioinform.
Lars Kiemer, Ole Lund, Søren Brunak, Nikolaj Blom
2004 J jnl
Bioinform.
Morten Nielsen, Claus Lundegaard, Peder Worning, Christina Sylvester-Hvid, Kasper Lamberth, Søren Buus, Søren Brunak, Ole Lund
2004 conf
ICARIS
Claus Lundegaard, Morten Nielsen, Kasper Lamberth, Peder Worning, Christina Sylvester-Hvid, Søren Buus, Søren Brunak, Ole Lund
2003 conf
Mathematical Methods for Protein Structure Analysis and Design
Claus Lundegaard, Thomas Nordahl Petersen, Morten Nielsen, Henrik Bohr, Jakob Bohr, Søren Brunak, Garry Gippert, Ole Lund
2003 J jnl
Neural Comput.
Jens Kaae Christensen, Kasper Lamberth, Morten Nielsen, Claus Lundegaard, Peder Worning, Sanne Lise Lauemøller, Søren Buus, Søren Brunak, Ole Lund
1999 J jnl
Bioinform.
Jan Gorodkin, Hans Henrik Stærfeldt, Ole Lund, Søren Brunak
1999 A conf
ISMB
Jan Gorodkin, Ole Lund, Claus A. F. Andersen, Søren Brunak
1998 J jnl
Nucleic Acids Res.
Jan E. Hansen, Ole Lund, Jette Nilsson, Kristoffer Rapacki, Søren Brunak
1997 J jnl
Nucleic Acids Res.
Jan E. Hansen, Ole Lund, Kristoffer Rapacki, Søren Brunak
1996 J jnl
Nucleic Acids Res.
Jan E. Hansen, Ole Lund, Jens O. Nielsen, John-E. S. Hansen, Søren Brunak
1993 J jnl
Simul. Pract. Theory
Ole Lund, Erik Mosekilde, Jan E. Hansen
1992 conf
EUROSIM
Ole Lund, Erik Mosekilde, Jan E. Hansen
tests/unit/test_apk_process_method.py
← Index tests/unit/test_apk_process_method.py python
"""Mock-based tests for APKCodeAnalyzer._process_method and androguard integration.

Tests the boundary between our code and androguard objects, covering:
- xref extraction (get_xref_from / get_xref_to) for both 4.x and 3.x APIs
- external method skipping
- library method filtering
- smali lookup and androguard fallback disassembly
- deduplication of content hashes
- full output population (all result dict keys)
- minimum instruction filtering
"""
from dataclasses import dataclass
from typing import List
from unittest.mock import MagicMock, Mock, patch, PropertyMock

import pytest

pytestmark = [pytest.mark.unit, pytest.mark.apk, pytest.mark.decompile]


# ---------------------------------------------------------------------------
# Helpers: build mock androguard objects
# ---------------------------------------------------------------------------

SAMPLE_SMALI_BODY = """\
.locals 2
const/4 v0, 0x0
invoke-virtual {p0, v0}, Lcom/example/Foo;->bar(I)V
iget-object v1, p0, Lcom/example/Foo;->name:Ljava/lang/String;
add-int v0, v0, v1
return-void
"""

SAMPLE_JAVA_SOURCE = """\
public void doStuff() {
    int x = 0;
    bar(x);
    String n = this.name;
    x = x + n;
}
"""


def _make_encoded_method(
    class_name="Lcom/example/Foo;",
    method_name="doStuff",
    descriptor="()V",
    code=None,
):
    """Create a mock EncodedMethod."""
    enc = MagicMock()
    enc.get_class_name.return_value = class_name
    enc.get_name.return_value = method_name
    enc.get_descriptor.return_value = descriptor
    enc.get_code.return_value = code
    return enc


def _make_xref_entry_4x(class_name, method_name, offset=0):
    """Create a mock xref tuple in androguard 4.x format.

    4.x: (ClassAnalysis, MethodAnalysis, offset)
    MethodAnalysis has .get_method() returning the EncodedMethod.
    """
    ref_class = MagicMock()
    ref_method = MagicMock()
    inner_enc = MagicMock()
    inner_enc.get_class_name.return_value = class_name
    inner_enc.get_name.return_value = method_name
    ref_method.get_method.return_value = inner_enc
    # Remove direct get_class_name/get_name to simulate 4.x behavior
    del ref_method.get_class_name
    del ref_method.get_name
    return (ref_class, ref_method, offset)


def _make_xref_entry_3x(class_name, method_name, offset=0):
    """Create a mock xref tuple in androguard 3.x format.

    3.x: (ClassAnalysis, EncodedMethod, offset)
    EncodedMethod has .get_class_name() and .get_name() directly.
    """
    ref_class = MagicMock()
    ref_method = MagicMock(spec=[
        "get_class_name", "get_name",
    ])
    ref_method.get_class_name.return_value = class_name
    ref_method.get_name.return_value = method_name
    return (ref_class, ref_method, offset)


def _make_method_analysis(
    encoded=None,
    is_external=False,
    xref_from=None,
    xref_to=None,
):
    """Create a mock MethodAnalysis."""
    method = MagicMock()
    method.is_external.return_value = is_external
    method.get_method.return_value = encoded or _make_encoded_method()
    method.get_xref_from.return_value = xref_from or []
    method.get_xref_to.return_value = xref_to or []
    return method


def _make_analyzer(min_instructions=1):
    """Create an APKCodeAnalyzer with mocked dependencies."""
    with patch(
        "redb.extractors.decompiler.apk.analyzer.JADXDecompiler"
    ), patch(
        "redb.extractors.decompiler.apk.analyzer.ApktoolDisassembler"
    ):
        from redb.extractors.decompiler.apk.analyzer import APKCodeAnalyzer
        analyzer = APKCodeAnalyzer("/fake/path.apk")
        analyzer.min_instructions = min_instructions
        analyzer.library_filter = MagicMock()
        analyzer.library_filter.is_library.return_value = False
        return analyzer


def _empty_results():
    """Create a fresh empty results dict."""
    return {
        "decompiled_content": [],
        "decompiled_refs": [],
        "smali_content": [],
        "smali_refs": [],
        "similarity_metrics": [],
        "cfg": [],
        "analysis_errors": [],
    }


def _make_smali_method(body=SAMPLE_SMALI_BODY, instruction_count=5):
    """Create a mock SmaliMethod."""
    m = MagicMock()
    m.body = body
    m.instruction_count = instruction_count
    m.register_count = 2
    return m


# ---------------------------------------------------------------------------
# Tests: xref extraction
# ---------------------------------------------------------------------------

class TestXrefExtraction:
    """Tests that xrefs are correctly extracted from androguard objects."""

    def test_xref_from_androguard_4x(self):
        """4.x: ref_method.get_method().get_class_name() path."""
        analyzer = _make_analyzer()
        results = _empty_results()
        method_key = "Lcom/example/Foo;->doStuff()V"

        xref_from = [
            _make_xref_entry_4x("Lcom/example/Caller;", "init", 42),
            _make_xref_entry_4x("Lcom/example/Other;", "run", 100),
        ]
        method = _make_method_analysis(xref_from=xref_from)

        smali_methods = {method_key: _make_smali_method()}
        java_methods = {"com.example.Foo.doStuff": SAMPLE_JAVA_SOURCE}

        analyzer._process_method(
            method, smali_methods, java_methods,
            results, set(), set(),
        )

        assert len(results["decompiled_refs"]) == 1
        ref = results["decompiled_refs"][0]
        assert ref["functions_caller"] == [
            "Lcom/example/Caller;->init",
            "Lcom/example/Other;->run",
        ]

    def test_xref_to_androguard_4x(self):
        """4.x: callees extracted via get_method() unwrap."""
        analyzer = _make_analyzer()
        results = _empty_results()
        method_key = "Lcom/example/Foo;->doStuff()V"

        xref_to = [
            _make_xref_entry_4x("Lcom/example/Dep;", "calculate", 10),
        ]
        method = _make_method_analysis(xref_to=xref_to)

        smali_methods = {method_key: _make_smali_method()}
        java_methods = {"com.example.Foo.doStuff": SAMPLE_JAVA_SOURCE}

        analyzer._process_method(
            method, smali_methods, java_methods,
            results, set(), set(),
        )

        ref = results["decompiled_refs"][0]
        assert ref["functions_call"] == ["Lcom/example/Dep;->calculate"]

    def test_xref_from_androguard_3x_fallback(self):
        """3.x: ref_method.get_class_name() direct access fallback."""
        analyzer = _make_analyzer()
        results = _empty_results()
        method_key = "Lcom/example/Foo;->doStuff()V"

        xref_from = [
            _make_xref_entry_3x("Lcom/example/OldCaller;", "legacy"),
        ]
        method = _make_method_analysis(xref_from=xref_from)

        smali_methods = {method_key: _make_smali_method()}
        java_methods = {"com.example.Foo.doStuff": SAMPLE_JAVA_SOURCE}

        analyzer._process_method(
            method, smali_methods, java_methods,
            results, set(), set(),
        )

        ref = results["decompiled_refs"][0]
        assert ref["functions_caller"] == ["Lcom/example/OldCaller;->legacy"]

    def test_xref_to_androguard_3x_fallback(self):
        """3.x: callees via direct access fallback."""
        analyzer = _make_analyzer()
        results = _empty_results()
        method_key = "Lcom/example/Foo;->doStuff()V"

        xref_to = [
            _make_xref_entry_3x("Lcom/example/OldDep;", "compute"),
        ]
        method = _make_method_analysis(xref_to=xref_to)

        smali_methods = {method_key: _make_smali_method()}
        java_methods = {"com.example.Foo.doStuff": SAMPLE_JAVA_SOURCE}

        analyzer._process_method(
            method, smali_methods, java_methods,
            results, set(), set(),
        )

        ref = results["decompiled_refs"][0]
        assert ref["functions_call"] == ["Lcom/example/OldDep;->compute"]

    def test_empty_xrefs(self):
        """No xrefs produces empty lists, not None."""
        analyzer = _make_analyzer()
        results = _empty_results()
        method_key = "Lcom/example/Foo;->doStuff()V"

        method = _make_method_analysis()
        smali_methods = {method_key: _make_smali_method()}
        java_methods = {"com.example.Foo.doStuff": SAMPLE_JAVA_SOURCE}

        analyzer._process_method(
            method, smali_methods, java_methods,
            results, set(), set(),
        )

        ref = results["decompiled_refs"][0]
        assert ref["functions_caller"] == []
        assert ref["functions_call"] == []

    def test_xref_exception_does_not_crash(self):
        """If get_xref_from() itself throws, method still processes."""
        analyzer = _make_analyzer()
        results = _empty_results()
        method_key = "Lcom/example/Foo;->doStuff()V"

        method = _make_method_analysis()
        method.get_xref_from.side_effect = RuntimeError("xref table corrupt")
        method.get_xref_to.side_effect = RuntimeError("xref table corrupt")

        smali_methods = {method_key: _make_smali_method()}
        java_methods = {"com.example.Foo.doStuff": SAMPLE_JAVA_SOURCE}

        analyzer._process_method(
            method, smali_methods, java_methods,
            results, set(), set(),
        )

        # Method should still be processed with empty xrefs
        assert len(results["smali_refs"]) == 1
        ref = results["decompiled_refs"][0]
        assert ref["functions_caller"] == []
        assert ref["functions_call"] == []

    def test_multiple_xrefs(self):
        """Multiple callers and callees are all captured."""
        analyzer = _make_analyzer()
        results = _empty_results()
        method_key = "Lcom/example/Foo;->doStuff()V"

        xref_from = [
            _make_xref_entry_4x("Lcom/A;", "a1"),
            _make_xref_entry_4x("Lcom/B;", "b1"),
            _make_xref_entry_4x("Lcom/C;", "c1"),
        ]
        xref_to = [
            _make_xref_entry_4x("Lcom/D;", "d1"),
            _make_xref_entry_4x("Lcom/E;", "e1"),
        ]
        method = _make_method_analysis(xref_from=xref_from, xref_to=xref_to)

        smali_methods = {method_key: _make_smali_method()}
        java_methods = {"com.example.Foo.doStuff": SAMPLE_JAVA_SOURCE}

        analyzer._process_method(
            method, smali_methods, java_methods,
            results, set(), set(),
        )

        ref = results["decompiled_refs"][0]
        assert len(ref["functions_caller"]) == 3
        assert len(ref["functions_call"]) == 2


# ---------------------------------------------------------------------------
# Tests: method filtering and skipping
# ---------------------------------------------------------------------------

class TestMethodFiltering:
    """Tests for external/library/min-instruction filtering."""

    def test_external_method_skipped(self):
        """External methods (no code body) produce no output."""
        analyzer = _make_analyzer()
        results = _empty_results()

        method = _make_method_analysis(is_external=True)

        analyzer._process_method(
            method, {}, {}, results, set(), set(),
        )

        assert all(len(v) == 0 for v in results.values())

    def test_library_method_skipped(self):
        """Library methods produce no output."""
        analyzer = _make_analyzer()
        analyzer.library_filter.is_library.return_value = True
        results = _empty_results()

        method = _make_method_analysis()

        analyzer._process_method(
            method, {}, {}, results, set(), set(),
        )

        assert all(len(v) == 0 for v in results.values())

    def test_min_instruction_filter(self):
        """Methods below min_instructions threshold are skipped."""
        analyzer = _make_analyzer(min_instructions=10)
        results = _empty_results()
        method_key = "Lcom/example/Foo;->doStuff()V"

        method = _make_method_analysis()
        # Only 3 instructions — below threshold of 10
        smali_methods = {method_key: _make_smali_method(instruction_count=3)}

        analyzer._process_method(
            method, smali_methods, {}, results, set(), set(),
        )

        assert all(len(v) == 0 for v in results.values())

    def test_method_above_min_instructions_processed(self):
        """Methods at or above threshold are processed."""
        analyzer = _make_analyzer(min_instructions=5)
        results = _empty_results()
        method_key = "Lcom/example/Foo;->doStuff()V"

        method = _make_method_analysis()
        smali_methods = {method_key: _make_smali_method(instruction_count=5)}

        analyzer._process_method(
            method, smali_methods, {}, results, set(), set(),
        )

        assert len(results["smali_content"]) == 1
        assert len(results["smali_refs"]) == 1


# ---------------------------------------------------------------------------
# Tests: smali body lookup and androguard fallback
# ---------------------------------------------------------------------------

class TestSmaliLookup:
    """Tests for smali body lookup from apktool and androguard fallback."""

    def test_apktool_smali_used_when_available(self):
        """When apktool smali is available, it's used."""
        analyzer = _make_analyzer()
        results = _empty_results()
        method_key = "Lcom/example/Foo;->doStuff()V"

        method = _make_method_analysis()
        smali_methods = {method_key: _make_smali_method()}

        analyzer._process_method(
            method, smali_methods, {}, results, set(), set(),
        )

        assert len(results["smali_content"]) == 1
        assert results["smali_content"][0]["smali_method"] == SAMPLE_SMALI_BODY

    def test_androguard_fallback_when_no_apktool(self):
        """When apktool smali is missing, _disassemble_with_androguard is used."""
        analyzer = _make_analyzer()
        results = _empty_results()

        # Create encoded method with code
        instruction1 = MagicMock()
        instruction1.get_name.return_value = "const/4"
        instruction1.get_output.return_value = "v0, 0x0"
        instruction2 = MagicMock()
        instruction2.get_name.return_value = "invoke-virtual"
        instruction2.get_output.return_value = "v0, Lcom/Foo;->bar()V"
        instruction3 = MagicMock()
        instruction3.get_name.return_value = "add-int"
        instruction3.get_output.return_value = "v0, v1, v2"
        instruction4 = MagicMock()
        instruction4.get_name.return_value = "sub-int"
        instruction4.get_output.return_value = "v3, v0, v1"
        instruction5 = MagicMock()
        instruction5.get_name.return_value = "return-void"
        instruction5.get_output.return_value = ""

        code = MagicMock()
        code.get_registers_size.return_value = 4
        bytecode = MagicMock()
        bytecode.get_instructions.return_value = [
            instruction1, instruction2, instruction3, instruction4, instruction5,
        ]
        code.get_bc.return_value = bytecode

        encoded = _make_encoded_method(code=code)
        method = _make_method_analysis(encoded=encoded)

        # Empty smali_methods — forces androguard fallback
        analyzer._process_method(
            method, {}, {}, results, set(), set(),
        )

        assert len(results["smali_content"]) == 1
        body = results["smali_content"][0]["smali_method"]
        assert "const/4" in body
        assert "return-void" in body

    def test_androguard_fallback_no_code(self):
        """When encoded method has no code, method is skipped."""
        analyzer = _make_analyzer()
        results = _empty_results()

        encoded = _make_encoded_method(code=None)
        method = _make_method_analysis(encoded=encoded)

        analyzer._process_method(
            method, {}, {}, results, set(), set(),
        )

        assert all(len(v) == 0 for v in results.values())

    def test_androguard_fallback_bytecode_exception(self):
        """When bytecode iteration throws, method is skipped gracefully."""
        analyzer = _make_analyzer()
        results = _empty_results()

        code = MagicMock()
        code.get_registers_size.return_value = 2
        bytecode = MagicMock()
        bytecode.get_instructions.side_effect = RuntimeError("bad bytecode")
        code.get_bc.return_value = bytecode

        encoded = _make_encoded_method(code=code)
        method = _make_method_analysis(encoded=encoded)

        analyzer._process_method(
            method, {}, {}, results, set(), set(),
        )

        # Should not crash, but no content produced
        assert len(results["smali_content"]) == 0


# ---------------------------------------------------------------------------
# Tests: output population and deduplication
# ---------------------------------------------------------------------------

class TestOutputPopulation:
    """Tests that all result dict keys are correctly populated."""

    def _process_standard_method(self, with_java=True):
        """Helper: process a standard method and return results."""
        analyzer = _make_analyzer()
        results = _empty_results()
        method_key = "Lcom/example/Foo;->doStuff()V"

        xref_from = [_make_xref_entry_4x("Lcom/Caller;", "call")]
        xref_to = [_make_xref_entry_4x("Lcom/Dep;", "dep")]
        method = _make_method_analysis(
            xref_from=xref_from, xref_to=xref_to
        )

        smali_methods = {method_key: _make_smali_method()}
        java_methods = {}
        if with_java:
            java_methods = {"com.example.Foo.doStuff": SAMPLE_JAVA_SOURCE}

        analyzer._process_method(
            method, smali_methods, java_methods,
            results, set(), set(),
        )
        return results

    def test_smali_content_populated(self):
        results = self._process_standard_method()
        assert len(results["smali_content"]) == 1
        entry = results["smali_content"][0]
        assert "smali_method_hash" in entry
        assert entry["smali_method"] == SAMPLE_SMALI_BODY
        assert entry["smali_method_type"] == "USER"
        assert entry["smali_instructions_count"] == 5
        assert isinstance(entry["smali_has_string_encryption"], bool)
        assert isinstance(entry["smali_has_reflection_calls"], bool)
        assert isinstance(entry["smali_excessive_goto_count"], bool)

    def test_smali_refs_populated(self):
        results = self._process_standard_method()
        assert len(results["smali_refs"]) == 1
        ref = results["smali_refs"][0]
        assert "smali_method_hash" in ref
        assert ref["smali_class_name"] == "com.example.Foo"
        assert ref["smali_method_name"] == "doStuff"
        assert ref["smali_method_signature"] == "()V"

    def test_decompiled_content_populated_with_java(self):
        results = self._process_standard_method(with_java=True)
        assert len(results["decompiled_content"]) == 1
        entry = results["decompiled_content"][0]
        assert "decompiled_method_hash" in entry
        assert entry["decompiled_method"] == SAMPLE_JAVA_SOURCE

    def test_decompiled_refs_populated_with_java(self):
        results = self._process_standard_method(with_java=True)
        assert len(results["decompiled_refs"]) == 1
        ref = results["decompiled_refs"][0]
        assert "decompiled_method_hash" in ref
        assert "smali_method_hash" in ref
        assert ref["decompiled_class_name"] == "com.example.Foo"
        assert ref["decompiled_method_name"] == "doStuff"
        assert "decompiled_method_prototype" in ref
        assert ref["functions_caller"] == ["Lcom/Caller;->call"]
        assert ref["functions_call"] == ["Lcom/Dep;->dep"]

    def test_no_decompiled_without_java(self):
        results = self._process_standard_method(with_java=False)
        assert len(results["decompiled_content"]) == 0
        assert len(results["decompiled_refs"]) == 0
        # Smali should still be there
        assert len(results["smali_content"]) == 1

    def test_similarity_metrics_populated(self):
        results = self._process_standard_method()
        assert len(results["similarity_metrics"]) == 1
        sim = results["similarity_metrics"][0]
        assert "smali_method_hash" in sim
        assert "cyclomatic_complexity" in sim
        assert "minhash" in sim
        assert isinstance(sim["minhash"], list)
        # block_count moved to cfg table
        assert "block_count" not in sim

    def test_cfg_entry_populated(self):
        results = self._process_standard_method()
        assert len(results["cfg"]) == 1
        cfg = results["cfg"][0]
        assert "smali_method_hash" in cfg
        assert "block_count" in cfg
        assert "cfg_topology_hash" in cfg
        assert "prime_product_smali" in cfg
        assert "wl_minhash" in cfg
        assert "bb_features" in cfg
        assert isinstance(cfg["bb_features"], list)
        for feat in cfg["bb_features"]:
            assert len(feat) == 8

    def test_smali_deduplication(self):
        """Same smali body processed twice produces one content entry."""
        analyzer = _make_analyzer()
        results = _empty_results()
        method_key = "Lcom/example/Foo;->doStuff()V"
        seen_smali = set()

        method = _make_method_analysis()
        smali_methods = {method_key: _make_smali_method()}

        # Process same method twice
        analyzer._process_method(
            method, smali_methods, {}, results, set(), seen_smali,
        )
        analyzer._process_method(
            method, smali_methods, {}, results, set(), seen_smali,
        )

        # Content deduplicated, but refs are per-call
        assert len(results["smali_content"]) == 1
        assert len(results["smali_refs"]) == 2

    def test_decompiled_deduplication(self):
        """Same Java source processed twice produces one content entry."""
        analyzer = _make_analyzer()
        results = _empty_results()
        method_key = "Lcom/example/Foo;->doStuff()V"
        seen_decompiled = set()
        seen_smali = set()

        method = _make_method_analysis()
        smali_methods = {method_key: _make_smali_method()}
        java_methods = {"com.example.Foo.doStuff": SAMPLE_JAVA_SOURCE}

        analyzer._process_method(
            method, smali_methods, java_methods,
            results, seen_decompiled, seen_smali,
        )
        analyzer._process_method(
            method, smali_methods, java_methods,
            results, seen_decompiled, seen_smali,
        )

        assert len(results["decompiled_content"]) == 1
        assert len(results["decompiled_refs"]) == 2


# ---------------------------------------------------------------------------
# Tests: _disassemble_with_androguard
# ---------------------------------------------------------------------------

class TestDisassembleWithAndroguard:
    """Tests for the androguard bytecode disassembly fallback."""

    def test_no_code_returns_none(self):
        from redb.extractors.decompiler.apk.analyzer import APKCodeAnalyzer
        encoded = _make_encoded_method(code=None)
        body, count, regs = APKCodeAnalyzer._disassemble_with_androguard(encoded)
        assert body is None
        assert count == 0
        assert regs == 0

    def test_no_bytecode_returns_none(self):
        from redb.extractors.decompiler.apk.analyzer import APKCodeAnalyzer
        code = MagicMock()
        code.get_registers_size.return_value = 3
        code.get_bc.return_value = None
        encoded = _make_encoded_method(code=code)

        body, count, regs = APKCodeAnalyzer._disassemble_with_androguard(encoded)
        assert body is None
        assert count == 0
        assert regs == 3

    def test_basic_disassembly(self):
        from redb.extractors.decompiler.apk.analyzer import APKCodeAnalyzer

        instructions = []
        for name, output in [
            ("const/4", "v0, 0x0"),
            ("invoke-virtual", "v0, Lcom/Foo;->bar()V"),
            ("return-void", ""),
        ]:
            instr = MagicMock()
            instr.get_name.return_value = name
            instr.get_output.return_value = output
            instructions.append(instr)

        code = MagicMock()
        code.get_registers_size.return_value = 2
        bytecode = MagicMock()
        bytecode.get_instructions.return_value = instructions
        code.get_bc.return_value = bytecode

        encoded = _make_encoded_method(code=code)
        body, count, regs = APKCodeAnalyzer._disassemble_with_androguard(encoded)

        assert body is not None
        assert count == 3
        assert regs == 2
        assert "const/4" in body
        assert "return-void" in body

    def test_invoke_operands_normalized(self):
        """Androguard invoke output gets braces added around registers."""
        from redb.extractors.decompiler.apk.analyzer import APKCodeAnalyzer

        instr = MagicMock()
        instr.get_name.return_value = "invoke-virtual"
        # Androguard format: no braces
        instr.get_output.return_value = "v0, v1, Lcom/Foo;->bar(I)V"

        code = MagicMock()
        code.get_registers_size.return_value = 2
        bytecode = MagicMock()
        bytecode.get_instructions.return_value = [instr]
        code.get_bc.return_value = bytecode

        encoded = _make_encoded_method(code=code)
        body, count, regs = APKCodeAnalyzer._disassemble_with_androguard(encoded)

        # Should be normalized to apktool format with braces
        assert "{v0, v1}" in body

    def test_bytecode_exception_returns_none(self):
        from redb.extractors.decompiler.apk.analyzer import APKCodeAnalyzer

        code = MagicMock()
        code.get_registers_size.return_value = 2
        bytecode = MagicMock()
        bytecode.get_instructions.side_effect = RuntimeError("corrupt")
        code.get_bc.return_value = bytecode

        encoded = _make_encoded_method(code=code)
        body, count, regs = APKCodeAnalyzer._disassemble_with_androguard(encoded)

        assert body is None
        assert regs == 2