Vebjorn Ljosa

16 papers A* 5B 1Journal 5Unranked 3
YearRankTypeTitle / Venue / Authors
2018 ch.
Encyclopedia of Database Systems (2nd ed.)
Arnab Bhattacharya, Vebjorn Ljosa
2016 J jnl
Bioinform.
David Dao, Adam Fraser, Jane Hung, Vebjorn Ljosa, Shantanu Singh, Anne E. Carpenter
2011 J jnl
Bioinform.
Lee Kamentsky, Thouis R. Jones, Adam Fraser, Mark-Anthony Bray, David J. Logan, Katherine L. Madden, Vebjorn Ljosa, Curtis Rueden, Kevin W. Eliceiri, Anne E. Carpenter
2010 conf
MICCAI (3)
Tammy Riklin Raviv, Vebjorn Ljosa, Annie L. Conery, Frederick M. Ausubel, Anne E. Carpenter, Polina Golland, Carolina Wählby
2010 conf
ISBI
Carolina Wählby, Tammy Riklin-Raviv, Vebjorn Ljosa, Annie L. Conery, Polina Golland, Frederick M. Ausubel, Anne E. Carpenter
2010 J jnl
CoRR
Mayank Kabra, Annie L. Conery, Eyleen J. O'Rourke, Xin Xie, Vebjorn Ljosa, Thouis R. Jones, Frederick M. Ausubel, Gary Ruvkun, Anne E. Carpenter, Yoav Freund
2009 ch.
Encyclopedia of Database Systems
Arnab Bhattacharya, Vebjorn Ljosa
2009 J jnl
PLoS Comput. Biol.
Vebjorn Ljosa, Anne E. Carpenter
2008 A* conf
ICDE
Vebjorn Ljosa, Ambuj K. Singh
2007 A* conf
ICDE
Vebjorn Ljosa, Ambuj K. Singh
2006 B conf
EDBT
Vebjorn Ljosa, Arnab Bhattacharya, Ambuj K. Singh
2006 A* conf
ICDE
Vebjorn Ljosa, Arnab Bhattacharya, Ambuj K. Singh
2006 A* conf
ICDM
Vebjorn Ljosa, Ambuj K. Singh
2005 conf
CSB Workshops
Ambuj K. Singh, Arnab Bhattacharya, Vebjorn Ljosa
2005 A* conf
ICDM
Arnab Bhattacharya, Vebjorn Ljosa, Jia-Yu Pan, Mark R. Verardo, Hyung-Jeong Yang, Christos Faloutsos, Ambuj K. Singh
2004 J jnl
Bioinform.
Tamer Kahveci, Vebjorn Ljosa, Ambuj K. Singh
tests/unit/test_decompile_medium_level.py
← Index tests/unit/test_decompile_medium_level.py python
# tests/unit/test_decompile_medium_level.py
"""Unit tests (mocked BN) for bninja/analysis/medium_level.py
   and bninja/analysis/medium_level_normalization.py."""
# tests/unit/test_decompile_medium_level.py
import sys
from unittest.mock import MagicMock, patch

# Installa gli stubs BN
from tests.unit.conftest_binja_stubs import install_binja_stubs
install_binja_stubs()

# ── Definisci MockMLILInstruction PRIMA di importare il modulo ──
class MockMLILInstruction:
    def __init__(self, operation, address=0, operands=None):
        self.operation = operation
        self.address = address
        self.operands = operands or []

# ── Patcha il modulo BN in modo che isinstance() funzioni ──
sys.modules["binaryninja"].MediumLevelILInstruction = MockMLILInstruction
sys.modules["binaryninja"].SSAVariable = type("SSAVariable", (), {})
sys.modules["binaryninja"].Variable = type("Variable", (), {})
sys.modules["binaryninja"].ILIntrinsic = type("ILIntrinsic", (), {})

# Ora importa il modulo — vede già i tipi corretti
from redb.extractors.decompiler.bninja.analysis.medium_level_normalization import (
    MediumLevelNormalization,
)	

class MockMLILFunction:
    def __init__(self, instructions):
        self._instructions = instructions

    @property
    def instructions(self):
        return iter(self._instructions)

    @property
    def basic_blocks(self):
        # one block containing all instructions, good enough for MinHasher
        block = MagicMock()
        block.__iter__ = lambda self_: iter([])  # not used by MediumLevelAnalysis
        return [block]


class MockFunction:
    def __init__(self, name="func", start=0x1000, mlil=None):
        self.name = name
        self.start = start
        self.mlil = mlil



class TestMediumLevelNormalization:
    def setup_method(self):
        from redb.extractors.decompiler.bninja.analysis.medium_level_normalization import (
            MediumLevelNormalization,
        )
        self.norm = MediumLevelNormalization()

    def test_normalize_skeleton_single_instruction(self):
        il = MockMLILInstruction(operation=42, operands=[])
        result = self.norm.normalize_instruction_all_levels(il)
        assert result == [42]

    def test_normalize_skeleton_nested(self):
        inner = MockMLILInstruction(operation=7, operands=[])
        outer = MockMLILInstruction(operation=1, operands=[inner])
        result = self.norm.normalize_instruction_all_levels(outer)
        assert result == [1, 7]

    def test_normalize_skeleton_with_list_operand(self):
        inner_a = MockMLILInstruction(operation=10, operands=[])
        inner_b = MockMLILInstruction(operation=11, operands=[])
        outer = MockMLILInstruction(operation=2, operands=[[inner_a, inner_b]])
        result = self.norm.normalize_instruction_all_levels(outer)
        assert result == [2, 10, 11]

    def test_normalize_skeleton_none(self):
        result = self.norm.normalize_instruction_all_levels(None)
        # collect on None should leave ops empty
        assert result == []

    def test_normalize_typed_appends_leaf_types(self):
        # operand is a plain int -> "CONST"
        il = MockMLILInstruction(operation=3, operands=[42])
        result = self.norm.normalize_instr_with_operands(il)
        assert result == [3, "CONST"]

    def test_normalize_typed_bool_before_int(self):
        # bool must be detected before int (since bool is an int subclass)
        il = MockMLILInstruction(operation=4, operands=[True])
        result = self.norm.normalize_instr_with_operands(il)
        assert result == [4, "BOOL"]

    def test_normalize_typed_float(self):
        il = MockMLILInstruction(operation=5, operands=[1.5])
        result = self.norm.normalize_instr_with_operands(il)
        assert result == [5, "FLOAT_CONST"]

    def test_normalize_typed_str(self):
        il = MockMLILInstruction(operation=6, operands=["hello"])
        result = self.norm.normalize_instr_with_operands(il)
        assert result == [6, "STR"]

    def test_normalize_typed_unknown_falls_back_to_typename(self):
        class Weird:
            pass
        il = MockMLILInstruction(operation=8, operands=[Weird()])
        result = self.norm.normalize_instr_with_operands(il)
        assert result == [8, "WEIRD"]

    def test_normalize_typed_nested_mlil(self):
        inner = MockMLILInstruction(operation=99, operands=[7])
        outer = MockMLILInstruction(operation=1, operands=[inner])
        result = self.norm.normalize_instr_with_operands(outer)
        assert result == [1, 99, "CONST"]

    def test_normalize_typed_list_mixed(self):
        inner = MockMLILInstruction(operation=50, operands=[])
        il = MockMLILInstruction(operation=2, operands=[[inner, 99]])
        result = self.norm.normalize_instr_with_operands(il)
        assert result == [2, 50, "CONST"]


class TestMediumLevelAnalysis:
    def _make_analysis(self, instructions=None, mlil=True, start=0x1000):
        from redb.extractors.decompiler.bninja.analysis.medium_level import (
            MediumLevelAnalysis,
        )
        mlil_func = MockMLILFunction(instructions or []) if mlil else None
        func = MockFunction(name="testfunc", start=start, mlil=mlil_func)
        bv = MagicMock()
        return MediumLevelAnalysis(func, bv, MagicMock())

    def test_collect_returns_empty_when_no_mlil(self):
        a = self._make_analysis(mlil=False)
        sk, sk_addr, ty, ty_addr = a._collect_mlil_skeleton_and_typed()
        assert sk == [] and sk_addr == [] and ty == [] and ty_addr == []

    def test_collect_skeleton_and_typed_basic(self):
        instrs = [
            MockMLILInstruction(operation=1, address=0x1000, operands=[]),
            MockMLILInstruction(operation=2, address=0x1004, operands=[42]),
        ]
        a = self._make_analysis(instructions=instrs, start=0x1000)
        sk, sk_addr, ty, ty_addr = a._collect_mlil_skeleton_and_typed()

        assert sk == [[1], [2]]
        assert ty == [[1], [2, "CONST"]]
        assert sk_addr == [(0, [1]), (4, [2])]
        assert ty_addr == [(0, [1]), (4, [2, "CONST"])]

    def test_collect_negative_offset_clamped_to_zero(self):
        instrs = [
            MockMLILInstruction(operation=1, address=0x900, operands=[]),
        ]
        a = self._make_analysis(instructions=instrs, start=0x1000)
        _, sk_addr, _, ty_addr = a._collect_mlil_skeleton_and_typed()
        assert sk_addr[0][0] == 0
        assert ty_addr[0][0] == 0

    def test_log_error_records_entry(self):
        a = self._make_analysis()
        a.log_error("boom", "fname", 0x1234, ValueError("x"), "loc")
        assert len(a.errors) == 1
        err = a.errors[0]
        assert err["function_name"] == "fname"
        assert err["function_address"] == "4660"  # hex 0x1234
        assert err["error_location"] == "loc"
        assert err["error_message"] == "boom"
        assert err["error_type"] == "ValueError"
        assert "timestamp" in err

    @patch(
        "redb.extractors.decompiler.bninja.analysis.medium_level.MinHasher"
    )
    def test_analyze_returns_expected_keys(self, mock_minhasher):
        mock_minhasher.return_value.calculateMinHash.return_value = [1, 2, 3]

        instrs = [
            MockMLILInstruction(operation=1, address=0x1000, operands=[]),
            MockMLILInstruction(operation=2, address=0x1004, operands=[42]),
            MockMLILInstruction(operation=3, address=0x1008, operands=[]),
        ]
        a = self._make_analysis(instructions=instrs, start=0x1000)
        result, errors = a.analyze()

        expected_keys = {
            "function_address",
            "body_mlil_skeleton_vector",
            "sha256_mlil_skeleton",
            "tlsh_mlil_skeleton",
            "minhash_mlil_skeleton",
            "body_mlil_typed_vector",
            "sha256_mlil_typed",
            "tlsh_mlil_typed",
            "minhash_mlil_typed",
        }
        assert set(result.keys()) == expected_keys
        assert result["function_address"] == 0x1000
        assert result["minhash_mlil_skeleton"] == [1, 2, 3]
        assert result["minhash_mlil_typed"] == [1, 2, 3]
        assert errors == []

    @patch(
        "redb.extractors.decompiler.bninja.analysis.medium_level.MinHasher"
    )
    def test_analyze_empty_mlil(self, mock_minhasher):
        mock_minhasher.return_value.calculateMinHash.return_value = []
        a = self._make_analysis(mlil=False)
        result, errors = a.analyze()
        assert result["body_mlil_skeleton_vector"] == []
        assert result["body_mlil_typed_vector"] == []
        assert errors == []

    @patch(
        "redb.extractors.decompiler.bninja.analysis.medium_level.MinHasher"
    )
    def test_analyze_sha256_differs_skeleton_vs_typed(self, mock_minhasher):
        mock_minhasher.return_value.calculateMinHash.return_value = []

        instrs = [
            MockMLILInstruction(operation=1, address=0x1000, operands=[42]),
            MockMLILInstruction(operation=2, address=0x1004, operands=["foo"]),
            MockMLILInstruction(operation=3, address=0x1008, operands=[True]),
        ]
        a = self._make_analysis(instructions=instrs)
        result, _ = a.analyze()
        # skeleton ignores operand leaves, typed includes them -> different hashes
        assert result["sha256_mlil_skeleton"] != result["sha256_mlil_typed"]


class TestMinHasherMLILKinds:
    def _make_func(self, instrs):
        # MinHasher iterates basic_blocks then over each block
        block = MagicMock()
        block.__iter__ = lambda self_: iter(instrs)
        f = MagicMock()
        f.basic_blocks = [block]
        return f

    def test_mlil_skeleton_uses_medium_normalizer(self):
        from redb.extractors.decompiler.bninja.similarity.minhasher import (
            MinHasher, TokenKind,
        )
        instrs = [
            MockMLILInstruction(operation=i, operands=[]) for i in range(5)
        ]
        func = self._make_func(instrs)
        hasher = MinHasher(seed=42, il_function=func, kind=TokenKind.MLIL)
        result = hasher.calculateMinHash()
        # 5 instructions -> 3 trigrams -> non-empty signature
        assert result != []

    def test_typed_mlil_differs_from_skeleton(self):
        from redb.extractors.decompiler.bninja.similarity.minhasher import (
            MinHasher, TokenKind,
        )
        instrs = [
            MockMLILInstruction(operation=1, operands=[42]),
            MockMLILInstruction(operation=2, operands=["s"]),
            MockMLILInstruction(operation=3, operands=[True]),
            MockMLILInstruction(operation=4, operands=[1.5]),
        ]
        func = self._make_func(instrs)
        skel = MinHasher(seed=42, il_function=func, kind=TokenKind.MLIL).calculateMinHash()
        typed = MinHasher(seed=42, il_function=func, kind=TokenKind.TYPED_MLIL).calculateMinHash()
        # Same seed, same instructions, but typed has extra leaf tokens
        # -> hashes should generally differ
        assert skel != typed

    def test_mlil_too_few_instructions(self):
        from redb.extractors.decompiler.bninja.similarity.minhasher import (
            MinHasher, TokenKind,
        )
        instrs = [MockMLILInstruction(operation=1, operands=[])] * 2
        func = self._make_func(instrs)
        hasher = MinHasher(seed=42, il_function=func, kind=TokenKind.MLIL)
        assert hasher.calculateMinHash() == []

    def test_unsupported_kind_raises(self):
        from redb.extractors.decompiler.bninja.similarity.minhasher import MinHasher
        func = self._make_func([])
        hasher = MinHasher(seed=42, il_function=func, kind="bogus")
        with pytest.raises(ValueError):
            hasher.calculateMinHash()