Makoto Jones

15 papers B 2Misc 2Journal 8Unranked 3
YearRankTypeTitle / Venue / Authors
2024 J jnl
BMC Medical Informatics Decis. Mak.
Everett Neil Rush, Özgür Özmen, Minsu Kim, Erin Rush Ortegon, Makoto Jones, Byung H. Park, Steven Pizer, Jodie Trafton, Lisa A. Brenner, Merry Ward, Jonathan R. Nebeker
2024 J jnl
J. Am. Medical Informatics Assoc.
Jorie M. Butler, Teresa Taft, Peter Taber, Elizabeth Rutter, Megan Fix, Alden Baker, Charlene R. Weir, McKenna Nevers, David C. Classen, Karen Cosby, Makoto Jones, Alec B. Chapman, Barbara E. Jones
2023 conf
MedInfo
Alec B. Chapman, Kelly S. Peterson, Elizabeth Rutter, McKenna Nevers, Jian Ying, David C. Classen, Makoto Jones, Matthew H. Samore, Barbara E. Jones
2023 Misc conf
Visualization and Data Analysis
Junghoon Chae, Byung H. Park, Minsu Kim, Everett Neil Rush, Özgür Özmen, Makoto Jones, Merry Ward, Jonathan R. Nebeker
2022 J jnl
J. Biomed. Informatics
Wathsala Widanagamaachchi, Kelly S. Peterson, Alec B. Chapman, David C. Classen, Makoto Jones
2021 J jnl
J. Biomed. Informatics
Alec B. Chapman, Audrey L. Jones, A. Taylor Kelley, Barbara E. Jones, Lori Gawron, Ann Elizabeth Montgomery, Thomas Byrne, Ying Suo, James Cook, Warren B. P. Pettey, Kelly S. Peterson, Makoto Jones, Richard Nelson
2021 Misc conf
AMIA
Andrea F. Kalvesmaki, Alec Chapman, Kelly S. Peterson, Mary Jo Pugh, Makoto Jones, Theresa Gleason
2020 B conf
CBMS
Everett Neil Rush, Özgür Özmen, Kathryn Knight, Byung H. Park, Clifton Baker, Makoto Jones, Merry Ward, Jonathan R. Nebeker
2020 B conf
CBMS
Junghoon Chae, Byung H. Park, Makoto Jones, Merry Ward, Jonathan R. Nebeker
2016 conf
ICHI
Don Roosan, Matthew H. Samore, Makoto Jones, Yarden Livnat, Justin Clutter
2016 J jnl
Appl. Clin. Inform.
Guilherme Del Fiol, Jorie Butler, Yarden Livnat, Jeanmarie Mayer, Matthew H. Samore, Makoto Jones, Charlene R. Weir, Don Roosan
2015 conf
MedInfo
Olga V. Patterson, Makoto Jones, Yiwen Yao, Benjamin Viernes, Patrick R. Alba, Theodore J. Iwashyna, Scott L. DuVall
2015 J jnl
BMC Medical Informatics Decis. Mak.
Roosan Islam, Charlene R. Weir, Makoto Jones, Guilherme Del Fiol, Matthew H. Samore
2012 J jnl
BMC Medical Informatics Decis. Mak.
Makoto Jones, Scott L. DuVall, Joshua Spuhl, Matthew H. Samore, Christopher D. Nielson, Michael A. Rubin
2009 J jnl
BMC Bioinform.
Brett R. South, Shuying Shen, Makoto Jones, Jennifer H. Garvin, Matthew H. Samore, Wendy Webber Chapman, Adi V. Gundlapalli
tests/unit/test_decompile_decompiler.py
← Index tests/unit/test_decompile_decompiler.py python
"""Unit tests (mocked BN) for bninja/decompiler.py — BinaryNinjaDecompiler."""
import sys
import json
import time
import pytest
from unittest.mock import MagicMock, patch, mock_open

from tests.unit.conftest_binja_stubs import (
    install_binja_stubs,
    MockFunction,
    MockBasicBlock,
    MockDisassemblyLine,
    MockToken,
    MockSymbol,
    MockBinaryView,
    MockEdge,
    SymbolType,
    InstructionTextTokenType,
    BranchType,
)

install_binja_stubs()

from redb.extractors.decompiler.bninja.decompiler import (
    BinaryNinjaDecompiler,
    is_lib_or_thunk,
)
from redb.extractors.decompiler.bninja.function_type import FunctionType


# ============================================================================
# 10a. BinaryNinjaDecompiler
# ============================================================================


class TestBinaryNinjaDecompilerLogError:
    def _make_decompiler(self):
        with patch.object(BinaryNinjaDecompiler, "__init__", lambda self, *a, **kw: None):
            d = BinaryNinjaDecompiler.__new__(BinaryNinjaDecompiler)
            d.log = MagicMock()
            d.errors = []
            d.filepath = "/fake/binary"
            d.bv = None
            d.analysis_results = None
            d.exporters = []
            d.index_prefix = None
            d.filetype = None
            d.goresym = None
            d.BNINJA_TIMEOUT = 60
            return d

    def test_log_error_appends(self):
        d = self._make_decompiler()
        d.log_error("test error", "func1", 0x1000, Exception("boom"), "extract")
        assert len(d.errors) == 1

    def test_log_error_schema(self):
        d = self._make_decompiler()
        d.log_error("test error", "func1", 0x1000, Exception("boom"), "extract")
        error = d.errors[0]
        expected_keys = [
            "function_name",
            "function_address",
            "error_location",
            "error_message",
            "error_details",
            "error_type",
            "timestamp",
        ]
        for key in expected_keys:
            assert key in error, f"Missing key: {key}"


class TestBinaryNinjaDecompilerIsTooFewBlocks:
    def _make_decompiler(self):
        with patch.object(BinaryNinjaDecompiler, "__init__", lambda self, *a, **kw: None):
            d = BinaryNinjaDecompiler.__new__(BinaryNinjaDecompiler)
            d.log = MagicMock()
            d.errors = []
            d.MIN_FUNCTION_SIZE = 10
            return d

    def test_is_too_few_blocks_none(self):
        d = self._make_decompiler()
        func = MagicMock()
        func.basic_blocks = None
        assert d.is_too_few_blocks(func) is False

    def test_is_too_few_blocks_empty(self):
        # Empty basic_blocks now returns True because Binja creates function
        # stubs with empty blocks before analysis completes — we no longer
        # skip these so they get filtered downstream instead.
        d = self._make_decompiler()
        func = MagicMock()
        func.basic_blocks = []
        assert d.is_too_few_blocks(func) is True

    def test_is_too_few_blocks_small_single(self):
        d = self._make_decompiler()
        block = MagicMock()
        block.disassembly_text = [MagicMock() for _ in range(5)]  # < 10
        func = MagicMock()
        func.basic_blocks = [block]
        assert d.is_too_few_blocks(func) is False

    def test_is_too_few_blocks_large_single(self):
        d = self._make_decompiler()
        block = MagicMock()
        block.disassembly_text = [MagicMock() for _ in range(15)]  # >= 10
        func = MagicMock()
        func.basic_blocks = [block]
        assert d.is_too_few_blocks(func) is True

    def test_is_too_few_blocks_multiple(self):
        d = self._make_decompiler()
        func = MagicMock()
        func.basic_blocks = [MagicMock(), MagicMock()]
        assert d.is_too_few_blocks(func) is True


class TestIsLibOrThunk:
    def test_is_lib_or_thunk_user(self):
        func = MagicMock()
        func.symbol.type = SymbolType.FunctionSymbol
        func.is_thunk = False
        assert is_lib_or_thunk(func) is True  # NOT filtered

    def test_is_lib_or_thunk_thunk(self):
        func = MagicMock()
        func.symbol.type = SymbolType.FunctionSymbol
        func.is_thunk = True
        assert is_lib_or_thunk(func) is False  # Filtered out

    def test_is_lib_or_thunk_external(self):
        func = MagicMock()
        func.symbol.type = SymbolType.ImportedFunctionSymbol
        func.is_thunk = False
        assert is_lib_or_thunk(func) is False  # Filtered out


class TestBinaryNinjaDecompilerExtract:
    def _make_decompiler(self):
        with patch.object(BinaryNinjaDecompiler, "__init__", lambda self, *a, **kw: None):
            d = BinaryNinjaDecompiler.__new__(BinaryNinjaDecompiler)
            d.log = MagicMock()
            d.errors = []
            d.filepath = "/fake/binary"
            d.bv = MagicMock()
            d.analysis_results = None
            d.exporters = []
            d.index_prefix = None
            d.filetype = None
            d.goresym = None
            d.BNINJA_TIMEOUT = 60
            d.arch = MagicMock()
            return d

    def test_extract_success(self):
        d = self._make_decompiler()
        mock_results = {
            "decompiled": [{"test": True}],
            "disassembled": [],
            "cfg": [],
            "llil": [],
            "errors": [],
            "strings": [],
            "mlil": [],
        }
        with patch.object(d, "analyze_binary", return_value=mock_results):
            result = d.extract()
            assert result is True
            assert d.analysis_results == mock_results

    def test_extract_failure(self):
        d = self._make_decompiler()
        with patch.object(d, "analyze_binary", return_value=None):
            result = d.extract()
            assert result is False

    def test_tag(self):
        d = self._make_decompiler()
        assert d.tag() == "DECOMPILED"


class TestBinaryNinjaDecompilerAnalyzeBinary:
    def _make_decompiler(self):
        with patch.object(BinaryNinjaDecompiler, "__init__", lambda self, *a, **kw: None):
            d = BinaryNinjaDecompiler.__new__(BinaryNinjaDecompiler)
            d.log = MagicMock()
            d.errors = []
            d.filepath = "/fake/binary"
            d.analysis_results = None
            d.exporters = []
            d.index_prefix = None
            d.filetype = None
            d.goresym = None
            d.BNINJA_TIMEOUT = 60
            d.arch = MagicMock()
            d.MIN_FUNCTION_SIZE = 10
            return d

    def test_analyze_binary_links_hlil_disasm(self):
        """Bi-directional hash linkage between decompiled and disassembled."""
        d = self._make_decompiler()
        d.bv = MagicMock()
        d.bv.functions = []
        # Mock methods to return controlled data
        with patch.object(d, "extract_hlil") as mock_hlil, \
             patch.object(d, "extract_disasm") as mock_disasm, \
             patch.object(d, "extract_cfg", return_value=None), \
             patch.object(d, "extract_lowlevel", return_value=None):

            mock_hlil.return_value = {
                "decompiled_function_hash": "HLIL_HASH",
                "decompiled_function_name": "test",
                "decompiled_function": "code",
            }
            mock_disasm.return_value = {
                "disassembled_function_hash": "DISASM_HASH",
                "disassembled_function_no_addresses": "asm",
            }

            # Manually feed one function
            mock_func = MagicMock()
            mock_func.symbol.type = SymbolType.FunctionSymbol
            mock_func.is_thunk = False
            mock_func.basic_blocks = [MagicMock(), MagicMock()]
            d.bv.functions = [mock_func]

            results = d.analyze_binary()
            if results and results["decompiled"]:
                hlil_r = results["decompiled"][0]
                disasm_r = results["disassembled"][0]
                assert hlil_r["disassembled_function_hash"] == "DISASM_HASH"
                assert disasm_r["decompiled_function_hash"] == "HLIL_HASH"

    def test_analyze_binary_links_llil_disasm(self):
        """Bi-directional linkage between LLIL and disassembly."""
        d = self._make_decompiler()
        d.bv = MagicMock()

        with patch.object(d, "extract_hlil", return_value=None), \
             patch.object(d, "extract_disasm") as mock_disasm, \
             patch.object(d, "extract_cfg", return_value=None), \
             patch.object(d, "extract_lowlevel") as mock_llil:

            mock_disasm.return_value = {
                "disassembled_function_hash": "DISASM_HASH",
                "disassembled_function_no_addresses": "asm",
            }
            mock_llil.return_value = {
                "sha256_llil": "LLIL_HASH",
                "tlsh_llil": "tlsh_val",
            }

            mock_func = MagicMock()
            mock_func.symbol.type = SymbolType.FunctionSymbol
            mock_func.is_thunk = False
            mock_func.basic_blocks = [MagicMock(), MagicMock()]
            d.bv.functions = [mock_func]

            results = d.analyze_binary()
            if results and results["llil"]:
                llil_r = results["llil"][0]
                assert llil_r["disassembled_function_hash"] == "DISASM_HASH"

    def test_analyze_binary_links_cfg_disasm(self):
        """CFG gets disassembled_function_hash."""
        d = self._make_decompiler()
        d.bv = MagicMock()

        with patch.object(d, "extract_hlil", return_value=None), \
             patch.object(d, "extract_disasm") as mock_disasm, \
             patch.object(d, "extract_cfg") as mock_cfg, \
             patch.object(d, "extract_lowlevel", return_value=None):

            mock_disasm.return_value = {
                "disassembled_function_hash": "DISASM_HASH",
                "disassembled_function_no_addresses": "asm",
            }
            mock_cfg.return_value = {
                "function_address": 0x1000,
                "cyclomatic_complexity": 3,
            }

            mock_func = MagicMock()
            mock_func.symbol.type = SymbolType.FunctionSymbol
            mock_func.is_thunk = False
            mock_func.basic_blocks = [MagicMock(), MagicMock()]
            d.bv.functions = [mock_func]

            results = d.analyze_binary()
            if results and results["cfg"]:
                cfg_r = results["cfg"][0]
                assert cfg_r["disassembled_function_hash"] == "DISASM_HASH"

    def test_analyze_binary_sets_cyclomatic(self):
        """cyclomatic_complexity set on disasm from CFG."""
        d = self._make_decompiler()
        d.bv = MagicMock()

        with patch.object(d, "extract_hlil", return_value=None), \
             patch.object(d, "extract_disasm") as mock_disasm, \
             patch.object(d, "extract_cfg") as mock_cfg, \
             patch.object(d, "extract_lowlevel", return_value=None):

            mock_disasm.return_value = {
                "disassembled_function_hash": "HASH",
                "disassembled_function_no_addresses": "asm",
            }
            mock_cfg.return_value = {
                "function_address": 0x1000,
                "cyclomatic_complexity": 7,
            }

            mock_func = MagicMock()
            mock_func.symbol.type = SymbolType.FunctionSymbol
            mock_func.is_thunk = False
            mock_func.basic_blocks = [MagicMock(), MagicMock()]
            d.bv.functions = [mock_func]

            results = d.analyze_binary()
            if results and results["disassembled"]:
                disasm_r = results["disassembled"][0]
                assert disasm_r.get("cyclomatic_complexity") == 7


class TestApplyGoReSym:
    def _make_decompiler(self):
        with patch.object(BinaryNinjaDecompiler, "__init__", lambda self, *a, **kw: None):
            d = BinaryNinjaDecompiler.__new__(BinaryNinjaDecompiler)
            d.log = MagicMock()
            d.errors = []
            d.bv = MagicMock()
            return d

    def test_apply_goresym_user_functions(self):
        d = self._make_decompiler()
        d.goresym = "/tmp/goresym.json"
        data = {
            "UserFunctions": [{"Start": 0x1000, "FullName": "main.main"}],
        }
        with patch("builtins.open", mock_open(read_data=json.dumps(data))):
            d._BinaryNinjaDecompiler__apply_goresym()
            d.bv.define_user_symbol.assert_called()

    def test_apply_goresym_std_functions(self):
        d = self._make_decompiler()
        d.goresym = "/tmp/goresym.json"
        data = {
            "StdFunctions": [{"Start": 0x2000, "FullName": "runtime.main"}],
        }
        with patch("builtins.open", mock_open(read_data=json.dumps(data))):
            d._BinaryNinjaDecompiler__apply_goresym()
            d.bv.define_user_symbol.assert_called()

    def test_apply_goresym_invalid_json(self):
        d = self._make_decompiler()
        d.goresym = "/tmp/goresym.json"
        with patch("builtins.open", mock_open(read_data="not json {")):
            d._BinaryNinjaDecompiler__apply_goresym()
            # Should log error but not crash
            d.log.log_error if hasattr(d.log, 'log_error') else None
            # Just verify no exception raised