Hannah Carter

15 papers Misc 4Journal 10Unranked 1
YearRankTypeTitle / Venue / Authors
2025 conf
I2MTC
Gabriella Butler, Hannah Carter, Dardan Bajrami, Sagar Shrestha, Donglu Shi, Mathias Bonmarin
2024 J jnl
Bioinform.
James V. Talwar, Adam R. Klie, Meghana S. Pagadala, Hannah Carter
2024 J jnl
Patterns
Eve Richardson, Raphael Trevizani, Jason A. Greenbaum, Hannah Carter, Morten Nielsen, Bjoern Peters
2023 J jnl
Nat. Comput. Sci.
Adam R. Klie, David Laub, James V. Talwar, Hayden Stites, Tobias Jores, Joe J. Solvason, Emma K. Farley, Hannah Carter
2023 J jnl
Nucleic Acids Res.
Zeynep Kosaloglu-Yalçin, Nina Blazeska, Randi Vita, Hannah Carter, Morten Nielsen, Stephen Schoenberger, Alessandro Sette, Bjoern Peters
2021 J jnl
Database J. Biol. Databases Curation
Adam R. Klie, Brian Tsui, Shamim Mollah, Dylan Skola, Michelle Dow, Chun-Nan Hsu, Hannah Carter
2019 Misc conf
PSB
Rachel M. Pyke, Raphael Genolet, Alexandre Harari, George Coukos, David Gfeller, Hannah Carter
2019 Misc conf
PSB
Brian Tsui, Michelle Dow, Dylan Skola, Hannah Carter
2019 J jnl
BMC Bioinform.
Alexandra R. Buckley, Trey Ideker, Hannah Carter, Nicholas J. Schork
2018 Misc conf
PSB
Billur Engin, Matan Hofree, Hannah Carter
2015 Misc conf
Pacific Symposium on Biocomputing
Billur Engin, Matan Hofree, Hannah Carter
2014 J jnl
PLoS Comput. Biol.
Yun-Ching Chen, Christopher Douville, Cheng Wang, Noushin Niknafs, Grace H. T. Yeo, Violeta Beleva Guthrie, Hannah Carter, Peter D. Stenson, David N. Cooper, Biao Li, Sean D. Mooney, Rachel Karchin
2013 J jnl
Bioinform.
Christopher Douville, Hannah Carter, Rick Kim, Noushin Niknafs, Mark Diekhans, Peter D. Stenson, David N. Cooper, Michael C. Ryan, Rachel Karchin
2011 J jnl
Bioinform.
Wing Chung Wong, Dewey Kim, Hannah Carter, Mark Diekhans, Michael C. Ryan, Rachel Karchin
2009 J jnl
Nucleic Acids Res.
Ursula Pieper, Narayanan Eswar, Ben M. Webb, David Eramian, Libusha Kelly, David T. Barkan, Hannah Carter, Parminder Mankoo, Rachel Karchin, Marc A. Martí-Renom, Fred P. Davis, Andrej Sali
tests/scripts/test_macho_extractors_local.py
← Index tests/scripts/test_macho_extractors_local.py python
#!/usr/bin/env python3
"""
Local MachO extractors test - test actual extractors without server connections
"""

import sys
import os
import logging
import hashlib
from datetime import datetime, timezone
from typing import Dict, Any, Optional
from unittest.mock import Mock, patch

# Add the redb directory to the path so we can import the extractors
sys.path.insert(0, os.path.join(os.path.dirname(__file__), 'redb'))

# Mock settings to avoid database connections
with patch.dict('os.environ', {'REDB_ENV': 'test'}):
    # Import the actual extractors
    from redb.extractors.macho_extractors.macho_features import MachOFeaturesExtractor
    from redb.extractors.macho_extractors.macho_segments import MachOSegmentExtractor
    from redb.extractors.macho_extractors.macho_imports import MachOImportExtractor
    from redb.extractors.macho_extractors.macho_exports import MachOExportExtractor
    from redb.extractors.macho_extractors.macho_dylibs import MachODylibExtractor
    from redb.extractors.macho_extractors.macho_signature import MachOSignatureExtractor
    from redb.extractors.macho_extractors.macho_universal import MachOUniversalExtractor

def setup_logging():
    """Setup basic logging configuration."""
    logging.basicConfig(
        level=logging.INFO,
        format='%(asctime)s - %(levelname)s - %(message)s'
    )
    return logging.getLogger(__name__)

class MockLogger:
    """Mock logger for testing without RedB dependencies."""
    def __init__(self):
        self.logger = logging.getLogger(__name__)
    
    def debug(self, msg):
        self.logger.debug(msg)
    
    def info(self, msg):
        self.logger.info(msg)
    
    def warning(self, msg):
        self.logger.warning(msg)
    
    def error(self, msg):
        self.logger.error(msg)

class MockExporter:
    """Mock exporter that does nothing."""
    def export(self, data):
        pass

def create_mock_extractor(extractor_class, filepath):
    """Create an extractor instance with mocked dependencies."""
    log = MockLogger()
    
    # Mock the exporters to avoid database connections
    mock_exporters = [MockExporter()]
    
    # Create the extractor with mocked dependencies
    extractor = extractor_class(
        filepath=filepath,
        log=log,
        exporters=mock_exporters,
        index_prefix="test",
        elastic_index="test_macho",
        known_benign=False,
        known_malicious=False
    )
    
    return extractor

def test_extractor(extractor_class, filepath, extractor_name):
    """Test a specific extractor."""
    log = setup_logging()
    log.info(f"Testing {extractor_name}...")
    
    try:
        # Create the extractor with mocked dependencies
        extractor = create_mock_extractor(extractor_class, filepath)
        
        if not extractor.macho:
            log.error(f"{extractor_name}: No MachO object created")
            return False

        # Test the actual extract method
        result = extractor.extract()
        
        if result:
            log.info(f"{extractor_name}: Successfully extracted data")
            print(f"\n{'='*60}")
            print(f"=== {extractor_name.upper()} RESULTS ===")
            print(f"{'='*60}")
            
            if isinstance(result, list):
                print(f"📊 Extracted {len(result)} items")
                print()
                for i, item in enumerate(result):
                    print(f"📦 Item {i+1}:")
                    print(f"   {'─'*40}")
                    # Handle dataclass objects in lists
                    if hasattr(item, '__dataclass_fields__'):
                        from dataclasses import asdict
                        item_dict = asdict(item)
                        for key, value in item_dict.items():
                            if isinstance(value, (list, dict)):
                                if isinstance(value, list):
                                    print(f"   🔹 {key}: List with {len(value)} items")
                                    print(f"      {value}")
                                elif isinstance(value, dict):
                                    print(f"   🔹 {key}: Dict with {len(value)} keys")
                                    for k, v in value.items():
                                        print(f"      {k}: {v}")
                            else:
                                print(f"   🔹 {key}: {value}")
                    else:
                        # Regular dict
                        for key, value in item.items():
                            if isinstance(value, (list, dict)):
                                if isinstance(value, list):
                                    print(f"   🔹 {key}: List with {len(value)} items")
                                    print(f"      {value}")
                                elif isinstance(value, dict):
                                    print(f"   🔹 {key}: Dict with {len(value)} keys")
                                    for k, v in value.items():
                                        print(f"      {k}: {v}")
                            else:
                                print(f"   🔹 {key}: {value}")
                    print()
            else:
                print("📊 Extracted data:")
                print()
                # Handle dataclass objects
                if hasattr(result, '__dataclass_fields__'):
                    # It's a dataclass, use dataclasses.asdict
                    from dataclasses import asdict
                    result_dict = asdict(result)
                    for key, value in result_dict.items():
                        if isinstance(value, (list, dict)):
                            if isinstance(value, list):
                                print(f"🔹 {key}: List with {len(value)} items")
                                print(f"   {value}")
                            elif isinstance(value, dict):
                                print(f"🔹 {key}: Dict with {len(value)} keys")
                                for k, v in value.items():
                                    print(f"   {k}: {v}")
                        else:
                            print(f"🔹 {key}: {value}")
                        print()
                else:
                    # It's a regular dict
                    for key, value in result.items():
                        if isinstance(value, (list, dict)):
                            if isinstance(value, list):
                                print(f"🔹 {key}: List with {len(value)} items")
                                print(f"   {value}")
                            elif isinstance(value, dict):
                                print(f"🔹 {key}: Dict with {len(value)} keys")
                                for k, v in value.items():
                                    print(f"   {k}: {v}")
                        else:
                            print(f"🔹 {key}: {value}")
                        print()
        else:
            log.warning(f"{extractor_name}: No data extracted")
            print(f"\n❌ {extractor_name}: No data extracted")
        
        return True
        
    except Exception as e:
        log.error(f"{extractor_name}: Error during extraction: {e}")
        import traceback
        traceback.print_exc()
        return False

def main():
    """Main function."""
    if len(sys.argv) < 2:
        print("Usage: python test_macho_extractors_local.py <macho_file> [extractor_name]")
        print("\nAvailable extractors:")
        print("  features    - Basic MachO header and metadata")
        print("  segments    - Segment information and analysis")
        print("  imports     - Imported functions and libraries")
        print("  exports     - Exported symbols")
        print("  dylibs      - Dynamic library dependencies")
        print("  signature   - Code signing information")
        print("  universal   - FAT/Universal binary information")
        print("  all         - Test all extractors")
        sys.exit(1)
    
    filepath = sys.argv[1]
    extractor_name = sys.argv[2] if len(sys.argv) > 2 else "all"
    
    if not os.path.exists(filepath):
        print(f"File not found: {filepath}")
        sys.exit(1)
    
    # Define extractors
    extractors = {
        'features': (MachOFeaturesExtractor, "MachO Features"),
        'segments': (MachOSegmentExtractor, "MachO Segments"),
        'imports': (MachOImportExtractor, "MachO Imports"),
        'exports': (MachOExportExtractor, "MachO Exports"),
        'dylibs': (MachODylibExtractor, "MachO Dylibs"),
        'signature': (MachOSignatureExtractor, "MachO Code Signature"),
        'universal': (MachOUniversalExtractor, "MachO Universal/FAT"),
    }
    
    if extractor_name == "all":
        print(f"Testing all extractors with file: {filepath}")
        success_count = 0
        for name, (extractor_class, display_name) in extractors.items():
            if test_extractor(extractor_class, filepath, display_name):
                success_count += 1
            print("-" * 50)
        
        print(f"\n✅ {success_count}/{len(extractors)} extractors completed successfully")
        
    elif extractor_name in extractors:
        extractor_class, display_name = extractors[extractor_name]
        success = test_extractor(extractor_class, filepath, display_name)
        
        if success:
            print(f"\n✅ {display_name} testing completed successfully")
        else:
            print(f"\n❌ {display_name} testing failed")
            sys.exit(1)
    else:
        print(f"Unknown extractor: {extractor_name}")
        print("Available extractors:", ", ".join(extractors.keys()) + ", all")
        sys.exit(1)

if __name__ == "__main__":
    main()