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{"parentUuid":"8407a037-7c93-48a3-b22e-de8f7592996b","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"1b2c28b5-75dc-4975-bcfb-c640069f26e6","version":"2.1.38","gitBranch":"main","slug":"synthetic-yawning-mountain","type":"user","message":{"role":"user","content":[{"tool_use_id":"toolu_01JHHpFKE1mTsJt4HGo54Y12","type":"tool_result","content":"The file /home/josie/development/personal/Vulnhalla/src/pipeline.py has been updated successfully."}]},"uuid":"dc768fe1-4788-4aad-801c-5a8f06c1eb82","timestamp":"2026-02-11T12:45:48.452Z","toolUseResult":{"filePath":"/home/josie/development/personal/Vulnhalla/src/pipeline.py","oldString":"    parser.add_argument(\"repo\", nargs=\"?\", help=\"GitHub repository in 'org/repo' format\")\n    parser.add_argument(\"--force\", \"-f\", action=\"store_true\", help=\"Re-download even if database exists\")\n    parser.add_argument(\"--local\", \"-l\", metavar=\"PATH\", help=\"Path to local CodeQL database (skips GitHub fetch)\")","newString":"    parser.add_argument(\"repo\", nargs=\"?\", help=\"GitHub repository in 'org/repo' format\")\n    parser.add_argument(\"--force\", \"-f\", action=\"store_true\", help=\"Re-download even if database exists\")\n    parser.add_argument(\"--local\", \"-l\", metavar=\"PATH\", help=\"Path to local CodeQL database (skips GitHub fetch)\")\n    parser.add_argument(\"--lang\", choices=[\"c\", \"go\"], default=\"c\", help=\"Programming language to analyze (default: c)\")","originalFile":"#!/usr/bin/env python3\n\"\"\"\nPipeline orchestration for Vulnhalla.\nThis module coordinates the complete analysis pipeline:\n1. Fetch CodeQL databases\n2. Run CodeQL queries\n3. Classify results with LLM\n4. Open UI (optional)\n\"\"\"\n# Ignore pydantic warnings\nimport warnings\nwarnings.filterwarnings(\"ignore\", category=UserWarning, module=\"pydantic\")\n\nimport argparse\nimport sys\nfrom pathlib import Path\nfrom typing import Optional\n\n# Add project root to Python path\nPROJECT_ROOT = Path(__file__).parent.parent\nif str(PROJECT_ROOT) not in sys.path:\n    sys.path.insert(0, str(PROJECT_ROOT))\n\nfrom src.codeql.fetch_repos import fetch_codeql_dbs\nfrom src.codeql.run_codeql_queries import compile_and_run_codeql_queries\nfrom src.utils.config import get_codeql_path\nfrom src.utils.config_validator import validate_and_exit_on_error\nfrom src.utils.logger import setup_logging, get_logger\nfrom src.utils.exceptions import (\n    CodeQLError, CodeQLConfigError, CodeQLExecutionError,\n    LLMError, LLMConfigError, LLMApiError,\n    VulnhallaError\n)\nfrom src.vulnhalla import IssueAnalyzer\nfrom src.ui.ui_app import main as ui_main\n\n# Initialize logging\nsetup_logging()\nlogger = get_logger(__name__)\n\n\ndef _log_exception_cause(e: Exception) -> None:\n    \"\"\"\n    Log the cause of an exception if available and not already included in the exception message.\n    Checks both e.cause (if set via constructor) and e.__cause__ (if set via 'from e').\n    \"\"\"\n    cause = getattr(e, 'cause', None) or getattr(e, '__cause__', None)\n    if cause:\n        # Only log cause if it's not already included in the exception message\n        cause_str = str(cause)\n        error_str = str(e)\n        if cause_str not in error_str:\n            logger.error(\"   Cause: %s\", cause)\n\n\ndef step1_fetch_codeql_dbs(lang: str, threads: int, repo: str, force: bool = False) -> str:\n    \"\"\"\n    Step 1: Fetch CodeQL databases from GitHub.\n    \n    Args:\n        lang: Programming language code.\n        threads: Number of threads for download operations.\n        repo: Repository name (e.g., \"redis/redis\").\n    \n    Returns:\n        str: Path to the directory containing downloaded databases.\n    \n    Raises:\n        CodeQLConfigError: If configuration is invalid (e.g., missing GitHub token).\n        CodeQLError: If database download or extraction fails.\n    \"\"\"\n    logger.info(\"\\nStep 1: Fetching CodeQL Databases\")\n    logger.info(\"-\" * 60)\n    logger.info(\"Fetching database for: %s\", repo)\n    \n    try:\n        dbs_dir = fetch_codeql_dbs(lang=lang, threads=threads, repo_name=repo, force=force)\n        if not dbs_dir:\n            raise CodeQLError(f\"No CodeQL databases were downloaded/found for {repo}\")\n        return dbs_dir\n    except CodeQLConfigError as e:\n        logger.error(\"[-] Step 1: Configuration error while fetching CodeQL databases: %s\", e)\n        _log_exception_cause(e)\n        logger.error(\"   Please check your GitHub token and permissions.\")\n        sys.exit(1)\n    except CodeQLError as e:\n        logger.error(\"[-] Step 1: Failed to fetch CodeQL databases: %s\", e)\n        _log_exception_cause(e)\n        logger.error(\"   Please check file permissions, disk space, and GitHub API access.\")\n        sys.exit(1)\n\n\ndef step2_run_codeql_queries(dbs_dir: str, lang: str, threads: int) -> None:\n    \"\"\"\n    Step 2: Run CodeQL queries on the downloaded databases.\n    \n    Args:\n        dbs_dir: Path to the directory containing CodeQL databases.\n        lang: Programming language code.\n        threads: Number of threads for query execution.\n    \n    Raises:\n        CodeQLConfigError: If CodeQL path configuration is invalid.\n        CodeQLExecutionError: If query execution fails.\n        CodeQLError: If other CodeQL-related errors occur (e.g., database access issues).\n    \"\"\"\n    logger.info(\"\\nStep 2: Running CodeQL Queries\")\n    logger.info(\"-\" * 60)\n    \n    try:\n        compile_and_run_codeql_queries(\n            codeql_bin=get_codeql_path(),\n            lang=lang,\n            threads=threads,\n            timeout=300,\n            dbs_dir=dbs_dir\n        )\n    except CodeQLConfigError as e:\n        logger.error(\"[-] Step 2: Configuration error while running CodeQL queries: %s\", e)\n        _log_exception_cause(e)\n        logger.error(\"   Please check your CODEQL_PATH configuration.\")\n        sys.exit(1)\n    except CodeQLExecutionError as e:\n        logger.error(\"[-] Step 2: Failed to execute CodeQL queries: %s\", e)\n        _log_exception_cause(e)\n        logger.error(\"   Please check your CodeQL installation and database files.\")\n        sys.exit(1)\n    except CodeQLError as e:\n        logger.error(\"[-] Step 2: CodeQL error while running queries: %s\", e)\n        _log_exception_cause(e)\n        logger.error(\"   Please check your CodeQL database files and query syntax.\")\n        sys.exit(1)\n    \n\ndef step3_classify_results_with_llm(dbs_dir: str, lang: str) -> None:\n    \"\"\"\n    Step 3: Classify CodeQL results using LLM analysis.\n    \n    Args:\n        dbs_dir: Path to the directory containing CodeQL databases.\n        lang: Programming language code.\n    \n    Raises:\n        LLMConfigError: If LLM configuration is invalid (e.g., missing API credentials).\n        LLMApiError: If LLM API call fails (e.g., network issues, rate limits).\n        LLMError: If other LLM-related errors occur.\n        CodeQLError: If reading CodeQL database files fails (YAML, ZIP, CSV).\n        VulnhallaError: If saving analysis results to disk fails.\n    \"\"\"\n    logger.info(\"\\nStep 3: Classifying Results with LLM\")\n    logger.info(\"-\" * 60)\n    \n    try:\n        analyzer = IssueAnalyzer(lang=lang)\n        analyzer.run(dbs_dir)\n    except LLMConfigError as e:\n        logger.error(\"[-] Step 3: LLM configuration error: %s\", e)\n        _log_exception_cause(e)\n        logger.error(\"   Please check your LLM configuration and API credentials in .env file.\")\n        sys.exit(1)\n    except LLMApiError as e:\n        logger.error(\"[-] Step 3: LLM API error: %s\", e)\n        _log_exception_cause(e)\n        logger.error(\"   Please check your API key, network connection, and rate limits.\")\n        sys.exit(1)\n    except LLMError as e:\n        logger.error(\"[-] Step 3: LLM error: %s\", e)\n        _log_exception_cause(e)\n        logger.error(\"   Please check your LLM provider settings and API status.\")\n        sys.exit(1)\n    except CodeQLError as e:\n        logger.error(\"[-] Step 3: CodeQL error while reading database files: %s\", e)\n        _log_exception_cause(e)\n        logger.error(\"   This step reads CodeQL database files (YAML, ZIP, CSV) to prepare data for LLM analysis.\")\n        logger.error(\"   Please check your CodeQL databases and files are accessible.\")\n        sys.exit(1)\n    except VulnhallaError as e:\n        logger.error(\"[-] Step 3: File system error while saving results: %s\", e)\n        _log_exception_cause(e)\n        logger.error(\"   This step writes analysis results to disk and creates output directories.\")\n        logger.error(\"   Please check file permissions and disk space.\")\n        sys.exit(1)\n\n\ndef step4_open_ui() -> None:\n    \"\"\"\n    Step 4: Open the results UI (optional).\n\n    Note:\n        This function does not raise exceptions. UI errors are handled internally by the UI module.\n    \"\"\"\n    logger.info(\"\\n[4/4] Opening UI\")\n    logger.info(\"-\" * 60)\n    logger.info(\"[+] Pipeline completed successfully!\")\n    logger.info(\"Opening results UI...\")\n    ui_main()\n\n\ndef main_analyze() -> None:\n    \"\"\"\n    CLI entry point for the complete analysis pipeline.\n    \n    Expected usage: \n        vulnhalla <org/repo> [--force]           # Fetch from GitHub\n        vulnhalla --local <path/to/db>           # Use local CodeQL database\n    \"\"\"\n    parser = argparse.ArgumentParser(\n        prog=\"vulnhalla\",\n        description=\"Vulnhalla - Automated CodeQL Analysis with LLM Classification\"\n    )\n    parser.add_argument(\"repo\", nargs=\"?\", help=\"GitHub repository in 'org/repo' format\")\n    parser.add_argument(\"--force\", \"-f\", action=\"store_true\", help=\"Re-download even if database exists\")\n    parser.add_argument(\"--local\", \"-l\", metavar=\"PATH\", help=\"Path to local CodeQL database (skips GitHub fetch)\")\n    \n    args = parser.parse_args()\n    \n    # Validate arguments\n    if args.local:\n        # Local database mode\n        local_path = Path(args.local)\n        if not local_path.exists():\n            parser.error(f\"Local database path does not exist: {args.local}\")\n        analyze_pipeline(repo=None, local_db_path=str(local_path))\n    elif args.repo:\n        # GitHub fetch mode\n        if \"/\" not in args.repo:\n            parser.error(\"Repository must be in format 'org/repo'\")\n        analyze_pipeline(repo=args.repo, force=args.force)\n    else:\n        parser.error(\"Either provide a repository (org/repo) or use --local <path>\")\n\n\ndef analyze_pipeline(\n    repo: Optional[str] = None,\n    lang: str = \"c\",\n    threads: int = 16,\n    open_ui: bool = True,\n    force: bool = False,\n    local_db_path: Optional[str] = None\n) -> None:\n    \"\"\"\n    Run the complete Vulnhalla pipeline: fetch, analyze, classify, and optionally open UI.\n    \n    Args:\n        repo: GitHub repository name (e.g., \"redis/redis\"). Required if local_db_path not provided.\n        lang: Programming language code. Defaults to \"c\".\n        threads: Number of threads for CodeQL operations. Defaults to 16.\n        open_ui: Whether to open the UI after completion. Defaults to True.\n        force: If True, re-download even if database exists. Defaults to False.\n        local_db_path: Path to local CodeQL database. If provided, skips GitHub fetch.\n    \n    Note:\n        This function catches and handles all exceptions internally, logging errors\n        and exiting with code 1 on failure. It does not raise exceptions.\n    \"\"\"\n    logger.info(\"🚀 Starting Vulnhalla Analysis Pipeline\")\n    logger.info(\"=\" * 60)\n    \n    # Validate configuration before starting\n    try:\n        validate_and_exit_on_error()\n    except (CodeQLConfigError, LLMConfigError, VulnhallaError) as e:\n        # Format error message for display\n        message = f\"\"\"\n[-] Configuration Validation Failed\n============================================================\n{str(e)}\n============================================================\nPlease fix the configuration errors above and try again.\nSee README.md for configuration reference.\n\"\"\"\n        logger.error(message)\n        _log_exception_cause(e)\n        sys.exit(1)\n    \n    # Step 1: Fetch CodeQL databases (or use local path)\n    if local_db_path:\n        logger.info(\"\\nStep 1: Using Local CodeQL Database\")\n        logger.info(\"-\" * 60)\n        logger.info(\"Database path: %s\", local_db_path)\n        dbs_dir = local_db_path\n    else:\n        dbs_dir = step1_fetch_codeql_dbs(lang, threads, repo, force)\n    \n    # Step 2: Run CodeQL queries\n    step2_run_codeql_queries(dbs_dir, lang, threads)\n    \n    # Step 3: Classify results with LLM\n    step3_classify_results_with_llm(dbs_dir, lang)\n    \n    # Step 4: Open UI (optional)\n    if open_ui:\n        step4_open_ui()\n\n\ndef main_ui() -> None:\n    \"\"\"\n    CLI entry point to open the UI without running analysis.\n    \n    Expected usage: vulnhalla-ui\n    \"\"\"\n    logger.info(\"Opening Vulnhalla UI...\")\n    ui_main()\n\n\ndef main_validate() -> None:\n    \"\"\"\n    CLI entry point to validate configuration.\n    \n    Expected usage: vulnhalla-validate\n    \"\"\"\n    from src.utils.config_validator import validate_all_config\n    \n    is_valid, errors = validate_all_config()\n    \n    if is_valid:\n        logger.info(\"[+] All configurations are valid!\")\n    else:\n        for error in errors:\n            logger.error(error)\n        sys.exit(1)\n\n\ndef main_list() -> None:\n    \"\"\"\n    CLI entry point to list analyzed repositories.\n    \n    Expected usage: vulnhalla-list\n    \"\"\"\n    from src.ui.results_loader import ResultsLoader\n    \n    results_dir = Path(\"output/results\")\n    if not results_dir.exists():\n        logger.info(\"No results found. Run 'vulnhalla <org/repo>' first.\")\n        return\n    \n    loader = ResultsLoader()\n    \n    # Currently only 'c' language is supported\n    lang = \"c\"\n    issues, _ = loader.load_all_issues(lang)\n    \n    if not issues:\n        logger.info(\"No analyzed repositories found.\")\n        return\n    \n    # Group issues by repo\n    repos = {}\n    for issue in issues:\n        repo = issue.repo\n        if repo not in repos:\n            repos[repo] = {\"true\": 0, \"false\": 0, \"needs_more_data to decide\": 0}\n        repos[repo][issue.status] += 1\n    \n    logger.info(\"Analyzed repositories:\")\n    logger.info(\"-\" * 50)\n    for repo, counts in sorted(repos.items()):\n        total = counts[\"true\"] + counts[\"false\"] + counts[\"needs_more_data to decide\"]\n        logger.info(\n            \"  %-30s %3d issues (%d True positive, %d False positive, %d Needs more data to decide)\",\n            repo, total, counts[\"true\"], counts[\"false\"], counts[\"needs_more_data to decide\"]\n        )\n\n\ndef main_example() -> None:\n    \"\"\"\n    CLI entry point to run the example pipeline.\n    \n    Expected usage: vulnhalla-example\n    \"\"\"\n    from examples.example import main as example_main\n    example_main()\n\n\nif __name__ == '__main__':\n    main_analyze()","structuredPatch":[{"oldStart":211,"oldLines":6,"newStart":211,"newLines":7,"lines":["     parser.add_argument(\"repo\", nargs=\"?\", help=\"GitHub repository in 'org/repo' format\")","     parser.add_argument(\"--force\", \"-f\", action=\"store_true\", help=\"Re-download even if database exists\")","     parser.add_argument(\"--local\", \"-l\", metavar=\"PATH\", help=\"Path to local CodeQL database (skips GitHub fetch)\")","+    parser.add_argument(\"--lang\", choices=[\"c\", \"go\"], default=\"c\", help=\"Programming language to analyze (default: c)\")","     ","     args = parser.parse_args()","     "]}],"userModified":false,"replaceAll":false},"sourceToolAssistantUUID":"8407a037-7c93-48a3-b22e-de8f7592996b"}
{"parentUuid":"dc768fe1-4788-4aad-801c-5a8f06c1eb82","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"1b2c28b5-75dc-4975-bcfb-c640069f26e6","version":"2.1.38","gitBranch":"main","slug":"synthetic-yawning-mountain","message":{"model":"claude-opus-4-6","id":"msg_01B7v3nGRc4p1X4dstHufW78","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_01NYkDSHzU3WpvzbZ3KkmNxs","name":"Edit","input":{"replace_all":false,"file_path":"/home/josie/development/personal/Vulnhalla/src/pipeline.py","old_string":"    # Validate arguments\n    if args.local:\n        # Local database mode\n        local_path = Path(args.local)\n        if not local_path.exists():\n            parser.error(f\"Local database path does not exist: {args.local}\")\n        analyze_pipeline(repo=None, local_db_path=str(local_path))\n    elif args.repo:\n        # GitHub fetch mode\n        if \"/\" not in args.repo:\n            parser.error(\"Repository must be in format 'org/repo'\")\n        analyze_pipeline(repo=args.repo, force=args.force)\n    else:\n        parser.error(\"Either provide a repository (org/repo) or use --local <path>\")","new_string":"    # Validate arguments\n    if args.local:\n        # Local database mode\n        local_path = Path(args.local)\n        if not local_path.exists():\n            parser.error(f\"Local database path does not exist: {args.local}\")\n        analyz