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{"parentUuid":"4c97c3e7-9a95-4512-964e-2b3e7d9375b9","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"assistant","timestamp":"2026-02-11T13:25:01.269Z","message":{"model":"claude-haiku-4-5-20251001","id":"msg_011TTpaCoKK7qWPybycXzzca","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_01QwVn7fx5y38Pw8ZCZedzQD","name":"Glob","input":{"pattern":"src/vulnhalla_setup.py"}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":3,"cache_creation_input_tokens":6960,"cache_read_input_tokens":9758,"cache_creation":{"ephemeral_5m_input_tokens":0,"ephemeral_1h_input_tokens":6960},"output_tokens":3,"service_tier":"standard","inference_geo":"not_available"},"context_management":null},"requestId":"req_011CY2Mc37PfrBTFNekHn9jT","uuid":"0f5e1980-5196-483f-b402-26130df4732a"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"28b3fa8b-cf4a-4b22-a6a8-df652ee0c101","timestamp":"2026-02-11T13:25:01.270Z"}
{"parentUuid":"28b3fa8b-cf4a-4b22-a6a8-df652ee0c101","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"user","message":{"role":"user","content":[{"type":"tool_result","content":"Sibling tool call errored","is_error":true,"tool_use_id":"toolu_01QwVn7fx5y38Pw8ZCZedzQD"}]},"uuid":"d67e6f7b-5a64-424d-a0a1-eecec254572a","timestamp":"2026-02-11T13:25:01.270Z","toolUseResult":"Sibling tool call errored"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"a094b1bc-6eaf-4697-8d21-e19f8324d20a","timestamp":"2026-02-11T13:25:01.270Z"}
{"parentUuid":"a094b1bc-6eaf-4697-8d21-e19f8324d20a","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"assistant","timestamp":"2026-02-11T13:25:01.413Z","message":{"model":"claude-haiku-4-5-20251001","id":"msg_011TTpaCoKK7qWPybycXzzca","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_01Xsef2YAxDLNLZQ3rWaLU1U","name":"Glob","input":{"pattern":"src/utils/config.py"}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":3,"cache_creation_input_tokens":6960,"cache_read_input_tokens":9758,"cache_creation":{"ephemeral_5m_input_tokens":0,"ephemeral_1h_input_tokens":6960},"output_tokens":3,"service_tier":"standard","inference_geo":"not_available"},"context_management":null},"requestId":"req_011CY2Mc37PfrBTFNekHn9jT","uuid":"f1dfadd6-45b1-41d2-9098-190de81d45d7"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"0756d4bc-f6d2-498e-a344-bfb4e8518147","timestamp":"2026-02-11T13:25:01.413Z"}
{"parentUuid":"0756d4bc-f6d2-498e-a344-bfb4e8518147","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"user","message":{"role":"user","content":[{"type":"tool_result","content":"Sibling tool call errored","is_error":true,"tool_use_id":"toolu_01Xsef2YAxDLNLZQ3rWaLU1U"}]},"uuid":"44e62858-90c2-4866-aa9f-bcde587bc92b","timestamp":"2026-02-11T13:25:01.413Z","toolUseResult":"Sibling tool call errored"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"eef43f66-beb5-4b63-8a41-afb4178d0057","timestamp":"2026-02-11T13:25:01.413Z"}
{"parentUuid":"eef43f66-beb5-4b63-8a41-afb4178d0057","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"assistant","timestamp":"2026-02-11T13:25:01.542Z","message":{"model":"claude-haiku-4-5-20251001","id":"msg_011TTpaCoKK7qWPybycXzzca","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_01DuTdhJ4SRP5S5N49dAHmJS","name":"Glob","input":{"pattern":"src/codeql/*.py"}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":3,"cache_creation_input_tokens":6960,"cache_read_input_tokens":9758,"cache_creation":{"ephemeral_5m_input_tokens":0,"ephemeral_1h_input_tokens":6960},"output_tokens":3,"service_tier":"standard","inference_geo":"not_available"},"context_management":null},"requestId":"req_011CY2Mc37PfrBTFNekHn9jT","uuid":"4edd66c9-57c6-49f5-92cb-29a760bb6497"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"e832c81d-f6b6-4455-b5e5-cf9cb9276621","timestamp":"2026-02-11T13:25:01.542Z"}
{"parentUuid":"e832c81d-f6b6-4455-b5e5-cf9cb9276621","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"user","message":{"role":"user","content":[{"type":"tool_result","content":"Sibling tool call errored","is_error":true,"tool_use_id":"toolu_01DuTdhJ4SRP5S5N49dAHmJS"}]},"uuid":"e5191d7e-43c5-4b98-9536-efc18a651d50","timestamp":"2026-02-11T13:25:01.542Z","toolUseResult":"Sibling tool call errored"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"ccb0dd2f-3000-4e59-8de1-77be66d1c0fb","timestamp":"2026-02-11T13:25:01.542Z"}
{"parentUuid":"ccb0dd2f-3000-4e59-8de1-77be66d1c0fb","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","message":{"model":"claude-opus-4-6","id":"msg_014rwsuJq2Vy4RedbBfZrLmL","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_01SBzXiYDFMSMi3vxEqQAeQd","name":"Task","input":{"description":"Explore query/template structure","prompt":"Explore the data directory structure for existing language support in Vulnhalla:\n\n1. List and read files in `data/queries/cpp/` - understand the query structure (issues/ and tools/ subdirs)\n2. List and read files in `data/queries/go/` - see how Go queries differ from C++\n3. List and read files in `data/templates/cpp/` - understand LLM prompt templates\n4. List and read files in `data/templates/go/` - see how Go templates differ\n5. Check if there are any qlpack.yml or similar CodeQL pack config files\n\nI need to understand the full pattern for adding a new language's queries and templates.","subagent_type":"Explore"}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":3,"cache_creation_input_tokens":10836,"cache_read_input_tokens":16746,"cache_creation":{"ephemeral_5m_input_tokens":0,"ephemeral_1h_input_tokens":10836},"output_tokens":12,"service_tier":"standard","inference_geo":"not_available"}},"requestId":"req_011CY2MbJfFTJGabZkwixbdo","type":"assistant","uuid":"defcfbe2-3e32-4c44-9224-6ab92d2a4cf7","timestamp":"2026-02-11T13:25:02.757Z"}
{"parentUuid":"defcfbe2-3e32-4c44-9224-6ab92d2a4cf7","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"type":"hook_progress","hookEvent":"PreToolUse","hookName":"PreToolUse:Task","command":"python3 ${CLAUDE_PLUGIN_ROOT}/hooks/pretooluse.py"},"toolUseID":"toolu_01SBzXiYDFMSMi3vxEqQAeQd","parentToolUseID":"toolu_01SBzXiYDFMSMi3vxEqQAeQd","uuid":"f8ddb17c-b75d-4c4a-9f70-e973b9594859","timestamp":"2026-02-11T13:25:02.759Z"}
{"parentUuid":"f8ddb17c-b75d-4c4a-9f70-e973b9594859","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"assistant","timestamp":"2026-02-11T13:25:02.818Z","message":{"model":"claude-haiku-4-5-20251001","id":"msg_01TQWbRySdrA4Ry3dXcnMAN6","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_01YKUiVA1M2dbm6qQrye5qXW","name":"Read","input":{"file_path":"/home/josie/development/personal/Vulnhalla/src/pipeline.py"}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":7,"cache_creation_input_tokens":768,"cache_read_input_tokens":16718,"cache_creation":{"ephemeral_5m_input_tokens":0,"ephemeral_1h_input_tokens":768},"output_tokens":1,"service_tier":"standard","inference_geo":"not_available"},"context_management":null},"requestId":"req_011CY2McDKYz2YQR93N53NDq","uuid":"c025a6a9-43f3-499e-8d7c-8bb26397a266"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"d1a774c8-3131-460f-88c3-91422a2a79ac","timestamp":"2026-02-11T13:25:02.818Z"}
{"parentUuid":"d1a774c8-3131-460f-88c3-91422a2a79ac","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"user","message":{"role":"user","content":[{"tool_use_id":"toolu_01YKUiVA1M2dbm6qQrye5qXW","type":"tool_result","content":" 1→#!/usr/bin/env python3\n 2→\"\"\"\n 3→Pipeline orchestration for Vulnhalla.\n 4→This module coordinates the complete analysis pipeline:\n 5→1. Fetch CodeQL databases\n 6→2. Run CodeQL queries\n 7→3. Classify results with LLM\n 8→4. Open UI (optional)\n 9→\"\"\"\n 10→# Ignore pydantic warnings\n 11→import warnings\n 12→warnings.filterwarnings(\"ignore\", category=UserWarning, module=\"pydantic\")\n 13→\n 14→import argparse\n 15→import sys\n 16→from pathlib import Path\n 17→from typing import Optional\n 18→\n 19→# Add project root to Python path\n 20→PROJECT_ROOT = Path(__file__).parent.parent\n 21→if str(PROJECT_ROOT) not in sys.path:\n 22→ sys.path.insert(0, str(PROJECT_ROOT))\n 23→\n 24→from src.codeql.fetch_repos import fetch_codeql_dbs\n 25→from src.codeql.run_codeql_queries import compile_and_run_codeql_queries\n 26→from src.utils.config import get_codeql_path\n 27→from src.utils.config_validator import validate_and_exit_on_error\n 28→from src.utils.logger import setup_logging, get_logger\n 29→from src.utils.exceptions import (\n 30→ CodeQLError, CodeQLConfigError, CodeQLExecutionError,\n 31→ LLMError, LLMConfigError, LLMApiError,\n 32→ VulnhallaError\n 33→)\n 34→from src.vulnhalla import IssueAnalyzer\n 35→from src.ui.ui_app import main as ui_main\n 36→\n 37→# Initialize logging\n 38→setup_logging()\n 39→logger = get_logger(__name__)\n 40→\n 41→\n 42→def _log_exception_cause(e: Exception) -> None:\n 43→ \"\"\"\n 44→ Log the cause of an exception if available and not already included in the exception message.\n 45→ Checks both e.cause (if set via constructor) and e.__cause__ (if set via 'from e').\n 46→ \"\"\"\n 47→ cause = getattr(e, 'cause', None) or getattr(e, '__cause__', None)\n 48→ if cause:\n 49→ # Only log cause if it's not already included in the exception message\n 50→ cause_str = str(cause)\n 51→ error_str = str(e)\n 52→ if cause_str not in error_str:\n 53→ logger.error(\" Cause: %s\", cause)\n 54→\n 55→\n 56→def step1_fetch_codeql_dbs(lang: str, threads: int, repo: str, force: bool = False) -> str:\n 57→ \"\"\"\n 58→ Step 1: Fetch CodeQL databases from GitHub.\n 59→ \n 60→ Args:\n 61→ lang: Programming language code.\n 62→ threads: Number of threads for download operations.\n 63→ repo: Repository name (e.g., \"redis/redis\").\n 64→ \n 65→ Returns:\n 66→ str: Path to the directory containing downloaded databases.\n 67→ \n 68→ Raises:\n 69→ CodeQLConfigError: If configuration is invalid (e.g., missing GitHub token).\n 70→ CodeQLError: If database download or extraction fails.\n 71→ \"\"\"\n 72→ logger.info(\"\\nStep 1: Fetching CodeQL Databases\")\n 73→ logger.info(\"-\" * 60)\n 74→ logger.info(\"Fetching database for: %s\", repo)\n 75→ \n 76→ try:\n 77→ dbs_dir = fetch_codeql_dbs(lang=lang, threads=threads, repo_name=repo, force=force)\n 78→ if not dbs_dir:\n 79→ raise CodeQLError(f\"No CodeQL databases were downloaded/found for {repo}\")\n 80→ return dbs_dir\n 81→ except CodeQLConfigError as e:\n 82→ logger.error(\"[-] Step 1: Configuration error while fetching CodeQL databases: %s\", e)\n 83→ _log_exception_cause(e)\n 84→ logger.error(\" Please check your GitHub token and permissions.\")\n 85→ sys.exit(1)\n 86→ except CodeQLError as e:\n 87→ logger.error(\"[-] Step 1: Failed to fetch CodeQL databases: %s\", e)\n 88→ _log_exception_cause(e)\n 89→ logger.error(\" Please check file permissions, disk space, and GitHub API access.\")\n 90→ sys.exit(1)\n 91→\n 92→\n 93→def step2_run_codeql_queries(dbs_dir: str, lang: str, threads: int) -> None:\n 94→ \"\"\"\n 95→ Step 2: Run CodeQL queries on the downloaded databases.\n 96→ \n 97→ Args:\n 98→ dbs_dir: Path to the directory containing CodeQL databases.\n 99→ lang: Programming language code.\n 100→ threads: Number of threads for query execution.\n 101→ \n 102→ Raises:\n 103→ CodeQLConfigError: If CodeQL path configuration is invalid.\n 104→ CodeQLExecutionError: If query execution fails.\n 105→ CodeQLError: If other CodeQL-related errors occur (e.g., database access issues).\n 106→ \"\"\"\n 107→ logger.info(\"\\nStep 2: Running CodeQL Queries\")\n 108→ logger.info(\"-\" * 60)\n 109→ \n 110→ try:\n 111→ compile_and_run_codeql_queries(\n 112→ codeql_bin=get_codeql_path(),\n 113→ lang=lang,\n 114→ threads=threads,\n 115→ timeout=300,\n 116→ dbs_dir=dbs_dir\n 117→ )\n 118→ except CodeQLConfigError as e:\n 119→ logger.error(\"[-] Step 2: Configuration error while running CodeQL queries: %s\", e)\n 120→ _log_exception_cause(e)\n 121→ logger.error(\" Please check your CODEQL_PATH configuration.\")\n 122→ sys.exit(1)\n 123→ except CodeQLExecutionError as e:\n 124→ logger.error(\"[-] Step 2: Failed to execute CodeQL queries: %s\", e)\n 125→ _log_exception_cause(e)\n 126→ logger.error(\" Please check your CodeQL installation and database files.\")\n 127→ sys.exit(1)\n 128→ except CodeQLError as e:\n 129→ logger.error(\"[-] Step 2: CodeQL error while running queries: %s\", e)\n 130→ _log_exception_cause(e)\n 131→ logger.error(\" Please check your CodeQL database files and query syntax.\")\n 132→ sys.exit(1)\n 133→ \n 134→\n 135→def step3_classify_results_with_llm(dbs_dir: str, lang: str) -> None:\n 136→ \"\"\"\n 137→ Step 3: Classify CodeQL results using LLM analysis.\n 138→ \n 139→ Args:\n 140→ dbs_dir: Path to the directory containing CodeQL databases.\n 141→ lang: Programming language code.\n 142→ \n 143→ Raises:\n 144→ LLMConfigError: If LLM configuration is invalid (e.g., missing API credentials).\n 145→ LLMApiError: If LLM API call fails (e.g., network issues, rate limits).\n 146→ LLMError: If other LLM-related errors occur.\n 147→ CodeQLError: If reading CodeQL database files fails (YAML, ZIP, CSV).\n 148→ VulnhallaError: If saving analysis results to disk fails.\n 149→ \"\"\"\n 150→ logger.info(\"\\nStep 3: Classifying Results with LLM\")\n 151→ logger.info(\"-\" * 60)\n 152→ \n 153→ try:\n 154→ analyzer = IssueAnalyzer(lang=lang)\n 155→ analyzer.run(dbs_dir)\n 156→ except LLMConfigError as e:\n 157→ logger.error(\"[-] Step 3: LLM configuration error: %s\", e)\n 158→ _log_exception_cause(e)\n 159→ logger.error(\" Please check your LLM configuration and API credentials in .env file.\")\n 160→ sys.exit(1)\n 161→ except LLMApiError as e:\n 162→ logger.error(\"[-] Step 3: LLM API error: %s\", e)\n 163→ _log_exception_cause(e)\n 164→ logger.error(\" Please check your API key, network connection, and rate limits.\")\n 165→ sys.exit(1)\n 166→ except LLMError as e:\n 167→ logger.error(\"[-] Step 3: LLM error: %s\", e)\n 168→ _log_exception_cause(e)\n 169→ logger.error(\" Please check your LLM provider settings and API status.\")\n 170→ sys.exit(1)\n 171→ except CodeQLError as e:\n 172→ logger.error(\"[-] Step 3: CodeQL error while reading database files: %s\", e)\n 173→ _log_exception_cause(e)\n 174→ logger.error(\" This step reads CodeQL database files (YAML, ZIP, CSV) to prepare data for LLM analysis.\")\n 175→ logger.error(\" Please check your CodeQL databases and files are accessible.\")\n 176→ sys.exit(1)\n 177→ except VulnhallaError as e:\n 178→ logger.error(\"[-] Step 3: File system error while saving results: %s\", e)\n 179→ _log_exception_cause(e)\n 180→ logger.error(\" This step writes analysis results to disk and creates output directories.\")\n 181→ logger.error(\" Please check file permissions and disk space.\")\n 182→ sys.exit(1)\n 183→\n 184→\n 185→def step4_open_ui() -> None:\n 186→ \"\"\"\n 187→ Step 4: Open the results UI (optional).\n 188→\n 189→ Note:\n 190→ This function does not raise exceptions. UI errors are handled internally by the UI module.\n 191→ \"\"\"\n 192→ logger.info(\"\\n[4/4] Opening UI\")\n 193→ logger.info(\"-\" * 60)\n 194→ logger.info(\"[+] Pipeline completed successfully!\")\n 195→ logger.info(\"Opening results UI...\")\n 196→ ui_main()\n 197→\n 198→\n 199→def main_analyze() -> None:\n 200→ \"\"\"\n 201→ CLI entry point for the complete analysis pipeline.\n 202→ \n 203→ Expected usage: \n 204→ vulnhalla [--force] # Fetch from GitHub\n 205→ vulnhalla --local # Use local CodeQL database\n 206→ \"\"\"\n 207→ parser = argparse.ArgumentParser(\n 208→ prog=\"vulnhalla\",\n 209→ description=\"Vulnhalla - Automated CodeQL Analysis with LLM Classification\"\n 210→ )\n 211→ parser.add_argument(\"repo\", nargs=\"?\", help=\"GitHub repository in 'org/repo' format\")\n 212→ parser.add_argument(\"--force\", \"-f\", action=\"store_true\", help=\"Re-download even if database exists\")\n 213→ parser.add_argument(\"--local\", \"-l\", metavar=\"PATH\", help=\"Path to local CodeQL database (skips GitHub fetch)\")\n 214→ parser.add_argument(\"--lang\", choices=[\"c\", \"go\"], default=\"c\", help=\"Programming language to analyze (default: c)\")\n 215→ \n 216→ args = parser.parse_args()\n 217→ \n 218→ # Validate arguments\n 219→ if args.local:\n 220→ # Local database mode\n 221→ local_path = Path(args.local)\n 222→ if not local_path.exists():\n 223→ parser.error(f\"Local database path does not exist: {args.local}\")\n 224→ analyze_pipeline(repo=None, lang=args.lang, local_db_path=str(local_path))\n 225→ elif args.repo:\n 226→ # GitHub fetch mode\n 227→ if \"/\" not in args.repo:\n 228→ parser.error(\"Repository must be in format 'org/repo'\")\n 229→ analyze_pipeline(repo=args.repo, lang=args.lang, force=args.force)\n 230→ else:\n 231→ parser.error(\"Either provide a repository (org/repo) or use --local \")\n 232→\n 233→\n 234→def analyze_pipeline(\n 235→ repo: Optional[str] = None,\n 236→ lang: str = \"c\",\n 237→ threads: int = 16,\n 238→ open_ui: bool = True,\n 239→ force: bool = False,\n 240→ local_db_path: Optional[str] = None\n 241→) -> None:\n 242→ \"\"\"\n 243→ Run the complete Vulnhalla pipeline: fetch, analyze, classify, and optionally open UI.\n 244→ \n 245→ Args:\n 246→ repo: GitHub repository name (e.g., \"redis/redis\"). Required if local_db_path not provided.\n 247→ lang: Programming language code. Defaults to \"c\".\n 248→ threads: Number of threads for CodeQL operations. Defaults to 16.\n 249→ open_ui: Whether to open the UI after completion. Defaults to True.\n 250→ force: If True, re-download even if database exists. Defaults to False.\n 251→ local_db_path: Path to local CodeQL database. If provided, skips GitHub fetch.\n 252→ \n 253→ Note:\n 254→ This function catches and handles all exceptions internally, logging errors\n 255→ and exiting with code 1 on failure. It does not raise exceptions.\n 256→ \"\"\"\n 257→ logger.info(\"🚀 Starting Vulnhalla Analysis Pipeline\")\n 258→ logger.info(\"=\" * 60)\n 259→ \n 260→ # Validate configuration before starting\n 261→ try:\n 262→ validate_and_exit_on_error()\n 263→ except (CodeQLConfigError, LLMConfigError, VulnhallaError) as e:\n 264→ # Format error message for display\n 265→ message = f\"\"\"\n 266→[-] Configuration Validation Failed\n 267→============================================================\n 268→{str(e)}\n 269→============================================================\n 270→Please fix the configuration errors above and try again.\n 271→See README.md for configuration reference.\n 272→\"\"\"\n 273→ logger.error(message)\n 274→ _log_exception_cause(e)\n 275→ sys.exit(1)\n 276→ \n 277→ # Step 1: Fetch CodeQL databases (or use local path)\n 278→ if local_db_path:\n 279→ logger.info(\"\\nStep 1: Using Local CodeQL Database\")\n 280→ logger.info(\"-\" * 60)\n 281→ logger.info(\"Database path: %s\", local_db_path)\n 282→ dbs_dir = local_db_path\n 283→ else:\n 284→ dbs_dir = step1_fetch_codeql_dbs(lang, threads, repo, force)\n 285→ \n 286→ # Step 2: Run CodeQL queries\n 287→ step2_run_codeql_queries(dbs_dir, lang, threads)\n 288→ \n 289→ # Step 3: Classify results with LLM\n 290→ step3_classify_results_with_llm(dbs_dir, lang)\n 291→ \n 292→ # Step 4: Open UI (optional)\n 293→ if open_ui:\n 294→ step4_open_ui()\n 295→\n 296→\n 297→def main_ui() -> None:\n 298→ \"\"\"\n 299→ CLI entry point to open the UI without running analysis.\n 300→ \n 301→ Expected usage: vulnhalla-ui\n 302→ \"\"\"\n 303→ logger.info(\"Opening Vulnhalla UI...\")\n 304→ ui_main()\n 305→\n 306→\n 307→def main_validate() -> None:\n 308→ \"\"\"\n 309→ CLI entry point to validate configuration.\n 310→ \n 311→ Expected usage: vulnhalla-validate\n 312→ \"\"\"\n 313→ from src.utils.config_validator import validate_all_config\n 314→ \n 315→ is_valid, errors = validate_all_config()\n 316→ \n 317→ if is_valid:\n 318→ logger.info(\"[+] All configurations are valid!\")\n 319→ else:\n 320→ for error in errors:\n 321→ logger.error(error)\n 322→ sys.exit(1)\n 323→\n 324→\n 325→def main_list() -> None:\n 326→ \"\"\"\n 327→ CLI entry point to list analyzed repositories.\n 328→ \n 329→ Expected usage: vulnhalla-list\n 330→ \"\"\"\n 331→ from src.ui.results_loader import ResultsLoader\n 332→ \n 333→ results_dir = Path(\"output/results\")\n 334→ if not results_dir.exists():\n 335→ logger.info(\"No results found. Run 'vulnhalla ' first.\")\n 336→ return\n 337→ \n 338→ loader = ResultsLoader()\n 339→ \n 340→ all_issues: list = []\n 341→ results_dir_path = Path(\"output/results\")\n 342→ for lang_dir in sorted(results_dir_path.iterdir()):\n 343→ if lang_dir.is_dir():\n 344→ issues, _ = loader.load_all_issues(lang_dir.name)\n 345→ all_issues.extend(issues)\n 346→ issues = all_issues\n 347→ \n 348→ if not issues:\n 349→ logger.info(\"No analyzed repositories found.\")\n 350→ return\n 351→ \n 352→ # Group issues by repo\n 353→ repos = {}\n 354→ for issue in issues:\n 355→ repo = issue.repo\n 356→ if repo not in repos:\n 357→ repos[repo] = {\"true\": 0, \"false\": 0, \"needs_more_data to decide\": 0}\n 358→ repos[repo][issue.status] += 1\n 359→ \n 360→ logger.info(\"Analyzed repositories:\")\n 361→ logger.info(\"-\" * 50)\n 362→ for repo, counts in sorted(repos.items()):\n 363→ total = counts[\"true\"] + counts[\"false\"] + counts[\"needs_more_data to decide\"]\n 364→ logger.info(\n 365→ \" %-30s %3d issues (%d True positive, %d False positive, %d Needs more data to decide)\",\n 366→ repo, total, counts[\"true\"], counts[\"false\"], counts[\"needs_more_data to decide\"]\n 367→ )\n 368→\n 369→\n 370→def main_example() -> None:\n 371→ \"\"\"\n 372→ CLI entry point to run the example pipeline.\n 373→ \n 374→ Expected usage: vulnhalla-example\n 375→ \"\"\"\n 376→ from examples.example import main as example_main\n 377→ example_main()\n 378→\n 379→\n 380→if __name__ == '__main__':\n 381→ main_analyze()\n\n\nWhenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.\n\n"}]},"uuid":"3e987e7e-6a5f-444f-b1de-863b015844b9","timestamp":"2026-02-11T13:25:02.874Z"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"e8e1df2b-cccf-46cf-9fc0-67b04d1c8848","timestamp":"2026-02-11T13:25:02.994Z"}
{"parentUuid":"e8e1df2b-cccf-46cf-9fc0-67b04d1c8848","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"assistant","timestamp":"2026-02-11T13:25:02.997Z","message":{"model":"claude-haiku-4-5-20251001","id":"msg_01TQWbRySdrA4Ry3dXcnMAN6","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_01VwwQjJFu4MacQNWvWoGXrq","name":"Read","input":{"file_path":"/home/josie/development/personal/Vulnhalla/src/vulnhalla_setup.py"}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":7,"cache_creation_input_tokens":768,"cache_read_input_tokens":16718,"cache_creation":{"ephemeral_5m_input_tokens":0,"ephemeral_1h_input_tokens":768},"output_tokens":1,"service_tier":"standard","inference_geo":"not_available"},"context_management":null},"requestId":"req_011CY2McDKYz2YQR93N53NDq","uuid":"4cd2efb1-be4a-4673-94a4-372dc9910276"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"5c3edd76-33dd-4a37-bf58-7c1c868db4fd","timestamp":"2026-02-11T13:25:02.997Z"}
{"parentUuid":"5c3edd76-33dd-4a37-bf58-7c1c868db4fd","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"user","message":{"role":"user","content":[{"type":"text","text":"Explore the data directory structure for existing language support in Vulnhalla:\n\n1. List and read files in `data/queries/cpp/` - understand the query structure (issues/ and tools/ subdirs)\n2. List and read files in `data/queries/go/` - see how Go queries differ from C++\n3. List and read files in `data/templates/cpp/` - understand LLM prompt templates\n4. List and read files in `data/templates/go/` - see how Go templates differ\n5. Check if there are any qlpack.yml or similar CodeQL pack config files\n\nI need to understand the full pattern for adding a new language's queries and templates."}]},"uuid":"550fb459-84c4-49b2-8d19-c7c7f4259df8","timestamp":"2026-02-11T13:25:02.798Z"},"normalizedMessages":[],"type":"agent_progress","prompt":"Explore the data directory structure for existing language support in Vulnhalla:\n\n1. List and read files in `data/queries/cpp/` - understand the query structure (issues/ and tools/ subdirs)\n2. List and read files in `data/queries/go/` - see how Go queries differ from C++\n3. List and read files in `data/templates/cpp/` - understand LLM prompt templates\n4. List and read files in `data/templates/go/` - see how Go templates differ\n5. Check if there are any qlpack.yml or similar CodeQL pack config files\n\nI need to understand the full pattern for adding a new language's queries and templates.","agentId":"affd883"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01SBzXiYDFMSMi3vxEqQAeQd","uuid":"6c868cc1-88bb-4e0b-9e61-2abbfc81e8bf","timestamp":"2026-02-11T13:25:02.798Z"}
{"parentUuid":"6c868cc1-88bb-4e0b-9e61-2abbfc81e8bf","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"user","message":{"role":"user","content":[{"tool_use_id":"toolu_01VwwQjJFu4MacQNWvWoGXrq","type":"tool_result","content":" 1→#!/usr/bin/env python3\n 2→\"\"\"\n 3→Vulnhalla Setup Command - CodeQL Configuration and Pack Installation\n 4→\n 5→This module provides the `vulnhalla-setup` Poetry CLI command that:\n 6→- Validates CodeQL configuration\n 7→- Installs required CodeQL packs\n 8→\n 9→Note: Python dependencies are managed by Poetry and should be installed via `poetry install`.\n 10→\"\"\"\n 11→\n 12→import os\n 13→import sys\n 14→import subprocess\n 15→import shutil\n 16→from pathlib import Path\n 17→\n 18→# Get project root\n 19→PROJECT_ROOT = Path(__file__).resolve().parent.parent\n 20→\n 21→# Initialize logging early\n 22→from src.utils.logger import setup_logging, get_logger\n 23→setup_logging()\n 24→logger = get_logger(__name__)\n 25→\n 26→\n 27→def main() -> None:\n 28→ \"\"\"\n 29→ Main entry point for vulnhalla-setup command.\n 30→ \n 31→ Validates CodeQL configuration and installs CodeQL packs.\n 32→ \"\"\"\n 33→ logger.info(\"Vulnhalla Setup\")\n 34→ logger.info(\"=\" * 50)\n 35→ \n 36→ # Install CodeQL packs\n 37→ # Check for CodeQL in PATH or .env\n 38→ codeql_cmd = None\n 39→ \n 40→ try:\n 41→ from src.utils.config import get_codeql_path\n 42→ from src.utils.config_validator import find_codeql_executable\n 43→ \n 44→ codeql_path = get_codeql_path()\n 45→ logger.debug(\"Checking CodeQL path: %s\", codeql_path)\n 46→ \n 47→ # Use helper function to find executable\n 48→ codeql_cmd = find_codeql_executable()\n 49→ \n 50→ if codeql_cmd:\n 51→ if codeql_path == \"codeql\":\n 52→ logger.debug(\"Checking if 'codeql' is in PATH...\")\n 53→ logger.info(\"[+] Found in PATH: %s\", codeql_cmd)\n 54→ else:\n 55→ logger.info(\"[+] Found CodeQL path: %s\", codeql_cmd)\n 56→ else:\n 57→ # Provide detailed error messages\n 58→ if codeql_path and codeql_path != \"codeql\":\n 59→ # Custom path specified - strip quotes if present\n 60→ codeql_path_clean = codeql_path.strip('\"').strip(\"'\")\n 61→ logger.error(\"[-] Path does not exist: %s\", codeql_path_clean)\n 62→ if os.name == 'nt':\n 63→ logger.debug(\"Also checked: %s.cmd\", codeql_path_clean)\n 64→ else:\n 65→ logger.debug(\"Checking if 'codeql' is in PATH...\")\n 66→ logger.error(\"[-] 'codeql' not found in PATH\")\n 67→ except Exception as e:\n 68→ # Fallback to checking PATH\n 69→ logger.error(\"[-] Error loading config: %s\", e)\n 70→ logger.debug(\"Falling back to PATH check...\")\n 71→ codeql_cmd = shutil.which(\"codeql\")\n 72→ if codeql_cmd:\n 73→ logger.info(\"[+] Found in PATH: %s\", codeql_cmd)\n 74→ \n 75→ if codeql_cmd:\n 76→ logger.info(\"Installing CodeQL packs... This may take a moment\")\n 77→ \n 78→ queries_root = PROJECT_ROOT / \"data\" / \"queries\"\n 79→ for lang_dir in sorted(queries_root.iterdir()):\n 80→ if not lang_dir.is_dir():\n 81→ continue\n 82→ for pack_type in [\"tools\", \"issues\"]:\n 83→ pack_dir = lang_dir / pack_type\n 84→ if (pack_dir / \"qlpack.yml\").exists():\n 85→ logger.info(\"Installing %s/%s pack...\", lang_dir.name, pack_type)\n 86→ os.chdir(str(pack_dir))\n 87→ result = subprocess.run([codeql_cmd, \"pack\", \"install\"], check=False, capture_output=True, text=True)\n 88→ if result.returncode != 0:\n 89→ logger.warning(\"Failed to install %s/%s pack: %s\", lang_dir.name, pack_type, result.stderr)\n 90→ os.chdir(str(PROJECT_ROOT))\n 91→ else:\n 92→ logger.error(\"[-] CodeQL CLI not found. Skipping CodeQL pack installation.\")\n 93→ logger.info(\"Install CodeQL CLI from: https://github.com/github/codeql-cli-binaries/releases\")\n 94→ logger.info(\"After installation, either add CodeQL to your PATH or set CODEQL_PATH in your .env file.\")\n 95→ logger.info(\"Then run: poetry run vulnhalla-setup or install packages manually\")\n 96→ return\n 97→ \n 98→ # Optional: Validate CodeQL configuration if .env file exists\n 99→ env_file = PROJECT_ROOT / \".env\"\n 100→ if env_file.exists():\n 101→ logger.debug(\"\\nValidating CodeQL configuration...\")\n 102→ try:\n 103→ from src.utils.config_validator import validate_codeql_path\n 104→ is_valid, error = validate_codeql_path()\n 105→ if is_valid:\n 106→ logger.info(\"[+] CodeQL configuration validated successfully!\")\n 107→ else:\n 108→ logger.warning(\"[-] CodeQL configuration issue detected:\")\n 109→ logger.warning(\"%s\", error.split(chr(10))[0]) # Print first line of error\n 110→ logger.warning(\"Please fix this before running the pipeline.\")\n 111→ except Exception as e:\n 112→ logger.warning(\"[-] Could not validate CodeQL configuration: %s\", e)\n 113→ logger.info(\"This is not critical - you can fix configuration later.\")\n 114→ \n 115→ logger.info(\"[+] Setup completed successfully!\")\n 116→ logger.info(\"Next steps:\")\n 117→ if not env_file.exists():\n 118→ logger.info(\"1. Create a .env file with all the required variables (see README.md)\")\n 119→ logger.info(\"2. Run one of the following commands to start the pipeline:\")\n 120→ else:\n 121→ logger.info(\"Run one of the following commands to start the pipeline:\")\n 122→ logger.info(\" • poetry run vulnhalla # Analyze a specific repository\")\n 123→ logger.info(\" • poetry run vulnhalla-example # See a full pipeline run\")\n 124→\n 125→\n 126→if __name__ == \"__main__\":\n 127→ main()\n 128→\n\n\nWhenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.\n\n"}]},"uuid":"89fdadb5-a244-4366-a6ae-d1086d73645f","timestamp":"2026-02-11T13:25:03.041Z"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"948525d7-ef5d-417f-992a-d8039c4b0152","timestamp":"2026-02-11T13:25:03.241Z"}
{"parentUuid":"948525d7-ef5d-417f-992a-d8039c4b0152","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"assistant","timestamp":"2026-02-11T13:25:03.346Z","message":{"model":"claude-haiku-4-5-20251001","id":"msg_01TQWbRySdrA4Ry3dXcnMAN6","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_01RkSTC31SkhHia6XbXTTG26","name":"Read","input":{"file_path":"/home/josie/development/personal/Vulnhalla/src/utils/config.py"}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":7,"cache_creation_input_tokens":768,"cache_read_input_tokens":16718,"cache_creation":{"ephemeral_5m_input_tokens":0,"ephemeral_1h_input_tokens":768},"output_tokens":1,"service_tier":"standard","inference_geo":"not_available"},"context_management":null},"requestId":"req_011CY2McDKYz2YQR93N53NDq","uuid":"03bb6084-7c6d-4bf5-856d-273fac4369dc"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"7fda2732-3772-492a-b4d3-78a8c180c1e4","timestamp":"2026-02-11T13:25:03.346Z"}
{"parentUuid":"7fda2732-3772-492a-b4d3-78a8c180c1e4","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"user","message":{"role":"user","content":[{"tool_use_id":"toolu_01RkSTC31SkhHia6XbXTTG26","type":"tool_result","content":" 1→#!/usr/bin/env python3\n 2→\"\"\"\n 3→Application Configuration Module\n 4→\n 5→Loads general application configuration from .env file or environment variables.\n 6→Handles CodeQL path, GitHub token, and other non-LLM settings.\n 7→\"\"\"\n 8→\n 9→import os\n 10→from pathlib import Path\n 11→from typing import Optional\n 12→from dotenv import load_dotenv\n 13→\n 14→# Load .env file if it exists, otherwise try .env.example\n 15→if Path(\".env\").exists():\n 16→ load_dotenv(\".env\")\n 17→elif Path(\".env.example\").exists():\n 18→ load_dotenv(\".env.example\")\n 19→\n 20→\n 21→def get_codeql_path() -> str:\n 22→ \"\"\"\n 23→ Get CodeQL executable path from .env file or environment variables.\n 24→ \n 25→ Returns:\n 26→ Path to CodeQL executable. Defaults to \"codeql\" if not set.\n 27→ \"\"\"\n 28→ path = os.getenv(\"CODEQL_PATH\", \"codeql\")\n 29→ # Strip quotes and Python raw string prefix if present\n 30→ if path and path != \"codeql\":\n 31→ path = path.strip('\"').strip(\"'\")\n 32→ # Remove 'r' prefix if present (Python raw string syntax, not valid in .env)\n 33→ if path.startswith(\"r\\\"\") or path.startswith(\"r'\"):\n 34→ path = path[2:]\n 35→ path = path.strip('\"').strip(\"'\")\n 36→ return path\n 37→\n 38→\n 39→def get_github_token() -> Optional[str]:\n 40→ \"\"\"\n 41→ Get GitHub API token from .env file or environment variables.\n 42→ \n 43→ Returns:\n 44→ GitHub token string if set, None otherwise.\n 45→ \"\"\"\n 46→ return os.getenv(\"GITHUB_TOKEN\")\n 47→\n 48→\n 49→def get_github_api_url() -> str:\n 50→ \"\"\"\n 51→ Get GitHub API base URL from .env file or environment variables.\n 52→ \n 53→ Supports both github.com and GitHub Enterprise Server.\n 54→ \n 55→ Returns:\n 56→ GitHub API base URL. Defaults to \"https://api.github.com\" for github.com.\n 57→ For GitHub Enterprise: \"https://github.example.com/api/v3\"\n 58→ \"\"\"\n 59→ url = os.getenv(\"GITHUB_API_URL\", \"https://api.github.com\")\n 60→ # Remove trailing slash for consistent URL construction\n 61→ return url.rstrip(\"/\")\n 62→\n 63→\n 64→def get_github_ssl_verify() -> bool:\n 65→ \"\"\"\n 66→ Get GitHub SSL verification setting from .env file or environment variables.\n 67→ \n 68→ For GitHub Enterprise with self-signed or internal CA certificates,\n 69→ set GITHUB_SSL_VERIFY=false to disable certificate verification.\n 70→ \n 71→ Returns:\n 72→ True to verify SSL certificates (default), False to skip verification.\n 73→ \"\"\"\n 74→ value = os.getenv(\"GITHUB_SSL_VERIFY\", \"true\").lower()\n 75→ return value not in (\"false\", \"0\", \"no\", \"off\")\n 76→\n 77→\n\n\nWhenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.\n\n"}]},"uuid":"cef441d7-a9a4-4384-8b82-85265eae254f","timestamp":"2026-02-11T13:25:03.404Z"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"dc8d8b2b-8202-40f6-b4e5-3b0a879b08e4","timestamp":"2026-02-11T13:25:03.442Z"}
{"parentUuid":"dc8d8b2b-8202-40f6-b4e5-3b0a879b08e4","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"assistant","timestamp":"2026-02-11T13:25:03.477Z","message":{"model":"claude-haiku-4-5-20251001","id":"msg_01TQWbRySdrA4Ry3dXcnMAN6","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_01WLnD6WLyt2DkKDHXMDGErE","name":"Bash","input":{"command":"find /home/josie/development/personal/Vulnhalla/src/codeql -name \"*.py\" -type f"}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":7,"cache_creation_input_tokens":768,"cache_read_input_tokens":16718,"cache_creation":{"ephemeral_5m_input_tokens":0,"ephemeral_1h_input_tokens":768},"output_tokens":1,"service_tier":"standard","inference_geo":"not_available"},"context_management":null},"requestId":"req_011CY2McDKYz2YQR93N53NDq","uuid":"ccf8c1ab-0a02-478b-85d5-2e0d2ff1bb98"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"d3556887-2f34-4aa8-996c-89d50aea9d2a","timestamp":"2026-02-11T13:25:03.478Z"}
{"parentUuid":"d3556887-2f34-4aa8-996c-89d50aea9d2a","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"user","message":{"role":"user","content":[{"tool_use_id":"toolu_01WLnD6WLyt2DkKDHXMDGErE","type":"tool_result","content":"/home/josie/development/personal/Vulnhalla/src/codeql/run_codeql_queries.py\n/home/josie/development/personal/Vulnhalla/src/codeql/fetch_repos.py\n/home/josie/development/personal/Vulnhalla/src/codeql/db_lookup.py","is_error":false}]},"uuid":"408274a1-e5af-4f94-a89c-738e5a5dced4","timestamp":"2026-02-11T13:25:03.549Z"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"69a1dd63-eb7d-4095-a77b-84a9eebf0a2f","timestamp":"2026-02-11T13:25:03.596Z"}
{"parentUuid":"69a1dd63-eb7d-4095-a77b-84a9eebf0a2f","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"assistant","timestamp":"2026-02-11T13:25:06.226Z","message":{"model":"claude-haiku-4-5-20251001","id":"msg_016w7rgerJHw4qTN3crNgEn8","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_016w1TSaFUxZcitD1ys7JiRu","name":"Read","input":{"file_path":"/home/josie/development/personal/Vulnhalla/src/codeql/fetch_repos.py"}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":7,"cache_creation_input_tokens":8960,"cache_read_input_tokens":17486,"cache_creation":{"ephemeral_5m_input_tokens":0,"ephemeral_1h_input_tokens":8960},"output_tokens":1,"service_tier":"standard","inference_geo":"not_available"},"context_management":null},"requestId":"req_011CY2McN6Pyp8Zqd3NBGzR8","uuid":"a9b233fa-ba1a-42a0-ab28-ff1f4fc246e0"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"5f4df92f-8a1b-45d8-965e-c8927373bd3d","timestamp":"2026-02-11T13:25:06.226Z"}
{"parentUuid":"5f4df92f-8a1b-45d8-965e-c8927373bd3d","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"assistant","timestamp":"2026-02-11T13:25:06.459Z","message":{"model":"claude-haiku-4-5-20251001","id":"msg_016w7rgerJHw4qTN3crNgEn8","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_01XevCfpzExhqoUWFs2Hxg69","name":"Read","input":{"file_path":"/home/josie/development/personal/Vulnhalla/src/codeql/run_codeql_queries.py"}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":7,"cache_creation_input_tokens":8960,"cache_read_input_tokens":17486,"cache_creation":{"ephemeral_5m_input_tokens":0,"ephemeral_1h_input_tokens":8960},"output_tokens":1,"service_tier":"standard","inference_geo":"not_available"},"context_management":null},"requestId":"req_011CY2McN6Pyp8Zqd3NBGzR8","uuid":"b89459d7-6f24-4e78-914c-a5bd07f2f148"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"ae173ce4-7c56-42a4-95af-1152805385ba","timestamp":"2026-02-11T13:25:06.459Z"}
{"parentUuid":"ae173ce4-7c56-42a4-95af-1152805385ba","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"user","message":{"role":"user","content":[{"tool_use_id":"toolu_016w1TSaFUxZcitD1ys7JiRu","type":"tool_result","content":" 1→#!/usr/bin/env python3\n 2→\"\"\"\n 3→Fetch repositories and their CodeQL databases from GitHub.\n 4→\n 5→Downloads a specific repository's CodeQL database.\n 6→\n 7→Example CLI usage:\n 8→ python fetch_repos.py myOrgName/myRepoName\n 9→\"\"\"\n 10→\n 11→from pathlib import Path\n 12→import sys\n 13→import json\n 14→import time\n 15→import zipfile\n 16→import requests\n 17→from typing import Any, Dict, List\n 18→from pySmartDL import SmartDL\n 19→\n 20→from src.utils.common_functions import read_file, write_file_text, get_all_dbs\n 21→from src.utils.config import get_github_token, get_github_api_url, get_github_ssl_verify\n 22→from src.utils.logger import get_logger\n 23→from src.utils.exceptions import CodeQLError, CodeQLConfigError\n 24→\n 25→logger = get_logger(__name__)\n 26→\n 27→LANG: str = \"c\"\n 28→\n 29→\n 30→def fetch_repos_from_github_api(url: str) -> Dict[str, Any]:\n 31→ \"\"\"\n 32→ Make a GET request to GitHub's API with optional rate-limit handling.\n 33→\n 34→ Args:\n 35→ url (str): The URL to be requested.\n 36→\n 37→ Returns:\n 38→ Dict[str, Any]: JSON response from the GitHub API as a Python dict.\n 39→ \n 40→ Raises:\n 41→ CodeQLConfigError: On 4xx client errors (invalid token, permissions, etc.).\n 42→ CodeQLError: On server errors or other unexpected errors.\n 43→ \"\"\"\n 44→ headers: Dict[str, str] = {}\n 45→ token = get_github_token()\n 46→ if token:\n 47→ headers[\"Authorization\"] = f'token {token}'\n 48→\n 49→ try:\n 50→ response = requests.get(url, headers=headers, verify=get_github_ssl_verify())\n 51→ # Check for HTTP errors\n 52→ try:\n 53→ response.raise_for_status()\n 54→ except requests.HTTPError as http_err:\n 55→ status = response.status_code\n 56→ # Request/config problem\n 57→ if 400 <= status < 500:\n 58→ error_msg = f\"GitHub API returned {status} for {url}\"\n 59→ if status == 401:\n 60→ error_msg += \". Please check your GitHub token - it may be invalid or expired.\"\n 61→ elif status == 403:\n 62→ error_msg += \". Please check your GitHub token permissions.\"\n 63→ else:\n 64→ error_msg += \". Please check your request parameters.\"\n 65→ raise CodeQLConfigError(error_msg) from http_err\n 66→ # CodeQLError\n 67→ raise CodeQLError(f\"GitHub API returned {status} for {url}\") from http_err\n 68→ \n 69→ remaining_requests = response.headers.get(\"X-RateLimit-Remaining\")\n 70→ reset_time = response.headers.get(\"X-RateLimit-Reset\")\n 71→\n 72→ # Approaching the rate limit, wait until reset\n 73→ if remaining_requests and reset_time and int(remaining_requests) < 7:\n 74→ logger.warning(\"Remaining requests: %s\", remaining_requests)\n 75→ logger.warning(\n 76→ \"Rate limit resets at: %s\",\n 77→ time.strftime('%Y-%m-%d %H:%M:%S', time.localtime(int(reset_time)))\n 78→ )\n 79→ wait_time = int(reset_time) - int(time.time())\n 80→ if wait_time > 0:\n 81→ logger.warning(\"Waiting for %.2f minutes until the rate limit resets.\", wait_time / 60)\n 82→ time.sleep(wait_time + 1)\n 83→ if int(remaining_requests) == 0:\n 84→ return fetch_repos_from_github_api(url)\n 85→\n 86→ return response.json()\n 87→ \n 88→ except CodeQLConfigError:\n 89→ raise\n 90→ except requests.RequestException as e:\n 91→ # Network errors\n 92→ raise CodeQLError(f\"Network error while accessing GitHub API: {e}\") from e\n 93→ except (ValueError, json.JSONDecodeError) as e:\n 94→ # Invalid JSON response\n 95→ raise CodeQLError(f\"Invalid response from GitHub API: {e}\") from e\n 96→\n 97→\n 98→def parse_github_search_result(url: str) -> List[Dict[str, Any]]:\n 99→ \"\"\"\n 100→ Retrieve repository information from GitHub search results.\n 101→\n 102→ Args:\n 103→ url (str): The GitHub API search endpoint URL.\n 104→\n 105→ Returns:\n 106→ List[Dict[str, Any]]: A list of repository metadata dictionaries.\n 107→ \n 108→ Raises:\n 109→ CodeQLConfigError: If GitHub API returns 4xx (invalid token, permissions, etc.).\n 110→ CodeQLError: If GitHub API returns 5xx or other errors.\n 111→ \"\"\"\n 112→ page = fetch_repos_from_github_api(url)\n 113→ repos = []\n 114→ for item in page.get(\"items\", []):\n 115→ repos.append(\n 116→ {\n 117→ \"html_url\": item[\"html_url\"],\n 118→ \"repo_name\": item[\"full_name\"],\n 119→ \"forks\": item[\"forks\"],\n 120→ \"stars\": item[\"watchers\"],\n 121→ }\n 122→ )\n 123→ return repos\n 124→\n 125→\n 126→def validate_rate_limit(threads: int) -> None:\n 127→ \"\"\"\n 128→ Check the GitHub rate limit and, if necessary, pause execution\n 129→ until the rate limit resets.\n 130→\n 131→ Args:\n 132→ threads (int): Number of download threads planned; used to estimate\n 133→ how many requests might be made.\n 134→ \n 135→ Raises:\n 136→ CodeQLError: If network error occurs while checking rate limit.\n 137→ \"\"\"\n 138→ try:\n 139→ rate_limit = requests.get(f\"{get_github_api_url()}/rate_limit\", verify=get_github_ssl_verify()).json()\n 140→ except requests.RequestException as e:\n 141→ raise CodeQLError(f\"Network error while checking GitHub rate limit: {e}\") from e\n 142→ except (ValueError, json.JSONDecodeError) as e:\n 143→ raise CodeQLError(f\"Invalid response from GitHub rate limit API: {e}\") from e\n 144→ \n 145→ remaining_requests = rate_limit[\"resources\"][\"core\"][\"remaining\"]\n 146→ reset_time = rate_limit[\"resources\"][\"core\"][\"reset\"]\n 147→ if int(remaining_requests) < threads + 3:\n 148→ logger.warning(\"Remaining requests: %s\", remaining_requests)\n 149→ logger.warning(\n 150→ \"Rate limit resets at: %s\",\n 151→ time.strftime('%Y-%m-%d %H:%M:%S', time.localtime(int(reset_time)))\n 152→ )\n 153→ wait_time = int(reset_time) - int(time.time()) + 120\n 154→ if wait_time > 0:\n 155→ logger.warning(\"Waiting for %.2f minutes until the rate limit resets.\", wait_time / 60)\n 156→ time.sleep(wait_time)\n 157→\n 158→\n 159→def custom_download(url: str, local_filename: str, max_attempts: int = 5, attempt: int = 1, force_full_download: bool = False) -> None:\n 160→ \"\"\"\n 161→ Download a file from GitHub (with optional resume and retry logic).\n 162→\n 163→ Args:\n 164→ url: Direct download URL.\n 165→ local_filename: Destination path on disk.\n 166→ max_attempts: Maximum number of retry attempts.\n 167→ attempt: Current attempt (used internally).\n 168→ force_full_download: If True, download from beginning even if file exists (skip Range header).\n 169→ \n 170→ Raises:\n 171→ CodeQLError: If download fails after all retry attempts, or on non-retryable errors.\n 172→ CodeQLConfigError: On 4xx client errors that indicate configuration issues (e.g., invalid token).\n 173→ \"\"\"\n 174→ # Check if file exists and validate it\n 175→ local_file_path = Path(local_filename)\n 176→ file_size = 0\n 177→ if local_file_path.exists() and not force_full_download:\n 178→ file_size = local_file_path.stat().st_size\n 179→ \n 180→ # Validate if existing file is a valid ZIP\n 181→ if file_size > 0:\n 182→ try:\n 183→ with zipfile.ZipFile(str(local_file_path), \"r\") as zip_ref:\n 184→ zip_ref.testzip() # Test if ZIP is valid\n 185→ except (zipfile.BadZipFile, zipfile.LargeZipFile):\n 186→ # File is corrupted, delete it and start again\n 187→ logger.warning(\"Existing file %s is corrupted. Deleting and starting fresh.\", local_filename)\n 188→ try:\n 189→ local_file_path.unlink()\n 190→ file_size = 0\n 191→ except (PermissionError, OSError) as e:\n 192→ raise CodeQLError(f\"Failed to delete corrupted file {local_filename}: {e}\") from e\n 193→\n 194→ # Set up headers\n 195→ headers = {\"Accept\": \"application/zip\"}\n 196→ token = get_github_token()\n 197→ if token:\n 198→ headers[\"Authorization\"] = f\"token {token}\"\n 199→ if file_size > 0 and not force_full_download:\n 200→ headers[\"Range\"] = f\"bytes={file_size}-\"\n 201→\n 202→ start_time = time.time()\n 203→\n 204→ try:\n 205→ with requests.get(url, headers=headers, stream=True, timeout=300, verify=get_github_ssl_verify()) as response:\n 206→ # Check for 416 Range Not Satisfiable error\n 207→ status = response.status_code\n 208→ if status == 416:\n 209→ # File changed on server, restart download from beginning\n 210→ if attempt < max_attempts:\n 211→ logger.debug(\"Server file changed, restarting download\")\n 212→ return custom_download(url, local_filename, max_attempts, attempt + 1, force_full_download=True)\n 213→ else:\n 214→ raise CodeQLError(\n 215→ f\"Failed to download {url} after {max_attempts} attempts. \"\n 216→ \"416 error suggests file on server may have changed.\"\n 217→ )\n 218→ \n 219→ # HTTP errors handling\n 220→ try:\n 221→ response.raise_for_status()\n 222→ except requests.HTTPError as http_err:\n 223→ status = http_err.response.status_code if http_err.response else None\n 224→ # Request/config problem \n 225→ if status is not None and 400 <= status < 500:\n 226→ raise CodeQLConfigError(\n 227→ f\"GitHub returned {status} while downloading {url}. \"\n 228→ \"Please check your GitHub token / permissions.\"\n 229→ ) from http_err\n 230→ # Handle level below\n 231→ raise\n 232→\n 233→ total_size = int(response.headers.get(\"content-length\", 0)) + file_size\n 234→ logger.debug(\"File size: %d bytes (%.2f MB)\", total_size, total_size / 1_000_000)\n 235→\n 236→ mode = \"ab\" if (file_size > 0 and not force_full_download) else \"wb\"\n 237→ with local_file_path.open(mode) as file:\n 238→ downloaded_size = file_size\n 239→ last_update = time.time()\n 240→\n 241→ for chunk in response.iter_content(chunk_size=8192):\n 242→ if not chunk:\n 243→ continue\n 244→\n 245→ file.write(chunk)\n 246→ downloaded_size += len(chunk)\n 247→\n 248→ current_time = time.time()\n 249→ if current_time - last_update >= 0.1 or downloaded_size == total_size:\n 250→ progress = (downloaded_size / total_size) * 100 if total_size > 0 else 0\n 251→ elapsed = current_time - start_time\n 252→ speed = downloaded_size / elapsed if elapsed > 0 else 0\n 253→\n 254→ downloaded_mb = downloaded_size / 1_000_000\n 255→ total_mb = total_size / 1_000_000\n 256→ speed_mb = speed / 1_000_000\n 257→\n 258→ bar_length = 20\n 259→ filled = int(bar_length * progress / 100)\n 260→ bar = \"█\" * filled + \"░\" * (bar_length - filled)\n 261→\n 262→ print(\n 263→ f\"\\rDownloading: [{bar}] {progress:.1f}% | \"\n 264→ f\"{downloaded_mb:.2f}/{total_mb:.2f} MB | {speed_mb:.2f} MB/s\",\n 265→ end=\"\",\n 266→ flush=True,\n 267→ )\n 268→ last_update = current_time\n 269→\n 270→ print()\n 271→\n 272→ time_taken = time.time() - start_time\n 273→ logger.debug(\"File downloaded successfully as %s\", local_filename)\n 274→ logger.info(\"Download completed in %.2f minutes.\", time_taken / 60)\n 275→\n 276→ except requests.RequestException as e:\n 277→ # Network errors\n 278→ if attempt >= max_attempts:\n 279→ raise CodeQLError(f\"Failed to download {url} after {max_attempts} attempts\") from e\n 280→\n 281→ backoff_time = min(2 ** attempt, 60)\n 282→ logger.warning(\n 283→ \"Network error during download (attempt %d/%d): %s. Retrying in %.1f seconds...\",\n 284→ attempt,\n 285→ max_attempts,\n 286→ e,\n 287→ backoff_time,\n 288→ )\n 289→ time.sleep(backoff_time)\n 290→ return custom_download(\n 291→ url,\n 292→ local_filename,\n 293→ max_attempts=max_attempts,\n 294→ attempt=attempt + 1,\n 295→ )\n 296→\n 297→ except (IOError, OSError) as e:\n 298→ # Disk write errors\n 299→ raise CodeQLError(f\"Failed to write downloaded content to {local_filename}: {e}\") from e\n 300→ except CodeQLConfigError:\n 301→ raise\n 302→ except Exception as e:\n 303→ raise CodeQLError(f\"Unexpected error during download of {url}: {e}\") from e\n 304→\n 305→\n 306→def multi_thread_db_download(url: str, repo_name: str, threads: int = 2) -> str:\n 307→ \"\"\"\n 308→ Download a CodeQL DB .zip file with multiple threads (if no token),\n 309→ or via custom_download (if using a token).\n 310→\n 311→ Args:\n 312→ url (str): The direct download URL.\n 313→ repo_name (str): The repository name used for constructing the .zip path.\n 314→ threads (int, optional): Number of threads for parallel download. Defaults to 2.\n 315→\n 316→ Returns:\n 317→ str: The local file system path to the downloaded .zip.\n 318→ \n 319→ Raises:\n 320→ CodeQLError: If directory creation fails or download fails.\n 321→ CodeQLConfigError: On 4xx client errors during download (if using token).\n 322→ \"\"\"\n 323→ dest_dir = Path(\"output/zip_dbs\") / LANG\n 324→ try:\n 325→ dest_dir.mkdir(parents=True, exist_ok=True)\n 326→ except PermissionError as e:\n 327→ raise CodeQLError(f\"Permission denied creating download directory: {dest_dir}\") from e\n 328→ except OSError as e:\n 329→ raise CodeQLError(f\"OS error creating download directory: {dest_dir}\") from e\n 330→ dest = dest_dir / f\"{repo_name}.zip\"\n 331→\n 332→ request_args = {\"headers\": {\"Accept\": \"application/zip\"}}\n 333→\n 334→ token = get_github_token()\n 335→ if token:\n 336→ custom_download(url, str(dest))\n 337→ return str(dest)\n 338→\n 339→ validate_rate_limit(threads)\n 340→ downloader = SmartDL(\n 341→ url, str(dest), request_args=request_args, threads=threads, progress_bar=False, verify=True\n 342→ )\n 343→ downloader.start()\n 344→ return downloader.get_dest()\n 345→\n 346→\n 347→def unzip_file(zip_path: str, extract_to: str) -> None:\n 348→ \"\"\"\n 349→ Unzip the specified .zip file into the target directory.\n 350→\n 351→ Args:\n 352→ zip_path (str): The path to the .zip file.\n 353→ extract_to (str): Directory path where files will be extracted.\n 354→ \n 355→ Raises:\n 356→ CodeQLError: If ZIP file is invalid, corrupted, or extraction fails.\n 357→ \"\"\"\n 358→ extract_to_path = Path(extract_to)\n 359→ try:\n 360→ extract_to_path.mkdir(parents=True, exist_ok=True)\n 361→ except PermissionError as e:\n 362→ raise CodeQLError(f\"Permission denied creating extraction directory: {extract_to}\") from e\n 363→ except OSError as e:\n 364→ raise CodeQLError(f\"OS error creating extraction directory: {extract_to}\") from e\n 365→ \n 366→ try:\n 367→ with zipfile.ZipFile(zip_path, \"r\") as zip_ref:\n 368→ zip_ref.extractall(str(extract_to_path))\n 369→ except zipfile.BadZipFile as e:\n 370→ raise CodeQLError(f\"Invalid or corrupted ZIP file: {zip_path}\") from e\n 371→ except zipfile.LargeZipFile as e:\n 372→ raise CodeQLError(f\"ZIP file too large to extract: {zip_path}\") from e\n 373→ except PermissionError as e:\n 374→ raise CodeQLError(f\"Permission denied extracting ZIP file: {zip_path}\") from e\n 375→ except OSError as e:\n 376→ raise CodeQLError(f\"OS error extracting ZIP file: {zip_path}\") from e\n 377→\n 378→\n 379→def filter_repos_by_db_and_lang(repos: List[Dict[str, Any]], lang: str) -> List[Dict[str, Any]]:\n 380→ \"\"\"\n 381→ For each repo, fetch available CodeQL databases from the GitHub API.\n 382→\n 383→ Args:\n 384→ repos (List[Dict[str, Any]]): A list of repository info dictionaries.\n 385→ lang (str): The language of interest (e.g., \"c\", \"cpp\").\n 386→\n 387→ Returns:\n 388→ List[Dict[str, Any]]: A list of dictionaries containing DB info\n 389→ for the matching language.\n 390→ \n 391→ Raises:\n 392→ CodeQLConfigError: If GitHub API returns 4xx (invalid token, permissions, etc.).\n 393→ CodeQLError: If GitHub API returns 5xx or other errors.\n 394→ \"\"\"\n 395→ repos_db = []\n 396→ # If language is 'c', the GH DB often has it as 'cpp'\n 397→ gh_lang = \"cpp\" if lang == \"c\" else lang\n 398→\n 399→ for repo in repos:\n 400→ try:\n 401→ db_info = fetch_repos_from_github_api(\n 402→ f\"{get_github_api_url()}/repos/{repo['repo_name']}/code-scanning/codeql/databases\"\n 403→ )\n 404→ except (CodeQLConfigError, CodeQLError):\n 405→ raise\n 406→ except Exception as e:\n 407→ raise CodeQLError(f\"Unexpected error while fetching databases for {repo['repo_name']}: {e}\") from e\n 408→ \n 409→ # db_info might be a list or empty list\n 410→ if not isinstance(db_info, list):\n 411→ # Check if it's an error response from GitHub API\n 412→ if isinstance(db_info, dict):\n 413→ error_msg = db_info.get(\"message\") or db_info.get(\"error\", \"Unknown error\")\n 414→ if \"message\" in db_info or \"error\" in db_info:\n 415→ raise CodeQLError(\n 416→ f\"GitHub API error for {repo['repo_name']}: {error_msg}\"\n 417→ )\n 418→ # If it's not a dict with error, log warning and continue\n 419→ logger.warning(\n 420→ \"Unexpected response format for %s databases: %s (type: %s)\",\n 421→ repo['repo_name'],\n 422→ db_info,\n 423→ type(db_info).__name__\n 424→ )\n 425→ continue\n 426→ \n 427→ for db in db_info:\n 428→ if \"language\" in db and db[\"language\"] == gh_lang:\n 429→ # Validate required fields exist\n 430→ if \"url\" not in db:\n 431→ logger.warning(\"Database entry missing 'url' field for %s, skipping\", repo['repo_name'])\n 432→ continue\n 433→ repos_db.append(\n 434→ {\n 435→ \"repo_name\": repo[\"repo_name\"],\n 436→ \"html_url\": repo[\"html_url\"],\n 437→ \"content_type\": db.get(\"content_type\", \"application/zip\"),\n 438→ \"size\": db.get(\"size\", 0),\n 439→ \"db_url\": db[\"url\"],\n 440→ \"forks\": repo[\"forks\"],\n 441→ \"stars\": repo[\"stars\"],\n 442→ }\n 443→ )\n 444→ return repos_db\n 445→\n 446→\n 447→def search_top_matching_repos(max_repos: int, lang: str) -> List[Dict[str, Any]]:\n 448→ \"\"\"\n 449→ Gather a list of repositories (sorted by stars) and retrieve\n 450→ their CodeQL DB info for the specified language.\n 451→\n 452→ Args:\n 453→ max_repos (int): Number of repositories to stop after collecting.\n 454→ lang (str): The programming language for which to search\n 455→ (e.g., \"c\" or \"cpp\").\n 456→\n 457→ Returns:\n 458→ List[Dict[str, Any]]: A list of dictionaries containing each repo's DB info.\n 459→ \n 460→ Raises:\n 461→ CodeQLConfigError: If GitHub API returns 4xx (invalid token, permissions, etc.).\n 462→ CodeQLError: If GitHub API returns 5xx or other errors.\n 463→ \"\"\"\n 464→ repos_db: List[Dict[str, Any]] = []\n 465→ curr_page = 1\n 466→\n 467→ while len(repos_db) < max_repos:\n 468→ # Search for top-starred repos by language\n 469→ search_url = (\n 470→ f\"{get_github_api_url()}/search/repositories\"\n 471→ f\"?q=language:{lang}&sort=stars&order=desc&page={curr_page}\"\n 472→ )\n 473→ all_repos = parse_github_search_result(search_url)\n 474→\n 475→ db_in_page = filter_repos_by_db_and_lang(all_repos, lang)\n 476→ repos_db += db_in_page\n 477→\n 478→ curr_page += 1\n 479→\n 480→ return repos_db[:max_repos]\n 481→\n 482→\n 483→def download_and_extract_db(repo: Dict[str, Any], threads: int, extract_folder: str) -> str:\n 484→ \"\"\"\n 485→ Handle the download and extraction of a single repository's CodeQL DB.\n 486→\n 487→ Args:\n 488→ repo (Dict[str, Any]): The repository DB info dictionary.\n 489→ threads (int): Number of threads for multi-threaded download.\n 490→ extract_folder (str): Where to extract the DB files.\n 491→ \n 492→ Returns:\n 493→ str: Path to the directory containing downloaded database.\n 494→ \n 495→ Raises:\n 496→ CodeQLError: If download, extraction, or folder rename fails.\n 497→ CodeQLConfigError: On 4xx client errors during download (e.g., invalid token).\n 498→ \"\"\"\n 499→ org_name, repo_name = repo[\"repo_name\"].split(\"/\")\n 500→ logger.info(\"Downloading repo %s/%s\", org_name, repo_name)\n 501→ zip_path = multi_thread_db_download(repo[\"db_url\"], repo_name, threads)\n 502→ db_path = Path(extract_folder) / repo_name\n 503→ unzip_file(zip_path, str(db_path))\n 504→ time.sleep(1) # Let file system sync\n 505→\n 506→ # Rename the extracted folder if needed (with retry for Windows file locking)\n 507→ source_path = None\n 508→ target_path = db_path / repo_name\n 509→ codeql_db_path = db_path / \"codeql_db\"\n 510→ lang_path = db_path / LANG\n 511→\n 512→ if codeql_db_path.exists():\n 513→ source_path = codeql_db_path\n 514→ elif lang_path.exists():\n 515→ source_path = lang_path\n 516→\n 517→ if source_path and not target_path.exists():\n 518→ # Retry rename with delays (Windows may lock files temporarily)\n 519→ for attempt in range(3):\n 520→ try:\n 521→ time.sleep(0.5 * (attempt + 1)) # Increasing delay: 0.5s, 1s, 1.5s\n 522→ source_path.rename(target_path)\n 523→ break\n 524→ except (PermissionError, OSError) as e:\n 525→ if attempt == 2:\n 526→ error_msg = (\n 527→ f\"Could not rename {source_path} to {target_path}. \"\n 528→ \"The folder may be locked. Please close any IDEs, File Explorer, \"\n 529→ \"or antivirus that might be accessing this folder, then run the script again.\"\n 530→ )\n 531→ raise CodeQLError(error_msg) from e\n 532→\n 533→ if target_path.exists():\n 534→ return str(target_path)\n 535→ return str(db_path)\n 536→\n 537→\n 538→def download_db_by_name(repo_name: str, lang: str, threads: int) -> str:\n 539→ \"\"\"\n 540→ Download the CodeQL database for a single repository.\n 541→\n 542→ Args:\n 543→ repo_name (str): The repository in 'org/repo' format.\n 544→ lang (str): The language to pass to GH DB detection (e.g., 'c').\n 545→ threads (int): Number of threads to use for download.\n 546→ \n 547→ Returns:\n 548→ str: Path to the directory containing downloaded database.\n 549→\n 550→ Raises:\n 551→ CodeQLConfigError: If GitHub API returns 4xx (invalid token, permissions, etc.) \n 552→ during database lookup or download.\n 553→ CodeQLError: If GitHub API returns 5xx, download fails, or other errors occur.\n 554→ \n 555→ Note:\n 556→ If no database is found for the specified language, a warning is logged\n 557→ and the function returns without raising an error.\n 558→ \"\"\"\n 559→ # Build a minimal repo dict to be processed\n 560→ repo = {\"stars\": 0, \"forks\": 0, \"repo_name\": repo_name, \"html_url\": \"\"}\n 561→ repo_db = filter_repos_by_db_and_lang([repo], lang)\n 562→ if not repo_db:\n 563→ logger.warning(\"No %s DB found for %s\", lang, repo_name)\n 564→ return []\n 565→ return download_and_extract_db(repo_db[0], threads, str(Path(\"output/databases\") / lang))\n 566→\n 567→\n 568→def fetch_codeql_dbs(\n 569→ lang: str = \"c\",\n 570→ threads: int = 4,\n 571→ repo_name: str | None = None,\n 572→ force: bool = False\n 573→) -> str:\n 574→ \"\"\"\n 575→ Fetch and download CodeQL databases for GitHub repositories.\n 576→\n 577→ Args:\n 578→ lang (str, optional): The programming language. Defaults to \"c\".\n 579→ threads (int, optional): Number of threads for multi-threaded download. Defaults to 4.\n 580→ repo_name (str, optional): Downloads this repository's DB.\n 581→ Format: \"org/repo\". Defaults to None.\n 582→ force (bool, optional): Re-download even if database exists. Defaults to False.\n 583→ \n 584→ Returns:\n 585→ str: Path to the directory containing downloaded database.\n 586→ \n 587→ Raises:\n 588→ CodeQLError: If directory creation, download, or extraction fails.\n 589→ CodeQLConfigError: On 4xx client errors (invalid token, permissions, etc.).\n 590→ \"\"\"\n 591→ # Ensure needed directories exist\n 592→ db_folder_path = Path(\"output/databases\") / lang\n 593→ try:\n 594→ db_folder_path.mkdir(parents=True, exist_ok=True)\n 595→ except PermissionError as e:\n 596→ raise CodeQLError(f\"Permission denied creating database directory: {db_folder_path}\") from e\n 597→ except OSError as e:\n 598→ raise CodeQLError(f\"OS error creating database directory: {db_folder_path}\") from e\n 599→\n 600→ zip_folder_path = Path(\"output/zip_dbs\") / lang\n 601→ try:\n 602→ zip_folder_path.mkdir(parents=True, exist_ok=True)\n 603→ except PermissionError as e:\n 604→ raise CodeQLError(f\"Permission denied creating ZIP directory: {zip_folder_path}\") from e\n 605→ except OSError as e:\n 606→ raise CodeQLError(f\"OS error creating ZIP directory: {zip_folder_path}\") from e\n 607→ \n 608→ # Check if database already exists\n 609→ _, just_repo_name = repo_name.split(\"/\")\n 610→ target_path = db_folder_path / just_repo_name\n 611→ if target_path.exists() and not force:\n 612→ logger.info(\"Database already exists at %s, skipping download (use --force to re-download)\", target_path)\n 613→ return str(target_path)\n 614→ \n 615→ # If force, delete existing ZIP to avoid resume issues\n 616→ if force and target_path.exists():\n 617→ zip_file = zip_folder_path / f\"{just_repo_name}.zip\"\n 618→ if zip_file.exists():\n 619→ zip_file.unlink()\n 620→ \n 621→ return download_db_by_name(repo_name, lang, threads)\n 622→\n 623→\n 624→def main_cli() -> None:\n 625→ \"\"\"\n 626→ CLI entry point. Downloads a specific repository's CodeQL database.\n 627→ Requires an argument 'org/repo' to specify which repository to fetch.\n 628→ \"\"\"\n 629→ logger.info(\"Current lang: %s\", LANG)\n 630→\n 631→ if len(sys.argv) == 1:\n 632→ raise CodeQLError(\"No arguments provided\")\n 633→ else:\n 634→ # If a single arg is provided, assume it's an 'org/repo' to fetch\n 635→ if \"/\" in sys.argv[1]:\n 636→ fetch_codeql_dbs(lang=LANG, threads=4, repo_name=sys.argv[1])\n 637→ else:\n 638→ logger.error(\"Usage:\\n python fetch_repos.py\\n or\\n python fetch_repos.py orgName/repoName\")\n 639→\n 640→\n 641→if __name__ == \"__main__\":\n 642→ main_cli()\n 643→\n\n\nWhenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.\n\n"}]},"uuid":"a4a0cf99-5909-4ccd-9279-3661f67f80bf","timestamp":"2026-02-11T13:25:06.518Z"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"9dc097e6-cdf0-4c56-bd80-0e0c6c9efc6f","timestamp":"2026-02-11T13:25:06.656Z"}
{"parentUuid":"9dc097e6-cdf0-4c56-bd80-0e0c6c9efc6f","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"user","message":{"role":"user","content":[{"tool_use_id":"toolu_01XevCfpzExhqoUWFs2Hxg69","type":"tool_result","content":" 1→#!/usr/bin/env python3\n 2→\"\"\"\n 3→Compile and run CodeQL queries on CodeQL databases for a specific language.\n 4→\n 5→Requires that CodeQL is installed or available under the CODEQL path.\n 6→By default, it compiles all .ql files under 'data/queries//tools' and\n 7→'data/queries//issues', then runs them on each CodeQL database located\n 8→in 'output/databases/'.\n 9→\n 10→Example:\n 11→ python src/codeql/run_codeql_queries.py\n 12→\"\"\"\n 13→\n 14→import subprocess\n 15→from pathlib import Path\n 16→from typing import List, Optional\n 17→\n 18→# Make sure your common_functions module is in your PYTHONPATH or same folder\n 19→from src.utils.common_functions import get_all_dbs\n 20→from src.utils.config import get_codeql_path\n 21→from src.utils.logger import get_logger\n 22→from src.utils.exceptions import CodeQLError, CodeQLConfigError, CodeQLExecutionError\n 23→\n 24→logger = get_logger(__name__)\n 25→\n 26→\n 27→# Default locations/values\n 28→DEFAULT_CODEQL = get_codeql_path()\n 29→DEFAULT_LANG = \"c\" # Mapped to data/queries/cpp for some tasks\n 30→\n 31→\n 32→def pre_compile_ql(file_name: str, threads: int, codeql_bin: str) -> None:\n 33→ \"\"\"\n 34→ Pre-compile a single .ql file using CodeQL.\n 35→\n 36→ Args:\n 37→ file_name (str): The path to the .ql query file.\n 38→ threads (int): Number of threads to use during compilation.\n 39→ codeql_bin (str): Full path to the 'codeql' executable.\n 40→ \n 41→ Raises:\n 42→ CodeQLConfigError: If CodeQL executable not found.\n 43→ CodeQLExecutionError: If query compilation fails.\n 44→ \"\"\"\n 45→ qlx_path = Path(str(file_name) + \"x\")\n 46→ if not qlx_path.exists():\n 47→ try:\n 48→ subprocess.run(\n 49→ [\n 50→ codeql_bin,\n 51→ \"query\",\n 52→ \"compile\",\n 53→ file_name,\n 54→ f'--threads={threads}',\n 55→ \"--precompile\"\n 56→ ],\n 57→ check=True,\n 58→ text=True,\n 59→ stdout=subprocess.DEVNULL,\n 60→ stderr=subprocess.DEVNULL\n 61→ )\n 62→ except FileNotFoundError as e:\n 63→ raise CodeQLConfigError(\n 64→ f\"CodeQL executable not found: {codeql_bin}. \"\n 65→ \"Please check your CODEQL_PATH configuration.\"\n 66→ ) from e\n 67→ except subprocess.CalledProcessError as e:\n 68→ raise CodeQLExecutionError(\n 69→ f\"Failed to compile query {file_name}: CodeQL returned exit code {e.returncode}\"\n 70→ ) from e\n 71→\n 72→\n 73→def compile_all_queries(queries_folder: str, threads: int, codeql_bin: str) -> None:\n 74→ \"\"\"\n 75→ Recursively pre-compile all .ql files in a folder.\n 76→\n 77→ Args:\n 78→ queries_folder (str): Directory containing .ql files (and possibly subdirectories).\n 79→ threads (int): Number of threads to use during compilation.\n 80→ codeql_bin (str): Full path to the 'codeql' executable.\n 81→ \n 82→ Raises:\n 83→ CodeQLConfigError: If CodeQL executable not found.\n 84→ CodeQLExecutionError: If query compilation fails.\n 85→ \"\"\"\n 86→ queries_folder_path = Path(queries_folder)\n 87→ for file_path in queries_folder_path.rglob(\"*\"):\n 88→ if file_path.is_file() and file_path.suffix.lower() == \".ql\":\n 89→ pre_compile_ql(str(file_path), threads, codeql_bin)\n 90→\n 91→\n 92→def run_one_query(\n 93→ query_file: str,\n 94→ curr_db: str,\n 95→ output_bqrs: str,\n 96→ output_csv: str,\n 97→ threads: int,\n 98→ codeql_bin: str\n 99→) -> None:\n 100→ \"\"\"\n 101→ Execute a single CodeQL query on a specific database and export the results.\n 102→\n 103→ Args:\n 104→ query_file (str): The path to the .ql file to run.\n 105→ curr_db (str): The path to the CodeQL database on which to run queries.\n 106→ output_bqrs (str): Where to write the intermediate BQRS output.\n 107→ output_csv (str): Where to write the CSV representation of the results.\n 108→ threads (int): Number of threads to use during query execution.\n 109→ codeql_bin (str): Full path to the 'codeql' executable.\n 110→ \n 111→ Raises:\n 112→ CodeQLConfigError: If CodeQL executable not found.\n 113→ CodeQLExecutionError: If query execution or BQRS decoding fails.\n 114→ \"\"\"\n 115→ # Run the query\n 116→ try:\n 117→ subprocess.run(\n 118→ [\n 119→ codeql_bin, \"query\", \"run\", query_file,\n 120→ f'--database={curr_db}',\n 121→ f'--output={output_bqrs}',\n 122→ f'--threads={threads}'\n 123→ ],\n 124→ check=True,\n 125→ text=True,\n 126→ stdout=subprocess.DEVNULL,\n 127→ stderr=subprocess.DEVNULL\n 128→ )\n 129→ except FileNotFoundError as e:\n 130→ raise CodeQLConfigError(\n 131→ f\"CodeQL executable not found: {codeql_bin}. \"\n 132→ \"Please check your CODEQL_PATH configuration.\"\n 133→ ) from e\n 134→ except subprocess.CalledProcessError as e:\n 135→ raise CodeQLExecutionError(\n 136→ f\"Failed to run query {query_file} on database {curr_db}: \"\n 137→ f\"CodeQL returned exit code {e.returncode}\"\n 138→ ) from e\n 139→\n 140→ # Decode BQRS to CSV\n 141→ try:\n 142→ subprocess.run(\n 143→ [\n 144→ codeql_bin, \"bqrs\", \"decode\", output_bqrs,\n 145→ '--format=csv', f'--output={output_csv}'\n 146→ ],\n 147→ check=True,\n 148→ text=True,\n 149→ stdout=subprocess.DEVNULL,\n 150→ stderr=subprocess.DEVNULL\n 151→ )\n 152→ except subprocess.CalledProcessError as e:\n 153→ raise CodeQLExecutionError(\n 154→ f\"Failed to decode BQRS file {output_bqrs} to CSV: \"\n 155→ f\"CodeQL returned exit code {e.returncode}\"\n 156→ ) from e\n 157→\n 158→\n 159→def run_queries_on_db(\n 160→ curr_db: str,\n 161→ tools_folder: str,\n 162→ queries_folder: str,\n 163→ threads: int,\n 164→ codeql_bin: str,\n 165→ timeout: int = 300\n 166→) -> None:\n 167→ \"\"\"\n 168→ Execute all tool queries in 'tools_folder' individually on a given database,\n 169→ then run 'database analyze' with all queries in 'queries_folder'.\n 170→\n 171→ Args:\n 172→ curr_db (str): The path to the CodeQL database.\n 173→ tools_folder (str): Folder containing individual .ql files to run.\n 174→ queries_folder (str): Folder containing .ql queries for database analysis.\n 175→ threads (int): Number of threads to use during query execution.\n 176→ codeql_bin (str): Full path to the 'codeql' executable.\n 177→ timeout (int, optional): Timeout in seconds for the 'database analyze' command.\n 178→ Defaults to 300.\n 179→ \n 180→ Raises:\n 181→ CodeQLConfigError: If CodeQL executable not found.\n 182→ CodeQLExecutionError: If query execution or database analysis fails.\n 183→ \"\"\"\n 184→ # 1) Run each .ql in tools_folder individually\n 185→ tools_folder_path = Path(tools_folder)\n 186→ if tools_folder_path.is_dir():\n 187→ for file_path in tools_folder_path.iterdir():\n 188→ if file_path.is_file() and file_path.suffix.lower() == \".ql\":\n 189→ file_stem = file_path.stem\n 190→ run_one_query(\n 191→ str(file_path),\n 192→ curr_db,\n 193→ str(Path(curr_db) / f\"{file_stem}.bqrs\"),\n 194→ str(Path(curr_db) / f\"{file_stem}.csv\"),\n 195→ threads,\n 196→ codeql_bin\n 197→ )\n 198→ else:\n 199→ logger.warning(\"Tools folder '%s' not found. Skipping individual queries.\", tools_folder)\n 200→\n 201→ # 2) Run the entire queries folder in one go using database analyze\n 202→ queries_folder_path = Path(queries_folder)\n 203→ if queries_folder_path.is_dir():\n 204→ try:\n 205→ subprocess.run(\n 206→ [\n 207→ codeql_bin,\n 208→ \"database\",\n 209→ \"analyze\",\n 210→ curr_db,\n 211→ queries_folder,\n 212→ f'--timeout={timeout}',\n 213→ '--format=csv',\n 214→ f'--output={str(Path(curr_db) / \"issues.csv\")}',\n 215→ f'--threads={threads}'\n 216→ ],\n 217→ check=True,\n 218→ text=True,\n 219→ stdout=subprocess.DEVNULL,\n 220→ stderr=subprocess.DEVNULL\n 221→ )\n 222→ except FileNotFoundError as e:\n 223→ raise CodeQLConfigError(\n 224→ f\"CodeQL executable not found: {codeql_bin}. \"\n 225→ \"Please check your CODEQL_PATH configuration.\"\n 226→ ) from e\n 227→ except subprocess.CalledProcessError as e:\n 228→ raise CodeQLExecutionError(\n 229→ f\"Failed to analyze database {curr_db} with queries from {queries_folder}: \"\n 230→ f\"CodeQL returned exit code {e.returncode}\"\n 231→ ) from e\n 232→ else:\n 233→ logger.warning(\"Queries folder '%s' not found. Skipping database analysis.\", queries_folder)\n 234→\n 235→\n 236→def compile_and_run_codeql_queries(\n 237→ codeql_bin: str = DEFAULT_CODEQL,\n 238→ lang: str = DEFAULT_LANG,\n 239→ threads: int = 16,\n 240→ timeout: int = 300,\n 241→ *,\n 242→ dbs_dir: str\n 243→) -> None:\n 244→ \"\"\"\n 245→ Compile and run CodeQL queries on CodeQL databases for a specific language.\n 246→\n 247→ 1. Pre-compile all .ql files in the tools and queries folders.\n 248→ 2. Enumerate all CodeQL DBs for the given language.\n 249→ 3. Run each DB against both the 'tools' and 'issues' queries folders.\n 250→\n 251→ Args:\n 252→ codeql_bin (str, optional): Full path to the 'codeql' executable. Defaults to DEFAULT_CODEQL.\n 253→ lang (str, optional): Language code. Defaults to 'c' (which maps to data/queries/cpp).\n 254→ threads (int, optional): Number of threads for compilation/execution. Defaults to 16.\n 255→ timeout (int, optional): Timeout in seconds for database analysis. Defaults to 300.\n 256→ dbs_dir (str): The path to the CodeQL databases.\n 257→ \n 258→ Raises:\n 259→ CodeQLConfigError: If CodeQL executable not found (from compilation or query execution).\n 260→ CodeQLExecutionError: If query compilation or execution fails.\n 261→ \"\"\"\n 262→ # Setup paths\n 263→ queries_subfolder = \"cpp\" if lang == \"c\" else lang\n 264→ queries_folder = str(Path(\"data/queries\") / queries_subfolder / \"issues\")\n 265→ tools_folder = str(Path(\"data/queries\") / queries_subfolder / \"tools\")\n 266→\n 267→ # Step 1: Pre-compile all queries\n 268→ compile_all_queries(tools_folder, threads, codeql_bin)\n 269→ compile_all_queries(queries_folder, threads, codeql_bin)\n 270→\n 271→ # Step 2: Run queries\n 272→ # Validate database directory exists and is accessible\n 273→ dbs_folder_path = Path(dbs_dir)\n 274→ if not dbs_folder_path.exists():\n 275→ logger.warning(\"Database folder '%s' does not exist. No databases to process.\", dbs_dir)\n 276→ logger.warning(\"Make sure databases were downloaded and extracted successfully.\")\n 277→ return\n 278→ \n 279→ if not dbs_folder_path.is_dir():\n 280→ logger.warning(\"Database path '%s' is not a directory. No databases to process.\", dbs_dir)\n 281→ return\n 282→ \n 283→ # List what's in the folder for debugging\n 284→ try:\n 285→ contents = list(dbs_folder_path.iterdir())\n 286→ if len(contents) == 0:\n 287→ logger.warning(\"Database folder '%s' is empty. No databases to process.\", dbs_dir)\n 288→ return\n 289→ logger.debug(\"Found %d item(s) in database folder: %s\", len(contents), [str(c) for c in contents])\n 290→ except OSError as e:\n 291→ logger.warning(\"Cannot access database folder '%s': %s. No databases to process.\", dbs_dir, e)\n 292→ return\n 293→ \n 294→ actual_dbs = get_all_dbs(dbs_dir)\n 295→\n 296→ if len(actual_dbs) == 0:\n 297→ logger.warning(\"No valid databases found in '%s'. Expected structure: ///codeql-database.yml\", dbs_dir)\n 298→ logger.warning(\"Make sure databases were downloaded and extracted successfully.\")\n 299→ return\n 300→\n 301→ for curr_db in actual_dbs:\n 302→ # Check if database folder is empty\n 303→ curr_db_path = Path(curr_db)\n 304→ if curr_db_path.is_dir():\n 305→ try:\n 306→ if len(list(curr_db_path.iterdir())) == 0:\n 307→ logger.warning(\"Database folder '%s' is empty. Skipping queries.\", curr_db)\n 308→ continue\n 309→ except OSError:\n 310→ logger.warning(\"Cannot access database folder '%s'. Skipping.\", curr_db)\n 311→ continue\n 312→ \n 313→ # If issues.csv was not generated yet, or FunctionTree.csv missing, run\n 314→ if (not (curr_db_path / \"FunctionTree.csv\").exists() or\n 315→ not (curr_db_path / \"issues.csv\").exists()):\n 316→ logger.info(\"Processing DB: %s\", curr_db)\n 317→ run_queries_on_db(\n 318→ curr_db,\n 319→ tools_folder,\n 320→ queries_folder,\n 321→ threads,\n 322→ codeql_bin,\n 323→ timeout\n 324→ )\n 325→ else:\n 326→ logger.info(\"Output files already exist for this DB, skipping...\")\n 327→\n 328→ logger.info(\"[+] done!\")\n 329→\n 330→\n 331→def main_cli() -> None:\n 332→ \"\"\"\n 333→ CLI entry point for running codeql queries with defaults.\n 334→ \"\"\"\n 335→ compile_and_run_codeql_queries(\n 336→ codeql_bin=DEFAULT_CODEQL,\n 337→ lang=DEFAULT_LANG,\n 338→ threads=16,\n 339→ timeout=300,\n 340→ dbs_dir=\"output/databases/c\"\n 341→ )\n 342→\n 343→\n 344→if __name__ == '__main__':\n 345→ # Initialize logging\n 346→ from src.utils.logger import setup_logging\n 347→ setup_logging()\n 348→ \n 349→ main_cli()\n 350→\n\n\nWhenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.\n\n"}]},"uuid":"4c94047d-f18f-472e-81f6-300efd18ea07","timestamp":"2026-02-11T13:25:06.505Z"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"0b8fbdbb-9733-406f-a81b-eb62c17420c3","timestamp":"2026-02-11T13:25:06.656Z"}
{"parentUuid":"0b8fbdbb-9733-406f-a81b-eb62c17420c3","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"assistant","timestamp":"2026-02-11T13:25:06.693Z","message":{"model":"claude-haiku-4-5-20251001","id":"msg_016w7rgerJHw4qTN3crNgEn8","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_01EdXJhUVAGDzMCbg1Phpkcc","name":"Read","input":{"file_path":"/home/josie/development/personal/Vulnhalla/src/codeql/db_lookup.py"}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":7,"cache_creation_input_tokens":8960,"cache_read_input_tokens":17486,"cache_creation":{"ephemeral_5m_input_tokens":0,"ephemeral_1h_input_tokens":8960},"output_tokens":1,"service_tier":"standard","inference_geo":"not_available"},"context_management":null},"requestId":"req_011CY2McN6Pyp8Zqd3NBGzR8","uuid":"294bf013-f8d9-4c72-bc9d-82c2dfc0053a"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"64f7acd8-aa7d-4a43-a78b-094bccac9e1e","timestamp":"2026-02-11T13:25:06.693Z"}
{"parentUuid":"64f7acd8-aa7d-4a43-a78b-094bccac9e1e","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"user","message":{"role":"user","content":[{"tool_use_id":"toolu_01EdXJhUVAGDzMCbg1Phpkcc","type":"tool_result","content":" 1→\"\"\"\n 2→CodeQL database lookup utilities.\n 3→\n 4→This module provides functions to query CodeQL CSV files (FunctionTree.csv,\n 5→Macros.csv, GlobalVars.csv, Classes.csv) and extract code snippets from\n 6→the source archive.\n 7→\"\"\"\n 8→\n 9→from pathlib import Path\n 10→from typing import Any, Dict, List, Optional, Tuple, Union\n 11→\n 12→from src.utils.exceptions import CodeQLError\n 13→from src.utils.common_functions import read_file_lines_from_zip\n 14→from src.utils.csv_parser import parse_csv_row\n 15→\n 16→\n 17→class CodeQLDBLookup:\n 18→ \"\"\"\n 19→ Encapsulates CodeQL database lookup operations for functions, macros,\n 20→ global variables, classes, and caller relationships.\n 21→ \"\"\"\n 22→\n 23→ def _iter_csv_lines(\n 24→ self,\n 25→ file_path: Union[str, Path],\n 26→ file_type_name: str\n 27→ ):\n 28→ \"\"\"\n 29→ Generator that yields lines from a CSV file, handling file I/O errors.\n 30→\n 31→ This helper centralizes CSV file opening, line iteration, and error handling.\n 32→ Each method can iterate over the yielded lines and apply method-specific logic.\n 33→\n 34→ Args:\n 35→ file_path: Path to the CSV file to read.\n 36→ file_type_name: Descriptive name for the file type (e.g., \"Function tree file\",\n 37→ \"Macros CSV\", \"GlobalVars CSV\") for error messages.\n 38→\n 39→ Yields:\n 40→ str: Each line from the CSV file (including newline characters).\n 41→\n 42→ Raises:\n 43→ CodeQLError: If file cannot be read (not found, permission denied, etc.).\n 44→ \"\"\"\n 45→ try:\n 46→ with Path(file_path).open(\"r\", encoding=\"utf-8\") as f:\n 47→ while True:\n 48→ line = f.readline()\n 49→ if not line:\n 50→ break\n 51→ yield line\n 52→ except (FileNotFoundError, PermissionError, OSError) as e:\n 53→ raise self._convert_csv_file_error(e, file_path, file_type_name) from e\n 54→\n 55→\n 56→ @staticmethod\n 57→ def _convert_csv_file_error(\n 58→ error: Exception,\n 59→ file_path: Union[str, Path],\n 60→ file_type_name: str\n 61→ ) -> CodeQLError:\n 62→ \"\"\"\n 63→ Convert file I/O exceptions to CodeQLError with consistent messaging.\n 64→\n 65→ Args:\n 66→ error: The original exception (FileNotFoundError, PermissionError, or OSError).\n 67→ file_path: Path to the CSV file that caused the error.\n 68→ file_type_name: Descriptive name for the file type (e.g., \"Function tree file\",\n 69→ \"Macros CSV\", \"GlobalVars CSV\") for error messages.\n 70→\n 71→ Returns:\n 72→ CodeQLError: Converted exception with appropriate message.\n 73→ \"\"\"\n 74→ file_path_str = str(file_path)\n 75→ if isinstance(error, FileNotFoundError):\n 76→ return CodeQLError(f\"{file_type_name} not found: {file_path_str}\")\n 77→ elif isinstance(error, PermissionError):\n 78→ return CodeQLError(f\"Permission denied reading {file_type_name}: {file_path_str}\")\n 79→ elif isinstance(error, OSError):\n 80→ return CodeQLError(f\"OS error while reading {file_type_name}: {file_path_str}\")\n 81→ else:\n 82→ # Fallback for unexpected exception types\n 83→ return CodeQLError(f\"Error reading {file_type_name}: {file_path_str}\")\n 84→\n 85→\n 86→ def get_function_by_line(\n 87→ self,\n 88→ function_tree_file: str,\n 89→ file: str,\n 90→ line: int\n 91→ ) -> Optional[Dict[str, str]]:\n 92→ \"\"\"\n 93→ Retrieve the function dictionary from a CSV (FunctionTree.csv) that matches\n 94→ the specified file and line coverage.\n 95→\n 96→ Args:\n 97→ function_tree_file (str): Path to the FunctionTree.csv file.\n 98→ file (str): Name of the file as it appears in the CSV row.\n 99→ line (int): A line number within the function's start_line and end_line range.\n 100→\n 101→ Returns:\n 102→ Optional[Dict[str, str]]: The matching function row as a dict, or None if not found.\n 103→ \n 104→ Raises:\n 105→ CodeQLError: If function tree file cannot be read (not found, permission denied, etc.).\n 106→ \"\"\"\n 107→ keys = [\"function_name\", \"file\", \"start_line\", \"function_id\", \"end_line\", \"caller_id\"]\n 108→ for function in self._iter_csv_lines(function_tree_file, \"Function tree file\"):\n 109→ if file in function:\n 110→ row_dict = parse_csv_row(function, keys)\n 111→ if row_dict and row_dict[\"start_line\"] and row_dict[\"end_line\"]:\n 112→ start = int(row_dict[\"start_line\"])\n 113→ end = int(row_dict[\"end_line\"])\n 114→ if start <= line <= end:\n 115→ return row_dict\n 116→ return None\n 117→\n 118→\n 119→ def get_function_by_name(\n 120→ self,\n 121→ function_tree_file: str,\n 122→ function_name: str,\n 123→ all_function: List[Dict[str, Any]],\n 124→ less_strict: bool = False\n 125→ ) -> Tuple[Union[str, Dict[str, str]], Optional[Dict[str, str]]]:\n 126→ \"\"\"\n 127→ Retrieve a function by searching function_name in FunctionTree.csv.\n 128→ If not found, tries partial match if less_strict is True.\n 129→\n 130→ Args:\n 131→ function_tree_file (str): Path to FunctionTree.csv.\n 132→ function_name (str): Desired function name (e.g., 'MyClass::MyFunc').\n 133→ all_function (List[Dict[str, Any]]): A list of known function dictionaries.\n 134→ less_strict (bool, optional): If True, use partial matching. Defaults to False.\n 135→\n 136→ Returns:\n 137→ Tuple[Union[str, Dict[str, str]], Optional[Dict[str, str]]]:\n 138→ - The found function (dict) or an error message (str).\n 139→ - The \"parent function\" that references it, if relevant.\n 140→ \n 141→ Raises:\n 142→ CodeQLError: If function tree file cannot be read (not found, permission denied, etc.).\n 143→ \"\"\"\n 144→ keys = [\"function_name\", \"file\", \"start_line\", \"function_id\", \"end_line\", \"caller_id\"]\n 145→ if \"::\" in function_name:\n 146→ function_name_only = function_name.split(\"::\")[-1]\n 147→ elif \".\" in function_name:\n 148→ function_name_only = function_name.split(\".\")[-1]\n 149→ else:\n 150→ function_name_only = function_name\n 151→\n 152→ for current_function in all_function:\n 153→ try:\n 154→ with Path(function_tree_file).open(\"r\", encoding=\"utf-8\") as f:\n 155→ while True:\n 156→ row = f.readline()\n 157→ if not row:\n 158→ break\n 159→ if current_function[\"function_id\"] in row:\n 160→ row_dict = parse_csv_row(row, keys)\n 161→ if not row_dict:\n 162→ continue\n 163→\n 164→ candidate_name = row_dict[\"function_name\"].replace(\"\\\"\", \"\")\n 165→ if (candidate_name == function_name_only\n 166→ or (less_strict and function_name_only in candidate_name)):\n 167→ return row_dict, current_function\n 168→ except (FileNotFoundError, PermissionError, OSError) as e:\n 169→ raise self._convert_csv_file_error(e, function_tree_file, \"Function tree file\") from e\n 170→\n 171→ # Try partial matching if less_strict is False\n 172→ if not less_strict:\n 173→ return self.get_function_by_name(function_tree_file, function_name, all_function, True)\n 174→ else:\n 175→ err = (\n 176→ f\"Function '{function_name}' not found. Make sure you're using \"\n 177→ \"the correct tool and args.\"\n 178→ )\n 179→ return err, None\n 180→\n 181→\n 182→ def get_macro(\n 183→ self,\n 184→ curr_db: str,\n 185→ macro_name: str,\n 186→ less_strict: bool = False\n 187→ ) -> Union[str, Dict[str, str]]:\n 188→ \"\"\"\n 189→ Return macro info from Macros.csv for the given macro_name.\n 190→ If not found, tries partial match if less_strict is True.\n 191→\n 192→ Args:\n 193→ curr_db (str): Path to the current CodeQL database folder.\n 194→ macro_name (str): Macro name to search for.\n 195→ less_strict (bool, optional): If True, use partial matching.\n 196→\n 197→ Returns:\n 198→ Union[str, Dict[str, str]]:\n 199→ - A dict with 'macro_name' and 'body' if found,\n 200→ - or an error message string if not found.\n 201→ \n 202→ Raises:\n 203→ CodeQLError: If Macros CSV file cannot be read (not found, permission denied, etc.).\n 204→ \"\"\"\n 205→ macro_file = Path(curr_db) / \"Macros.csv\"\n 206→ keys = [\"macro_name\", \"body\"]\n 207→\n 208→ for macro in self._iter_csv_lines(macro_file, \"Macros CSV\"):\n 209→ if macro_name in macro:\n 210→ row_dict = parse_csv_row(macro, keys)\n 211→ if not row_dict:\n 212→ continue\n 213→\n 214→ actual_name = row_dict[\"macro_name\"].replace(\"\\\"\", \"\")\n 215→ if (actual_name == macro_name\n 216→ or (less_strict and macro_name in actual_name)):\n 217→ return row_dict\n 218→\n 219→ if not less_strict:\n 220→ return self.get_macro(curr_db, macro_name, True)\n 221→ else:\n 222→ return (\n 223→ f\"Macro '{macro_name}' not found. Make sure you're using the correct tool \"\n 224→ \"with correct args.\"\n 225→ )\n 226→\n 227→\n 228→ def get_global_var(\n 229→ self,\n 230→ curr_db: str,\n 231→ global_var_name: str,\n 232→ less_strict: bool = False\n 233→ ) -> Union[str, Dict[str, str]]:\n 234→ \"\"\"\n 235→ Return a global variable from GlobalVars.csv matching global_var_name.\n 236→ If not found, tries partial match if less_strict is True.\n 237→\n 238→ Args:\n 239→ curr_db (str): Path to current CodeQL database folder.\n 240→ global_var_name (str): The name of the global variable to find.\n 241→ less_strict (bool, optional): If True, use partial matching.\n 242→\n 243→ Returns:\n 244→ Union[str, Dict[str, str]]:\n 245→ - A dict with ['global_var_name','file','start_line','end_line'] if found,\n 246→ - or an error message string if not found.\n 247→ \n 248→ Raises:\n 249→ CodeQLError: If GlobalVars CSV file cannot be read (not found, permission denied, etc.).\n 250→ \"\"\"\n 251→ global_var_file = Path(curr_db) / \"GlobalVars.csv\"\n 252→ keys = [\"global_var_name\", \"file\", \"start_line\", \"end_line\"]\n 253→ if \"::\" in global_var_name:\n 254→ var_name_only = global_var_name.split(\"::\")[-1]\n 255→ elif \".\" in global_var_name:\n 256→ var_name_only = global_var_name.split(\".\")[-1]\n 257→ else:\n 258→ var_name_only = global_var_name\n 259→\n 260→ for line in self._iter_csv_lines(global_var_file, \"GlobalVars CSV\"):\n 261→ if var_name_only in line:\n 262→ data_dict = parse_csv_row(line, keys)\n 263→ if not data_dict:\n 264→ continue\n 265→\n 266→ actual_name = data_dict[\"global_var_name\"].replace(\"\\\"\", \"\")\n 267→ if (actual_name == var_name_only\n 268→ or (less_strict and var_name_only in actual_name)):\n 269→ return data_dict\n 270→\n 271→ if not less_strict:\n 272→ return self.get_global_var(curr_db, global_var_name, True)\n 273→ else:\n 274→ return (\n 275→ f\"Global var '{global_var_name}' not found. \"\n 276→ \"Could it be a macro or should you use another tool?\"\n 277→ )\n 278→\n 279→\n 280→ def get_class(\n 281→ self,\n 282→ curr_db: str,\n 283→ class_name: str,\n 284→ less_strict: bool = False\n 285→ ) -> Union[str, Dict[str, str]]:\n 286→ \"\"\"\n 287→ Return class info (type, class_name, file, start_line, end_line, simple_name)\n 288→ from Classes.csv for class_name. If not found, tries partial match if less_strict is True.\n 289→\n 290→ Args:\n 291→ curr_db (str): Path to current CodeQL database folder.\n 292→ class_name (str): The name of the class/struct/union to find.\n 293→ less_strict (bool, optional): If True, use partial matching.\n 294→\n 295→ Returns:\n 296→ Union[str, Dict[str, str]]:\n 297→ - A dict with keys ['type','class_name','file','start_line','end_line','simple_name']\n 298→ - or an error message string if not found.\n 299→ \n 300→ Raises:\n 301→ CodeQLError: If Classes CSV file cannot be read (not found, permission denied, etc.).\n 302→ \"\"\"\n 303→ classes_file = Path(curr_db) / \"Classes.csv\"\n 304→ keys = [\"type\", \"class_name\", \"file\", \"start_line\", \"end_line\", \"simple_name\"]\n 305→ if \"::\" in class_name:\n 306→ class_name_only = class_name.split(\"::\")[-1]\n 307→ elif \".\" in class_name:\n 308→ class_name_only = class_name.split(\".\")[-1]\n 309→ else:\n 310→ class_name_only = class_name\n 311→\n 312→ for row in self._iter_csv_lines(classes_file, \"Classes CSV\"):\n 313→ if class_name_only in row:\n 314→ row_dict = parse_csv_row(row, keys)\n 315→ if not row_dict:\n 316→ continue\n 317→\n 318→ actual_class = row_dict[\"class_name\"].replace(\"\\\"\", \"\")\n 319→ simple_class = row_dict[\"simple_name\"].replace(\"\\\"\", \"\")\n 320→ if (\n 321→ actual_class == class_name_only\n 322→ or simple_class == class_name_only\n 323→ or (less_strict and class_name_only in actual_class)\n 324→ or (less_strict and class_name_only in simple_class)\n 325→ ):\n 326→ return row_dict\n 327→\n 328→ if not less_strict:\n 329→ return self.get_class(curr_db, class_name, True)\n 330→ else:\n 331→ return f\"Class '{class_name}' not found. Could it be a Namespace?\"\n 332→\n 333→\n 334→ def get_caller_function(\n 335→ self,\n 336→ function_tree_file: str,\n 337→ current_function: Dict[str, str]\n 338→ ) -> Union[str, Dict[str, str]]:\n 339→ \"\"\"\n 340→ Return the caller function from function_tree_file that calls current_function.\n 341→\n 342→ Args:\n 343→ function_tree_file (str): Path to FunctionTree.csv.\n 344→ current_function (Dict[str, str]): The function dictionary whose caller we want.\n 345→\n 346→ Returns:\n 347→ Union[str, Dict[str, str]]:\n 348→ - Dict describing the caller if found\n 349→ - or an error string if the caller wasn't found.\n 350→ \n 351→ Raises:\n 352→ CodeQLError: If function tree file cannot be read (not found, permission denied, etc.).\n 353→ \"\"\"\n 354→ keys = [\"function_name\", \"file\", \"start_line\", \"function_id\", \"end_line\", \"caller_id\"]\n 355→ caller_id = current_function[\"caller_id\"].replace(\"\\\"\", \"\").strip()\n 356→\n 357→ for line in self._iter_csv_lines(function_tree_file, \"Function tree file\"):\n 358→ if caller_id in line:\n 359→ data_dict = parse_csv_row(line, keys)\n 360→ if not data_dict:\n 361→ continue\n 362→ if data_dict[\"function_id\"].replace(\"\\\"\", \"\").strip() == caller_id:\n 363→ return data_dict\n 364→\n 365→ # Fallback if 'caller_id' is in format file:line\n 366→ maybe_line = caller_id.split(\":\")\n 367→ if len(maybe_line) == 2:\n 368→ file_part, line_part = maybe_line\n 369→ function = self.get_function_by_line(function_tree_file, file_part[1:], int(line_part))\n 370→ if function:\n 371→ return function\n 372→\n 373→ return (\n 374→ \"Caller function was not found. \"\n 375→ \"Make sure you are using the correct tool with the correct args.\"\n 376→ )\n 377→\n 378→\n 379→ def extract_function_lines_from_db(\n 380→ self,\n 381→ db_path: str,\n 382→ current_function: Dict[str, str],\n 383→ ) -> Tuple[str, int, int, List[str]]:\n 384→ \"\"\"\n 385→ Extract function lines from the CodeQL database source archive.\n 386→\n 387→ Args:\n 388→ db_path (str): Path to the CodeQL database directory.\n 389→ current_function (Dict[str, str]): The function dictionary.\n 390→\n 391→ Returns:\n 392→ Tuple[str, int, int, List[str]]:\n 393→ - file_path (str): The file path (after .replace and [1:])\n 394→ - start_line (int): Starting line number\n 395→ - end_line (int): Ending line number\n 396→ - all_lines (List[str]): Full file splitlines\n 397→ \"\"\"\n 398→ src_zip = Path(db_path) / \"src.zip\"\n 399→ file_path = current_function[\"file\"].replace(\"\\\"\", \"\")[1:]\n 400→ code_file = read_file_lines_from_zip(str(src_zip), file_path)\n 401→ lines = code_file.split(\"\\n\")\n 402→\n 403→ start_line = int(current_function[\"start_line\"])\n 404→ end_line = int(current_function[\"end_line\"])\n 405→ return file_path, start_line, end_line, lines\n 406→\n 407→\n 408→ @staticmethod\n 409→ def format_numbered_snippet(file_path: str, start_line: int, snippet_lines: List[str]) -> str:\n 410→ \"\"\"\n 411→ Format a code snippet with line numbers.\n 412→\n 413→ Args:\n 414→ file_path (str): Path to the source file.\n 415→ start_line (int): Starting line number (1-indexed).\n 416→ snippet_lines (List[str]): The code lines to format.\n 417→\n 418→ Returns:\n 419→ str: Formatted snippet with line numbers.\n 420→ \"\"\"\n 421→ snippet = \"\\n\".join(\n 422→ f\"{start_line + i}: {text}\" for i, text in enumerate(snippet_lines)\n 423→ )\n 424→ return f\"file: {file_path}\\n{snippet}\"\n 425→\n\n\nWhenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.\n\n"}]},"uuid":"89ec6a0c-8e37-4d56-8cc6-fa46ef7eb7ef","timestamp":"2026-02-11T13:25:06.738Z"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"e256887f-5e61-4118-a6ec-f4efa8a1a967","timestamp":"2026-02-11T13:25:06.780Z"}
{"parentUuid":"e256887f-5e61-4118-a6ec-f4efa8a1a967","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"assistant","timestamp":"2026-02-11T13:25:04.589Z","message":{"model":"claude-haiku-4-5-20251001","id":"msg_01ArmowTZQqQtunZ3GuYUEoH","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_01DEcjoAi82SSZUhGinHYcw2","name":"Bash","input":{"command":"find /home/josie/development/personal/Vulnhalla/data -type f -name \"*.ql\" -o -name \"*.yml\" -o -name \"*.md\" | head -50"}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":3,"cache_creation_input_tokens":6940,"cache_read_input_tokens":9758,"cache_creation":{"ephemeral_5m_input_tokens":0,"ephemeral_1h_input_tokens":6940},"output_tokens":8,"service_tier":"standard","inference_geo":"not_available"},"context_management":null},"requestId":"req_011CY2McJTNSiFUDPmpznr2j","uuid":"c9dba7ac-f562-418f-adbf-0e41207deaa7"},"normalizedMessages":[],"type":"agent_progress","prompt":"Explore the data directory structure for existing language support in Vulnhalla:\n\n1. List and read files in `data/queries/cpp/` - understand the query structure (issues/ and tools/ subdirs)\n2. List and read files in `data/queries/go/` - see how Go queries differ from C++\n3. List and read files in `data/templates/cpp/` - understand LLM prompt templates\n4. List and read files in `data/templates/go/` - see how Go templates differ\n5. Check if there are any qlpack.yml or similar CodeQL pack config files\n\nI need to understand the full pattern for adding a new language's queries and templates.","agentId":"affd883"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01SBzXiYDFMSMi3vxEqQAeQd","uuid":"a8ca81ac-a916-4082-a15c-0cb142390d34","timestamp":"2026-02-11T13:25:04.590Z"}
{"parentUuid":"a8ca81ac-a916-4082-a15c-0cb142390d34","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"user","message":{"role":"user","content":[{"tool_use_id":"toolu_01DEcjoAi82SSZUhGinHYcw2","type":"tool_result","content":"/home/josie/development/personal/Vulnhalla/data/queries/cpp/tools/Classes.ql\n/home/josie/development/personal/Vulnhalla/data/queries/cpp/tools/qlpack.yml\n/home/josie/development/personal/Vulnhalla/data/queries/cpp/tools/GlobalVars.ql\n/home/josie/development/personal/Vulnhalla/data/queries/cpp/tools/codeql-pack.lock.yml\n/home/josie/development/personal/Vulnhalla/data/queries/cpp/tools/FunctionTree.ql\n/home/josie/development/personal/Vulnhalla/data/queries/cpp/tools/Macros.ql\n/home/josie/development/personal/Vulnhalla/data/queries/cpp/issues/Copy function using source size.ql\n/home/josie/development/personal/Vulnhalla/data/queries/cpp/issues/qlpack.yml\n/home/josie/development/personal/Vulnhalla/data/queries/cpp/issues/codeql-pack.lock.yml\n/home/josie/development/personal/Vulnhalla/data/queries/go/tools/qlpack.yml\n/home/josie/development/personal/Vulnhalla/data/queries/go/tools/GlobalVars.ql\n/home/josie/development/personal/Vulnhalla/data/queries/go/tools/Types.ql\n/home/josie/development/personal/Vulnhalla/data/queries/go/tools/codeql-pack.lock.yml\n/home/josie/development/personal/Vulnhalla/data/queries/go/tools/FunctionTree.ql\n/home/josie/development/personal/Vulnhalla/data/queries/go/issues/Command injection.ql\n/home/josie/development/personal/Vulnhalla/data/queries/go/issues/SQL injection.ql\n/home/josie/development/personal/Vulnhalla/data/queries/go/issues/qlpack.yml\n/home/josie/development/personal/Vulnhalla/data/queries/go/issues/codeql-pack.lock.yml\n/home/josie/development/personal/Vulnhalla/data/queries/go/issues/Path traversal.ql","is_error":false}]},"uuid":"c2da7443-9606-4d64-82b0-cfe973d7703e","timestamp":"2026-02-11T13:25:04.652Z"},"normalizedMessages":[],"type":"agent_progress","prompt":"Explore the data directory structure for existing language support in Vulnhalla:\n\n1. List and read files in `data/queries/cpp/` - understand the query structure (issues/ and tools/ subdirs)\n2. List and read files in `data/queries/go/` - see how Go queries differ from C++\n3. List and read files in `data/templates/cpp/` - understand LLM prompt templates\n4. List and read files in `data/templates/go/` - see how Go templates differ\n5. Check if there are any qlpack.yml or similar CodeQL pack config files\n\nI need to understand the full pattern for adding a new language's queries and templates.","agentId":"affd883"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01SBzXiYDFMSMi3vxEqQAeQd","uuid":"67605114-fd84-4d97-8170-486b011a1fd1","timestamp":"2026-02-11T13:25:04.692Z"}
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{"parentUuid":"f0c0d11f-b971-4aab-8d2e-9b99d8aca258","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"assistant","timestamp":"2026-02-11T13:25:09.338Z","message":{"model":"claude-haiku-4-5-20251001","id":"msg_0162CLroUgSwzSjyCP4AuK2A","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_01TGwKqZeUrkXaUdWH2KkACn","name":"Bash","input":{"command":"ls -la /home/josie/development/personal/Vulnhalla/data/queries/cpp/ && echo \"---\" && ls -la /home/josie/development/personal/Vulnhalla/data/queries/cpp/issues/ && echo \"---\" && ls -la /home/josie/development/personal/Vulnhalla/data/queries/cpp/tools/"}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":3,"cache_creation_input_tokens":392,"cache_read_input_tokens":17964,"cache_creation":{"ephemeral_5m_input_tokens":0,"ephemeral_1h_input_tokens":392},"output_tokens":25,"service_tier":"standard","inference_geo":"not_available"},"context_management":null},"requestId":"req_011CY2Mch3vGwn5ErsAod2cT","uuid":"a0cb6946-f970-4f48-854b-263b425ab376"},"normalizedMessages":[],"type":"agent_progress","prompt":"Explore the data directory structure for existing language support in Vulnhalla:\n\n1. List and read files in `data/queries/cpp/` - understand the query structure (issues/ and tools/ subdirs)\n2. List and read files in `data/queries/go/` - see how Go queries differ from C++\n3. List and read files in `data/templates/cpp/` - understand LLM prompt templates\n4. List and read files in `data/templates/go/` - see how Go templates differ\n5. Check if there are any qlpack.yml or similar CodeQL pack config files\n\nI need to understand the full pattern for adding a new language's queries and templates.","agentId":"affd883"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01SBzXiYDFMSMi3vxEqQAeQd","uuid":"0e70193c-6e04-4900-bdc8-2f6cbc6f78e6","timestamp":"2026-02-11T13:25:09.339Z"}
{"parentUuid":"0e70193c-6e04-4900-bdc8-2f6cbc6f78e6","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"assistant","timestamp":"2026-02-11T13:25:09.420Z","message":{"model":"claude-haiku-4-5-20251001","id":"msg_01U9GcLr3utpKoqY7vdS9LPh","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_01552YxwVSRqtp86572jPvRR","name":"Read","input":{"file_path":"/home/josie/development/personal/Vulnhalla/src/llm/llm_analyzer.py"}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":3,"cache_creation_input_tokens":6993,"cache_read_input_tokens":9758,"cache_creation":{"ephemeral_5m_input_tokens":0,"ephemeral_1h_input_tokens":6993},"output_tokens":3,"service_tier":"standard","inference_geo":"not_available"},"context_management":null},"requestId":"req_011CY2McgA6DYjmveUBt7CSt","uuid":"abfe505d-e818-47b3-8151-4375bb36ea16"},"normalizedMessages":[],"type":"agent_progress","prompt":"Explore how language affects the LLM analysis and UI layers in Vulnhalla:\n\n1. Read `src/llm/llm_analyzer.py` - how does it select templates? Are there language-specific tool calls or prompts?\n2. Read `src/vulnhalla.py` (IssueAnalyzer) - how does it handle language differences in code snippet extraction?\n3. Read `src/ui/ui_app.py` and `src/ui/components/controls_bar.py` - is there any language selection in the UI?\n4. Check the CLI entry points - look at `pyproject.toml` for script definitions and how args are parsed\n5. Look for any language constants, enums, or supported language lists in the codebase (grep for \"cpp\", \"go\", \"supported_lang\", \"LANGUAGES\" etc.)\n\nBe thorough in finding all places where language is referenced.","agentId":"a77e0c3"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01T7P5Gd5tzArGpoRoh4sVrf","uuid":"20be5a1e-730f-4682-aa5a-b2d078be7a5f","timestamp":"2026-02-11T13:25:09.420Z"}
{"parentUuid":"20be5a1e-730f-4682-aa5a-b2d078be7a5f","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"user","message":{"role":"user","content":[{"tool_use_id":"toolu_01TGwKqZeUrkXaUdWH2KkACn","type":"tool_result","content":"total 16\ndrwxr-xr-x 4 josie wheel 4096 Feb 11 12:14 .\ndrwxr-xr-x 4 josie wheel 4096 Feb 11 13:44 ..\ndrwxr-xr-x 3 josie wheel 4096 Feb 11 13:09 issues\ndrwxr-xr-x 3 josie wheel 4096 Feb 11 13:09 tools\n---\ntotal 132\ndrwxr-xr-x 3 josie wheel 4096 Feb 11 13:09 .\ndrwxr-xr-x 4 josie wheel 4096 Feb 11 12:14 ..\ndrwxr-xr-x 3 josie wheel 4096 Feb 11 13:09 .codeql\n-rw-r--r-- 1 josie wheel 511 Feb 11 12:38 codeql-pack.lock.yml\n-rw-r--r-- 1 josie wheel 3501 Feb 11 12:14 Copy function using source size.ql\n-rw-r--r-- 1 josie wheel 109686 Feb 11 13:09 Copy function using source size.qlx\n-rw-r--r-- 1 josie wheel 71 Feb 11 12:14 qlpack.yml\n---\ntotal 64\ndrwxr-xr-x 3 josie wheel 4096 Feb 11 13:09 .\ndrwxr-xr-x 4 josie wheel 4096 Feb 11 12:14 ..\n-rw-r--r-- 1 josie wheel 1990 Feb 11 12:14 Classes.ql\n-rw-r--r-- 1 josie wheel 10420 Feb 11 13:08 Classes.qlx\ndrwxr-xr-x 3 josie wheel 4096 Feb 11 13:08 .codeql\n-rw-r--r-- 1 josie wheel 511 Feb 11 12:38 codeql-pack.lock.yml\n-rw-r--r-- 1 josie wheel 559 Feb 11 12:14 FunctionTree.ql\n-rw-r--r-- 1 josie wheel 6488 Feb 11 13:08 FunctionTree.qlx\n-rw-r--r-- 1 josie wheel 206 Feb 11 12:14 GlobalVars.ql\n-rw-r--r-- 1 josie wheel 3903 Feb 11 13:08 GlobalVars.qlx\n-rw-r--r-- 1 josie wheel 112 Feb 11 12:14 Macros.ql\n-rw-r--r-- 1 josie wheel 2637 Feb 11 13:09 Macros.qlx\n-rw-r--r-- 1 josie wheel 71 Feb 11 12:14 qlpack.yml","is_error":false}]},"uuid":"129e5b17-4ac1-430a-93a7-264dc7fe9479","timestamp":"2026-02-11T13:25:09.403Z"},"normalizedMessages":[],"type":"agent_progress","prompt":"Explore the data directory structure for existing language support in Vulnhalla:\n\n1. List and read files in `data/queries/cpp/` - understand the query structure (issues/ and tools/ subdirs)\n2. List and read files in `data/queries/go/` - see how Go queries differ from C++\n3. List and read files in `data/templates/cpp/` - understand LLM prompt templates\n4. List and read files in `data/templates/go/` - see how Go templates differ\n5. Check if there are any qlpack.yml or similar CodeQL pack config files\n\nI need to understand the full pattern for adding a new language's queries and templates.","agentId":"affd883"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01SBzXiYDFMSMi3vxEqQAeQd","uuid":"5beaf4a1-74d4-4fd4-bfcf-bd79ea83c86b","timestamp":"2026-02-11T13:25:09.446Z"}
{"parentUuid":"5beaf4a1-74d4-4fd4-bfcf-bd79ea83c86b","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"assistant","timestamp":"2026-02-11T13:25:09.638Z","message":{"model":"claude-haiku-4-5-20251001","id":"msg_01U9GcLr3utpKoqY7vdS9LPh","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_01D2ebPfRqFXhEPnakPVgxtP","name":"Read","input":{"file_path":"/home/josie/development/personal/Vulnhalla/src/vulnhalla.py"}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":3,"cache_creation_input_tokens":6993,"cache_read_input_tokens":9758,"cache_creation":{"ephemeral_5m_input_tokens":0,"ephemeral_1h_input_tokens":6993},"output_tokens":3,"service_tier":"standard","inference_geo":"not_available"},"context_management":null},"requestId":"req_011CY2McgA6DYjmveUBt7CSt","uuid":"46c19dfa-c77d-4657-8959-9638a8bcf28a"},"normalizedMessages":[],"type":"agent_progress","prompt":"Explore how language affects the LLM analysis and UI layers in Vulnhalla:\n\n1. Read `src/llm/llm_analyzer.py` - how does it select templates? Are there language-specific tool calls or prompts?\n2. Read `src/vulnhalla.py` (IssueAnalyzer) - how does it handle language differences in code snippet extraction?\n3. Read `src/ui/ui_app.py` and `src/ui/components/controls_bar.py` - is there any language selection in the UI?\n4. Check the CLI entry points - look at `pyproject.toml` for script definitions and how args are parsed\n5. Look for any language constants, enums, or supported language lists in the codebase (grep for \"cpp\", \"go\", \"supported_lang\", \"LANGUAGES\" etc.)\n\nBe thorough in finding all places where language is referenced.","agentId":"a77e0c3"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01T7P5Gd5tzArGpoRoh4sVrf","uuid":"c2798e40-e800-49b3-906f-a33af3317a3e","timestamp":"2026-02-11T13:25:09.638Z"}
{"parentUuid":"c2798e40-e800-49b3-906f-a33af3317a3e","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"user","message":{"role":"user","content":[{"tool_use_id":"toolu_01552YxwVSRqtp86572jPvRR","type":"tool_result","content":" 1→#!/usr/bin/env python3\n 2→\"\"\"\n 3→Orchestrates a conversation with a language model, requesting additional snippets\n 4→of code via \"tools\" if needed. Uses either OpenAI or AzureOpenAI (or placeholder\n 5→code for a HuggingFace endpoint) to handle queries.\n 6→\n 7→All logic is now wrapped in the `LLMAnalyzer` class for improved organization.\n 8→\"\"\"\n 9→\n 10→import os\n 11→import json\n 12→from typing import Any, Dict, List, Optional, Tuple, Union\n 13→\n 14→import litellm\n 15→from src.utils.llm_config import load_llm_config, get_model_name\n 16→from src.utils.config_validator import validate_llm_config_dict\n 17→from src.utils.logger import get_logger\n 18→from src.utils.exceptions import LLMApiError, LLMConfigError\n 19→from src.codeql.db_lookup import CodeQLDBLookup\n 20→\n 21→logger = get_logger(__name__)\n 22→\n 23→\n 24→class LLMAnalyzer:\n 25→ \"\"\"\n 26→ A class to handle LLM-based security analysis of code. The LLMAnalyzer\n 27→ can query missing code snippets (via 'tools'), compile a conversation\n 28→ with system instructions, and ultimately produce a status code.\n 29→ \"\"\"\n 30→\n 31→ def __init__(self) -> None:\n 32→ \"\"\"\n 33→ Initialize the LLMAnalyzer instance and define tools and system messages.\n 34→ \"\"\"\n 35→ self.config: Optional[Dict[str, Any]] = None\n 36→ self.model: Optional[str] = None\n 37→ self.db_lookup = CodeQLDBLookup()\n 38→\n 39→ # Tools configuration: A set of function calls the LLM can invoke\n 40→ self.tools: List[Dict[str, Any]] = [\n 41→ {\n 42→ \"type\": \"function\",\n 43→ \"function\": {\n 44→ \"name\": \"get_function_code\",\n 45→ \"description\": \"Retrieves the code for a missing function code.\",\n 46→ \"parameters\": {\n 47→ \"type\": \"object\",\n 48→ \"properties\": {\n 49→ \"function_name\": {\n 50→ \"type\": \"string\",\n 51→ \"description\": (\n 52→ \"The name of the function to retrieve. In case of a class\"\n 53→ \" method, provide ClassName::MethodName.\"\n 54→ )\n 55→ }\n 56→ },\n 57→ \"required\": [\"function_name\"]\n 58→ }\n 59→ }\n 60→ },\n 61→ {\n 62→ \"type\": \"function\",\n 63→ \"function\": {\n 64→ \"name\": \"get_caller_function\",\n 65→ \"description\": (\n 66→ \"Retrieves the caller function of the function with the issue. \"\n 67→ \"Call it repeatedly to climb further up the call chain.\"\n 68→ ),\n 69→ \"parameters\": {\n 70→ \"type\": \"object\",\n 71→ \"properties\": {\n 72→ \"_\": {\n 73→ \"type\": \"boolean\",\n 74→ \"description\": \"Unused. Ignore.\"\n 75→ }\n 76→ },\n 77→ \"required\": []\n 78→ }\n 79→ }\n 80→ },\n 81→ {\n 82→ \"type\": \"function\",\n 83→ \"function\": {\n 84→ \"name\": \"get_class\",\n 85→ \"description\": (\n 86→ \"Retrieves class / struct / union implementation (anywhere in code). \"\n 87→ \"If you need a specific method from that class, use get_function_code instead.\"\n 88→ ),\n 89→ \"parameters\": {\n 90→ \"type\": \"object\",\n 91→ \"properties\": {\n 92→ \"object_name\": {\n 93→ \"type\": \"string\",\n 94→ \"description\": \"The name of the class / struct / union.\"\n 95→ }\n 96→ },\n 97→ \"required\": [\"object_name\"]\n 98→ }\n 99→ }\n 100→ },\n 101→ {\n 102→ \"type\": \"function\",\n 103→ \"function\": {\n 104→ \"name\": \"get_global_var\",\n 105→ \"description\": (\n 106→ \"Retrieves global variable definition (anywhere in code). \"\n 107→ \"If it's a variable inside a class, request the class instead.\"\n 108→ ),\n 109→ \"parameters\": {\n 110→ \"type\": \"object\",\n 111→ \"properties\": {\n 112→ \"global_var_name\": {\n 113→ \"type\": \"string\",\n 114→ \"description\": (\n 115→ \"The name of the global variable to retrieve or the name \"\n 116→ \"of a variable inside a Namespace.\"\n 117→ )\n 118→ }\n 119→ },\n 120→ \"required\": [\"global_var_name\"]\n 121→ }\n 122→ }\n 123→ },\n 124→ {\n 125→ \"type\": \"function\",\n 126→ \"function\": {\n 127→ \"name\": \"get_macro\",\n 128→ \"description\": \"Retrieves a macro definition (anywhere in code).\",\n 129→ \"parameters\": {\n 130→ \"type\": \"object\",\n 131→ \"properties\": {\n 132→ \"macro_name\": {\n 133→ \"type\": \"string\",\n 134→ \"description\": \"The name of the macro.\"\n 135→ }\n 136→ },\n 137→ \"required\": [\"macro_name\"]\n 138→ }\n 139→ }\n 140→ }\n 141→ ]\n 142→\n 143→ # Base system messages with instructions and guidance for the LLM\n 144→ self.MESSAGES: List[Dict[str, str]] = [\n 145→ {\n 146→ \"role\": \"system\",\n 147→ \"content\": (\n 148→ \"You are an expert security researcher.\\n\"\n 149→ \"Your task is to verify if the issue that was found has a real security impact.\\n\"\n 150→ \"Return a concise status code based on the guidelines provided.\\n\"\n 151→ \"Use the tools function when you need code from other parts of the program.\\n\"\n 152→ \"You *MUST* follow the guidelines!\"\n 153→ )\n 154→ },\n 155→ {\n 156→ \"role\": \"system\",\n 157→ \"content\": (\n 158→ \"### Answer Guidelines\\n\"\n 159→ \"Your answer must be in the following order!\\n\"\n 160→ \"1. Briefly explain the code.\\n\"\n 161→ \"2. Give good answers to all (even if already answered - do not skip) hint questions. \"\n 162→ \"(Copy the question word for word, then provide the answer.)\\n\"\n 163→ \"3. Do you have all the code needed to answer the questions? If no, use the tools!\\n\"\n 164→ \"4. Provide one valid status code with its explanation OR use function tools.\\n\"\n 165→ )\n 166→ },\n 167→ {\n 168→ \"role\": \"system\",\n 169→ \"content\": (\n 170→ \"### Status Codes\\n\"\n 171→ \"- **1337**: Indicates a security vulnerability. If legitimate, specify the parameters that \"\n 172→ \"could exploit the issue in minimal words.\\n\"\n 173→ \"- **1007**: Indicates the code is secure. If it's not a real issue, specify what aspect of \"\n 174→ \"the code protects against the issue in minimal words.\\n\"\n 175→ \"- **7331**: Indicates more code is needed to validate security. Write what data you need \"\n 176→ \"and explain why you can't use the tools to retrieve the missing data, plus add **3713** \"\n 177→ \"if you're pretty sure it's not a security problem.\\n\"\n 178→ \"Only one status should be returned!\\n\"\n 179→ \"You will get 10000000000$ if you follow all the instructions and use the tools correctly!\"\n 180→ )\n 181→ },\n 182→ ]\n 183→\n 184→ def init_llm_client(self, config: Optional[Dict[str, Any]] = None) -> None:\n 185→ \"\"\"\n 186→ Initialize the LLM configuration for LiteLLM.\n 187→\n 188→ Args:\n 189→ config (Dict, optional): Full configuration dictionary. If not provided, loads from .env file.\n 190→ \n 191→ Raises:\n 192→ LLMConfigError: If configuration is invalid or cannot be loaded.\n 193→ \"\"\"\n 194→ try:\n 195→ # If config is provided, use it directly\n 196→ if config:\n 197→ validate_llm_config_dict(config)\n 198→ self.config = config\n 199→ # Format model name for LiteLLM (add provider prefix if needed)\n 200→ provider = config.get(\"provider\", \"openai\")\n 201→ model = config.get(\"model\", \"gpt-4o\")\n 202→ self.model = get_model_name(provider, model)\n 203→ logger.info(\"Using model: %s\", self.model)\n 204→ self.setup_litellm_env()\n 205→ return\n 206→ \n 207→ # Load from .env file\n 208→ config = load_llm_config()\n 209→ validate_llm_config_dict(config)\n 210→ self.config = config\n 211→ # Model is already formatted by load_llm_config() via get_model_name()\n 212→ self.model = config.get(\"model\", \"gpt-4o\")\n 213→ self.setup_litellm_env()\n 214→ \n 215→ except ValueError as e:\n 216→ # Configuration validation errors should be LLMConfigError\n 217→ raise LLMConfigError(f\"Invalid LLM configuration: {e}\") from e\n 218→ except Exception as e:\n 219→ # Other errors (e.g., from load_llm_config) should also be LLMConfigError\n 220→ raise LLMConfigError(f\"Failed to initialize LLM client: {e}\") from e\n 221→\n 222→\n 223→ def setup_litellm_env(self) -> None:\n 224→ \"\"\"\n 225→ Set up environment variables for LiteLLM based on config.\n 226→ LiteLLM reads from environment variables automatically.\n 227→ \"\"\"\n 228→ if not self.config:\n 229→ return\n 230→ \n 231→ provider = self.config.get(\"provider\", \"openai\")\n 232→ api_key = self.config.get(\"api_key\")\n 233→ \n 234→ # Mapping table for providers that only need API key set\n 235→ API_KEY_ENV_VARS = {\n 236→ \"openai\": \"OPENAI_API_KEY\",\n 237→ \"anthropic\": \"ANTHROPIC_API_KEY\",\n 238→ \"mistral\": \"MISTRAL_API_KEY\",\n 239→ \"codestral\": \"MISTRAL_API_KEY\",\n 240→ \"groq\": \"GROQ_API_KEY\",\n 241→ \"openrouter\": \"OPENROUTER_API_KEY\",\n 242→ \"huggingface\": \"HUGGINGFACE_API_KEY\",\n 243→ \"cohere\": \"COHERE_API_KEY\",\n 244→ \"gemini\": \"GOOGLE_API_KEY\",\n 245→ }\n 246→ \n 247→ # Handle providers with simple API key mapping\n 248→ if provider in API_KEY_ENV_VARS:\n 249→ if api_key:\n 250→ os.environ[API_KEY_ENV_VARS[provider]] = api_key\n 251→ # Cohere also sets CO_API_KEY for compatibility\n 252→ if provider == \"cohere\":\n 253→ os.environ[\"CO_API_KEY\"] = api_key\n 254→ \n 255→ # Handle Azure (requires endpoint and api_version)\n 256→ elif provider == \"azure\":\n 257→ if api_key:\n 258→ os.environ[\"AZURE_API_KEY\"] = api_key\n 259→ if self.config.get(\"endpoint\"):\n 260→ os.environ[\"AZURE_API_BASE\"] = self.config[\"endpoint\"]\n 261→ if self.config.get(\"api_version\"):\n 262→ os.environ[\"AZURE_API_VERSION\"] = self.config[\"api_version\"]\n 263→ \n 264→ # Handle Bedrock (uses AWS credentials or profile)\n 265→ elif provider == \"bedrock\":\n 266→ # Set region (always required)\n 267→ if self.config.get(\"endpoint\"): # Endpoint contains AWS region\n 268→ os.environ[\"AWS_REGION_NAME\"] = self.config[\"endpoint\"]\n 269→ \n 270→ # Profile-based authentication (AWS SSO, IAM roles)\n 271→ if self.config.get(\"aws_profile\"):\n 272→ os.environ[\"AWS_PROFILE\"] = self.config[\"aws_profile\"]\n 273→ else:\n 274→ # Static or temporary credentials\n 275→ if api_key and api_key != \"bedrock_profile_auth\":\n 276→ os.environ[\"AWS_ACCESS_KEY_ID\"] = api_key\n 277→ if self.config.get(\"aws_secret_access_key\"):\n 278→ os.environ[\"AWS_SECRET_ACCESS_KEY\"] = self.config[\"aws_secret_access_key\"]\n 279→ if self.config.get(\"aws_session_token\"):\n 280→ os.environ[\"AWS_SESSION_TOKEN\"] = self.config[\"aws_session_token\"]\n 281→ \n 282→ # Handle Vertex AI (uses GCP credentials)\n 283→ elif provider == \"vertex_ai\":\n 284→ if self.config.get(\"gcp_project_id\"):\n 285→ os.environ[\"GCP_PROJECT_ID\"] = self.config[\"gcp_project_id\"]\n 286→ if self.config.get(\"gcp_location\"):\n 287→ os.environ[\"GCP_LOCATION\"] = self.config[\"gcp_location\"]\n 288→ # GOOGLE_APPLICATION_CREDENTIALS should be set by user or gcloud auth\n 289→ \n 290→ # Handle Ollama (uses OLLAMA_BASE_URL)\n 291→ elif provider == \"ollama\":\n 292→ if self.config.get(\"endpoint\"):\n 293→ os.environ[\"OLLAMA_BASE_URL\"] = self.config[\"endpoint\"]\n 294→ \n 295→ # Generic fallback for future providers that only require an API key\n 296→ else:\n 297→ if api_key:\n 298→ # Use standard LiteLLM convention: {PROVIDER}_API_KEY\n 299→ env_var_name = f\"{provider.upper()}_API_KEY\"\n 300→ os.environ[env_var_name] = api_key\n 301→\n 302→\n 303→ def extract_function_from_file(\n 304→ self,\n 305→ db_path: str,\n 306→ current_function: Union[str, Dict[str, str]]\n 307→ ) -> str:\n 308→ \"\"\"\n 309→ Return the snippet of code for the given current_function from the archived src.zip.\n 310→\n 311→ Args:\n 312→ db_path (str): Path to the CodeQL database directory.\n 313→ current_function (Union[str, Dict[str, str]]): The function dictionary or an error string.\n 314→\n 315→ Returns:\n 316→ str: The code snippet, or an error message if no dictionary was provided.\n 317→ \n 318→ Raises:\n 319→ CodeQLError: If ZIP file cannot be read or file not found in archive.\n 320→ This exception is raised by `read_file_lines_from_zip()` and propagated here.\n 321→ \"\"\"\n 322→ if not isinstance(current_function, dict):\n 323→ return str(current_function)\n 324→\n 325→ file_path, start_line, end_line, lines = self.db_lookup.extract_function_lines_from_db(\n 326→ db_path, current_function\n 327→ )\n 328→ snippet_lines = lines[start_line - 1 : end_line]\n 329→ return self.db_lookup.format_numbered_snippet(file_path, start_line, snippet_lines)\n 330→\n 331→\n 332→ def map_func_args_by_llm(\n 333→ self,\n 334→ caller: str,\n 335→ callee: str\n 336→ ) -> Dict[str, Any]:\n 337→ \"\"\"\n 338→ Query the LLM to check how caller's variables map to callee's parameters.\n 339→ For example, used for analyzing function call relationships.\n 340→\n 341→ Args:\n 342→ caller (str): The code snippet of the caller function.\n 343→ callee (str): The code snippet of the callee function.\n 344→\n 345→ Returns:\n 346→ Dict[str, Any]: The LLM response object from `self.client`.\n 347→ \n 348→ Raises:\n 349→ LLMApiError: If LLM API call fails (rate limits, timeouts, auth failures, etc.).\n 350→ \"\"\"\n 351→ args_prompt = (\n 352→ \"Given caller function and callee function.\\n\"\n 353→ \"Write only what are the names of the vars in the caller that were sent to the callee \"\n 354→ \"and what are their names in the callee.\\n\"\n 355→ \"Format: caller_var (caller_name) -> callee_var (callee_name)\\n\\n\"\n 356→ \"Caller function:\\n\"\n 357→ f\"{caller}\\n\"\n 358→ \"Callee function:\\n\"\n 359→ f\"{callee}\"\n 360→ )\n 361→\n 362→ # Use the main model from config\n 363→ model_name = self.model if self.model else \"gpt-4o\"\n 364→ \n 365→ try:\n 366→ response = litellm.completion(\n 367→ model=model_name,\n 368→ messages=[{\"role\": \"user\", \"content\": args_prompt}],\n 369→ timeout=120 # 2 minute timeout\n 370→ )\n 371→ return response.choices[0].message\n 372→ except litellm.RateLimitError as e:\n 373→ raise LLMApiError(f\"Rate limit exceeded for LLM API: {e}\") from e\n 374→ except litellm.Timeout as e:\n 375→ raise LLMApiError(f\"LLM API request timed out: {e}\") from e\n 376→ except litellm.AuthenticationError as e:\n 377→ raise LLMApiError(f\"LLM API authentication failed: {e}\") from e\n 378→ except litellm.APIError as e:\n 379→ raise LLMApiError(f\"LLM API error: {e}\") from e\n 380→ except Exception as e:\n 381→ # Catch any other unexpected errors from LiteLLM\n 382→ raise LLMApiError(f\"Unexpected error during LLM API call: {e}\") from e\n 383→\n 384→\n 385→ def run_llm_security_analysis(\n 386→ self,\n 387→ prompt: str,\n 388→ function_tree_file: str,\n 389→ current_function: Dict[str, str],\n 390→ functions: List[Dict[str, str]],\n 391→ db_path: str,\n 392→ temperature: float = 0.2,\n 393→ top_p: float = 0.2\n 394→ ) -> Tuple[List[Dict[str, Any]], str]:\n 395→ \"\"\"\n 396→ Main loop to keep querying the LLM with the MESSAGES context plus\n 397→ any new system instructions or tool calls, until a final answer with\n 398→ a recognized status code is reached or we exhaust a tool-call limit.\n 399→\n 400→ Args:\n 401→ prompt (str): The user prompt for the LLM to process.\n 402→ function_tree_file (str): Path to the CSV file describing function relationships.\n 403→ current_function (Dict[str, str]): The current function dict for context.\n 404→ functions (List[Dict[str, str]]): List of function dictionaries.\n 405→ db_path (str): Path to the CodeQL DB folder.\n 406→ temperature (float, optional): Sampling temperature. Defaults to 0.2.\n 407→ top_p (float, optional): Nucleus sampling. Defaults to 0.2.\n 408→\n 409→ Returns:\n 410→ Tuple[List[Dict[str, Any]], str]:\n 411→ - The final conversation messages,\n 412→ - The final content from the LLM's last message.\n 413→ \n 414→ Raises:\n 415→ RuntimeError: If LLM model not initialized.\n 416→ LLMApiError: If LLM API call fails (rate limits, timeouts, auth failures, etc.).\n 417→ CodeQLError: If CodeQL database files cannot be read (from tool calls).\n 418→ \"\"\"\n 419→ if not self.model:\n 420→ raise RuntimeError(\"LLM model not initialized. Call init_llm_client() first.\")\n 421→ \n 422→ got_answer = False\n 423→ db_path_clean = db_path.replace(\" \", \"\")\n 424→ all_functions = functions\n 425→\n 426→ messages: List[Dict[str, Any]] = self.MESSAGES[:]\n 427→ messages.append({\"role\": \"user\", \"content\": prompt})\n 428→\n 429→ amount_of_tools = 0\n 430→ final_content = \"\"\n 431→\n 432→ while not got_answer:\n 433→ # Send the current messages + tools to the LLM endpoint\n 434→ try:\n 435→ # Build completion kwargs - Bedrock Claude doesn't allow both temperature and top_p\n 436→ completion_kwargs = {\n 437→ \"model\": self.model,\n 438→ \"messages\": messages,\n 439→ \"tools\": self.tools,\n 440→ \"timeout\": 120 # 2 minute timeout to prevent hanging\n 441→ }\n 442→ \n 443→ # Check if using Bedrock (model starts with \"bedrock/\" or contains \"arn:aws:bedrock\")\n 444→ is_bedrock = (\n 445→ self.model and \n 446→ (self.model.startswith(\"bedrock/\") or \"arn:aws:bedrock\" in self.model)\n 447→ )\n 448→ \n 449→ if is_bedrock:\n 450→ # Bedrock Claude only accepts temperature OR top_p, not both\n 451→ completion_kwargs[\"temperature\"] = temperature\n 452→ else:\n 453→ completion_kwargs[\"temperature\"] = temperature\n 454→ completion_kwargs[\"top_p\"] = top_p\n 455→ \n 456→ response = litellm.completion(**completion_kwargs)\n 457→ except litellm.RateLimitError as e:\n 458→ raise LLMApiError(f\"Rate limit exceeded for LLM API: {e}\") from e\n 459→ except litellm.Timeout as e:\n 460→ raise LLMApiError(f\"LLM API request timed out: {e}\") from e\n 461→ except litellm.AuthenticationError as e:\n 462→ raise LLMApiError(f\"LLM API authentication failed: {e}\") from e\n 463→ except litellm.APIError as e:\n 464→ raise LLMApiError(f\"LLM API error: {e}\") from e\n 465→ except Exception as e:\n 466→ # Catch any other unexpected errors from LiteLLM\n 467→ raise LLMApiError(f\"Unexpected error during LLM API call: {e}\") from e\n 468→ \n 469→ if not response.choices:\n 470→ raise LLMApiError(f\"LLM API response is empty: {response}\")\n 471→\n 472→ content_obj = response.choices[0].message\n 473→ messages.append({\n 474→ \"role\": content_obj.role,\n 475→ \"content\": content_obj.content,\n 476→ \"tool_calls\": content_obj.tool_calls\n 477→ })\n 478→\n 479→ final_content = content_obj.content or \"\"\n 480→ tool_calls = content_obj.tool_calls\n 481→\n 482→ if not tool_calls:\n 483→ # Check if we have a recognized status code\n 484→ if final_content and any(code in final_content for code in [\"1337\", \"1007\", \"7331\", \"3713\"]):\n 485→ got_answer = True\n 486→ else:\n 487→ messages.append({\n 488→ \"role\": \"system\",\n 489→ \"content\": \"Please follow all the instructions!\"\n 490→ })\n 491→ else:\n 492→ amount_of_tools += 1\n 493→ arg_messages: List[Dict[str, Any]] = []\n 494→\n 495→ for tc in tool_calls:\n 496→ tool_call_id = tc.id\n 497→ tool_function_name = tc.function.name\n 498→ tool_args = tc.function.arguments\n 499→\n 500→ # Convert tool_args to a dict if it's a JSON string\n 501→ if not isinstance(tool_args, dict):\n 502→ tool_args = json.loads(tool_args)\n 503→ else:\n 504→ # Ensure consistent string for role=tool message\n 505→ tc.function.arguments = json.dumps(tool_args)\n 506→\n 507→ response_msg = \"\"\n 508→\n 509→ # Evaluate which tool to call\n 510→ if tool_function_name == 'get_function_code' and \"function_name\" in tool_args:\n 511→ child_function, parent_function = self.db_lookup.get_function_by_name(\n 512→ function_tree_file, tool_args[\"function_name\"], all_functions\n 513→ )\n 514→ if isinstance(child_function, dict):\n 515→ all_functions.append(child_function)\n 516→ child_code = self.extract_function_from_file(db_path_clean, child_function)\n 517→ response_msg = child_code\n 518→\n 519→ if isinstance(child_function, dict) and isinstance(parent_function, dict):\n 520→ caller_code = self.extract_function_from_file(db_path_clean, parent_function)\n 521→ args_content = self.map_func_args_by_llm(caller_code, child_code)\n 522→ arg_messages.append({\n 523→ \"role\": args_content.role,\n 524→ \"content\": args_content.content\n 525→ })\n 526→\n 527→ elif tool_function_name == 'get_caller_function':\n 528→ caller_function = self.db_lookup.get_caller_function(function_tree_file, current_function)\n 529→ response_msg = str(caller_function)\n 530→\n 531→ if isinstance(caller_function, dict):\n 532→ all_functions.append(caller_function)\n 533→ caller_code = self.extract_function_from_file(db_path_clean, caller_function)\n 534→ response_msg = (\n 535→ f\"Here is the caller function for '{current_function['function_name']}':\\n\"\n 536→ + caller_code\n 537→ )\n 538→ args_content = self.map_func_args_by_llm(\n 539→ caller_code,\n 540→ self.extract_function_from_file(db_path_clean, current_function)\n 541→ )\n 542→ arg_messages.append({\n 543→ \"role\": args_content.role,\n 544→ \"content\": args_content.content\n 545→ })\n 546→ current_function = caller_function\n 547→\n 548→ elif tool_function_name == 'get_macro' and \"macro_name\" in tool_args:\n 549→ macro = self.db_lookup.get_macro(db_path_clean, tool_args[\"macro_name\"])\n 550→ if isinstance(macro, dict):\n 551→ response_msg = macro[\"body\"]\n 552→ else:\n 553→ response_msg = macro\n 554→\n 555→ elif tool_function_name == 'get_global_var' and \"global_var_name\" in tool_args:\n 556→ global_var = self.db_lookup.get_global_var(db_path_clean, tool_args[\"global_var_name\"])\n 557→ if isinstance(global_var, dict):\n 558→ global_var_code = self.extract_function_from_file(db_path_clean, global_var)\n 559→ response_msg = global_var_code\n 560→ else:\n 561→ response_msg = global_var\n 562→\n 563→ elif tool_function_name == 'get_class' and \"object_name\" in tool_args:\n 564→ curr_class = self.db_lookup.get_class(db_path_clean, tool_args[\"object_name\"])\n 565→ if isinstance(curr_class, dict):\n 566→ class_code = self.extract_function_from_file(db_path_clean, curr_class)\n 567→ response_msg = class_code\n 568→ else:\n 569→ response_msg = curr_class\n 570→\n 571→ else:\n 572→ response_msg = (\n 573→ f\"No matching tool '{tool_function_name}' or invalid args {tool_args}. \"\n 574→ \"Try again.\"\n 575→ )\n 576→\n 577→ messages.append({\n 578→ \"role\": \"tool\",\n 579→ \"tool_call_id\": tool_call_id,\n 580→ \"name\": tool_function_name,\n 581→ \"content\": response_msg\n 582→ })\n 583→\n 584→ messages += arg_messages\n 585→\n 586→ if amount_of_tools >= 6:\n 587→ messages.append({\n 588→ \"role\": \"system\",\n 589→ \"content\": (\n 590→ \"You called too many tools! If you still can't give a clear answer, \"\n 591→ \"return the 'more data' status.\"\n 592→ )\n 593→ })\n 594→\n 595→ return messages, final_content\n\n\nWhenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.\n\n"}]},"uuid":"ac476494-3d3f-4bc2-a7e1-d63614142b32","timestamp":"2026-02-11T13:25:09.664Z"},"normalizedMessages":[],"type":"agent_progress","prompt":"Explore how language affects the LLM analysis and UI layers in Vulnhalla:\n\n1. Read `src/llm/llm_analyzer.py` - how does it select templates? Are there language-specific tool calls or prompts?\n2. Read `src/vulnhalla.py` (IssueAnalyzer) - how does it handle language differences in code snippet extraction?\n3. Read `src/ui/ui_app.py` and `src/ui/components/controls_bar.py` - is there any language selection in the UI?\n4. Check the CLI entry points - look at `pyproject.toml` for script definitions and how args are parsed\n5. Look for any language constants, enums, or supported language lists in the codebase (grep for \"cpp\", \"go\", \"supported_lang\", \"LANGUAGES\" etc.)\n\nBe thorough in finding all places where language is referenced.","agentId":"a77e0c3"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01T7P5Gd5tzArGpoRoh4sVrf","uuid":"9f66fe9c-c93a-424d-9f8a-3253fe20e98d","timestamp":"2026-02-11T13:25:09.840Z"}
{"parentUuid":"9f66fe9c-c93a-424d-9f8a-3253fe20e98d","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"assistant","timestamp":"2026-02-11T13:25:09.846Z","message":{"model":"claude-haiku-4-5-20251001","id":"msg_01U9GcLr3utpKoqY7vdS9LPh","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_01FPx8tWy9Q3UnxQWPz3aSxn","name":"Read","input":{"file_path":"/home/josie/development/personal/Vulnhalla/src/ui/ui_app.py"}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":3,"cache_creation_input_tokens":6993,"cache_read_input_tokens":9758,"cache_creation":{"ephemeral_5m_input_tokens":0,"ephemeral_1h_input_tokens":6993},"output_tokens":3,"service_tier":"standard","inference_geo":"not_available"},"context_management":null},"requestId":"req_011CY2McgA6DYjmveUBt7CSt","uuid":"a946839f-06e2-46e8-8031-3820389e7cd1"},"normalizedMessages":[],"type":"agent_progress","prompt":"Explore how language affects the LLM analysis and UI layers in Vulnhalla:\n\n1. Read `src/llm/llm_analyzer.py` - how does it select templates? Are there language-specific tool calls or prompts?\n2. Read `src/vulnhalla.py` (IssueAnalyzer) - how does it handle language differences in code snippet extraction?\n3. Read `src/ui/ui_app.py` and `src/ui/components/controls_bar.py` - is there any language selection in the UI?\n4. Check the CLI entry points - look at `pyproject.toml` for script definitions and how args are parsed\n5. Look for any language constants, enums, or supported language lists in the codebase (grep for \"cpp\", \"go\", \"supported_lang\", \"LANGUAGES\" etc.)\n\nBe thorough in finding all places where language is referenced.","agentId":"a77e0c3"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01T7P5Gd5tzArGpoRoh4sVrf","uuid":"0765835a-bf5f-4a0b-b4ae-c33228c4b8a8","timestamp":"2026-02-11T13:25:09.846Z"}
{"parentUuid":"0765835a-bf5f-4a0b-b4ae-c33228c4b8a8","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"user","message":{"role":"user","content":[{"tool_use_id":"toolu_01D2ebPfRqFXhEPnakPVgxtP","type":"tool_result","content":" 1→#!/usr/bin/env python3\n 2→\"\"\"\n 3→Core analysis engine for Vulnhalla.\n 4→\n 5→This module coordinates the aggregation of raw CodeQL findings and their\n 6→classification by an LLM. It loads issues from CodeQL result files,\n 7→groups them by issue type, runs LLM-based analysis to decide whether\n 8→each finding is a true positive, false positive, or needs more data,\n 9→and writes structured result files for further inspection (e.g. in the UI).\n 10→\n 11→Analysis Pipeline Algorithm:\n 12→ 1. Collect DBs via get_all_dbs(dbs_folder), parse issues.csv, group by issue['name'].\n 13→ 2. For each issue: find containing function via find_function_by_line() (smallest line range).\n 14→ 3. Extract snippet and full function code.\n 15→ 4. Replace bracket references in the message; if references point outside current function, append those functions' code.\n 16→ 5. Build prompt; save *_raw.json; run LLM analysis; save *_final.json.\n 17→ 6. Classify by substring: \"1337\" → true, \"1007\" → false, else → more; log stats.\n 18→\"\"\"\n 19→\n 20→from pathlib import Path, PurePosixPath\n 21→import csv\n 22→import re\n 23→import json\n 24→from typing import Any, Callable, Dict, List, Optional, Tuple\n 25→from src.utils.common_functions import (\n 26→ get_all_dbs,\n 27→ read_file_lines_from_zip,\n 28→ read_file as read_file_utf8,\n 29→ write_file_ascii,\n 30→ read_yml\n 31→)\n 32→\n 33→# LLM analyzer for security analysis\n 34→from src.llm.llm_analyzer import LLMAnalyzer\n 35→from src.utils.config_validator import validate_and_exit_on_error\n 36→from src.utils.logger import get_logger\n 37→from src.utils.exceptions import VulnhallaError, CodeQLError, LLMApiError\n 38→\n 39→logger = get_logger(__name__)\n 40→\n 41→\n 42→class IssueAnalyzer:\n 43→ \"\"\"\n 44→ Analyzes all issues in CodeQL databases, fetches relevant code snippets,\n 45→ and forwards them to an LLM (via llm_analyzer) for triage.\n 46→ \"\"\"\n 47→\n 48→ def __init__(self, lang: str = \"c\", config: Optional[Dict[str, Any]] = None) -> None:\n 49→ \"\"\"\n 50→ Initialize the IssueAnalyzer with default parameters.\n 51→\n 52→ Args:\n 53→ lang (str, optional): The language code. Defaults to 'c'.\n 54→ config (Dict, optional): Full LLM configuration dictionary. If not provided, loads from .env file.\n 55→ \"\"\"\n 56→ self.lang = lang\n 57→ self.db_path: Optional[str] = None\n 58→ self.code_path: Optional[str] = None\n 59→ self.config = config\n 60→\n 61→ # ----------------------------------------------------------------------\n 62→ # 1. CSV Parsing and Data Gathering\n 63→ # ----------------------------------------------------------------------\n 64→\n 65→ def parse_issues_csv(self, file_name: str) -> List[Dict[str, str]]:\n 66→ \"\"\"\n 67→ Reads the issues.csv file produced by CodeQL (with a custom or default\n 68→ set of columns) and returns a list of dicts.\n 69→\n 70→ Args:\n 71→ file_name (str): The path to 'issues.csv'.\n 72→\n 73→ Returns:\n 74→ List[Dict[str, str]]: A list of issue objects parsed from CSV rows.\n 75→ \n 76→ Raises:\n 77→ CodeQLError: If file cannot be read (not found, permission denied, etc.).\n 78→ \"\"\"\n 79→ field_names = [\n 80→ \"name\", \"help\", \"type\", \"message\",\n 81→ \"file\", \"start_line\", \"start_offset\",\n 82→ \"end_line\", \"end_offset\"\n 83→ ]\n 84→ issues = []\n 85→ try:\n 86→ with Path(file_name).open(\"r\", encoding=\"utf-8\") as f:\n 87→ csv_reader = csv.DictReader(f, fieldnames=field_names)\n 88→ for row in csv_reader:\n 89→ issues.append(row)\n 90→ except FileNotFoundError as e:\n 91→ raise CodeQLError(f\"Issues CSV file not found: {file_name}\") from e\n 92→ except PermissionError as e:\n 93→ raise CodeQLError(f\"Permission denied reading issues CSV: {file_name}\") from e\n 94→ except OSError as e:\n 95→ raise CodeQLError(f\"OS error while reading issues CSV: {file_name}\") from e\n 96→ return issues\n 97→\n 98→ def collect_issues_from_databases(self, dbs_dir: str) -> Dict[str, List[Dict[str, str]]]:\n 99→ \"\"\"\n 100→ Searches through all CodeQL databases in `dbs_folder`, collects issues\n 101→ from each DB, and groups them by issue name.\n 102→\n 103→ Args:\n 104→ dbs_folder (str): The folder containing the language-specific databases.\n 105→\n 106→ Returns:\n 107→ Dict[str, List[Dict[str, str]]]: All issues, grouped by issue name.\n 108→ \n 109→ Raises:\n 110→ CodeQLError: If database folder cannot be accessed or issues cannot be read.\n 111→ \"\"\"\n 112→ issues_statistics: Dict[str, List[Dict[str, str]]] = {}\n 113→ \n 114→ actual_dbs = get_all_dbs(dbs_dir)\n 115→ for curr_db in actual_dbs:\n 116→ logger.info(\"Processing DB: %s\", curr_db)\n 117→ curr_db_path = Path(curr_db)\n 118→ function_tree_csv = curr_db_path / \"FunctionTree.csv\"\n 119→ issues_file = curr_db_path / \"issues.csv\"\n 120→ if function_tree_csv.exists() and issues_file.exists():\n 121→ # parse_issues_csv() raises CodeQLError on errors\n 122→ issues = self.parse_issues_csv(str(issues_file))\n 123→ for issue in issues:\n 124→ if issue[\"name\"] not in issues_statistics:\n 125→ issues_statistics[issue[\"name\"]] = []\n 126→ issue[\"db_path\"] = curr_db\n 127→ issues_statistics[issue[\"name\"]].append(issue)\n 128→ else:\n 129→ logger.error(\"Error: Execute run_codeql_queries.py first!\")\n 130→ continue\n 131→\n 132→ return issues_statistics\n 133→\n 134→ # ----------------------------------------------------------------------\n 135→ # 2. Function and Snippet Extraction\n 136→ # ----------------------------------------------------------------------\n 137→\n 138→ def find_function_by_line(self, function_tree_file: str, file_path: str, line: int) -> Optional[Dict[str, str]]:\n 139→ \"\"\"\n 140→ Finds the most specific (smallest) function containing the given file and line number.\n 141→\n 142→ Algorithm:\n 143→ - Iterate rows where file_path substring appears\n 144→ - Keep rows where start_line <= line <= end_line and file_path in function[\"file\"]\n 145→ - Return function with smallest (end_line - start_line), else None\n 146→\n 147→ Args:\n 148→ function_tree_file (str): Path to the 'FunctionTree.csv' file.\n 149→ file_path (str): File path substring to match (uses substring containment).\n 150→ line (int): The line number to check within function range.\n 151→\n 152→ Returns:\n 153→ Optional[Dict[str, str]]: The best matching function dictionary, or None if not found.\n 154→ \n 155→ Raises:\n 156→ CodeQLError: If function tree file cannot be read (not found, permission denied, etc.).\n 157→ \"\"\"\n 158→ keys = [\"function_name\", \"file\", \"start_line\", \"function_id\", \"end_line\", \"caller_id\"]\n 159→ best_function = None\n 160→ smallest_range = float('inf')\n 161→\n 162→ try:\n 163→ with Path(function_tree_file).open(\"r\", encoding=\"utf-8\") as f:\n 164→ for row in f:\n 165→ if file_path in row:\n 166→ fields = re.split(r',(?=(?:[^\"]*\"[^\"]*\")*[^\"]*$)', row.strip())\n 167→ if len(fields) != len(keys):\n 168→ continue # Skip malformed rows\n 169→\n 170→ function = dict(zip(keys, fields))\n 171→ try:\n 172→ start_line = int(function[\"start_line\"])\n 173→ end_line = int(function[\"end_line\"])\n 174→ except ValueError:\n 175→ continue # Skip if lines aren't integers\n 176→\n 177→ # Check if the target line falls within this function's range\n 178→ if start_line <= line <= end_line:\n 179→ if file_path in function[\"file\"]:\n 180→ # Greedy selection: track the function with smallest range\n 181→ # (most specific/nested function containing the line)\n 182→ size = end_line - start_line\n 183→ if size < smallest_range:\n 184→ best_function = function\n 185→ smallest_range = size\n 186→ except FileNotFoundError as e:\n 187→ raise CodeQLError(f\"Function tree file not found: {function_tree_file}\") from e\n 188→ except PermissionError as e:\n 189→ raise CodeQLError(f\"Permission denied reading function tree file: {function_tree_file}\") from e\n 190→ except OSError as e:\n 191→ raise CodeQLError(f\"OS error while reading function tree file: {function_tree_file}\") from e\n 192→\n 193→ return best_function\n 194→\n 195→ def extract_function_code(self, code_file: List[str], function_dict: Dict[str, str]) -> str:\n 196→ \"\"\"\n 197→ Produces lines of the function's code from a list of lines.\n 198→\n 199→ Args:\n 200→ code_file (List[str]): A list of lines for the entire file.\n 201→ function_dict (Dict[str, str]): The dictionary describing the function.\n 202→\n 203→ Returns:\n 204→ str: A snippet string of code for the function.\n 205→ \"\"\"\n 206→ if not function_dict:\n 207→ return \"\"\n 208→ start_line_idx = int(function_dict[\"start_line\"]) - 1 # Index for array access\n 209→ start_line_display = int(function_dict[\"start_line\"]) # Index for display\n 210→ end_line = int(function_dict[\"end_line\"])\n 211→ snippet_lines = code_file[start_line_idx:end_line]\n 212→ snippet = \"\\n\".join(\n 213→ f\"{start_line_display + i}: {s.replace(chr(9), ' ')}\"\n 214→ for i, s in enumerate(snippet_lines)\n 215→ )\n 216→ return snippet\n 217→\n 218→ # ----------------------------------------------------------------------\n 219→ # 3. Text Replacement & Prompt Building\n 220→ # ----------------------------------------------------------------------\n 221→\n 222→ def create_bracket_reference_replacer(\n 223→ self,\n 224→ db_path: str,\n 225→ code_path: str\n 226→ ) -> Callable[[re.Match], str]:\n 227→ \"\"\"\n 228→ Creates a replacement callback for re.sub to transform CodeQL bracket references\n 229→ into readable code snippets.\n 230→\n 231→ Algorithm:\n 232→ - Parse (variable, path_type, file_path, line, offsets)\n 233→ - Resolve path: relative:// → code_path + file_path; else strip leading '/'\n 234→ - Read from src.zip, slice snippet, return \"var 'snippet' (filename:line)\"\n 235→\n 236→ Args:\n 237→ db_path (str): Path to the current CodeQL database.\n 238→ code_path (str): Base path to the code. May differ on Windows vs. Linux.\n 239→\n 240→ Returns:\n 241→ Callable[[re.Match], str]: A function that can be used with `re.sub`.\n 242→ \n 243→ Note:\n 244→ The returned callback function may raise `CodeQLError` if ZIP file cannot be read.\n 245→ \"\"\"\n 246→ def replacement(match):\n 247→ variable = match.group(1)\n 248→ path_type = match.group(2)\n 249→ file_path = match.group(3)\n 250→ line_number = match.group(4)\n 251→ start_offset = match.group(5)\n 252→ end_offset = match.group(6)\n 253→\n 254→ if path_type == \"relative://\":\n 255→ full_path = code_path + file_path\n 256→ else:\n 257→ full_path = file_path[1:] if file_path.startswith(\"/\") else file_path\n 258→\n 259→ code_text = read_file_lines_from_zip(\n 260→ str(Path(db_path) / \"src.zip\"),\n 261→ full_path\n 262→ )\n 263→ code_lines = code_text.split(\"\\n\")\n 264→ snippet = code_lines[int(line_number) - 1][int(start_offset) - 1:int(end_offset)]\n 265→\n 266→ file_name = PurePosixPath(file_path).name\n 267→ return f\"{variable} '{snippet}' ({file_name}:{int(line_number)})\"\n 268→\n 269→ return replacement\n 270→\n 271→ def build_prompt_by_template(\n 272→ self,\n 273→ issue: Dict[str, str],\n 274→ message: str,\n 275→ snippet: str,\n 276→ code: str\n 277→ ) -> str:\n 278→ \"\"\"\n 279→ Builds the final 'prompt' template to feed into an LLM, combining\n 280→ the code snippet, code content, and a set of hints.\n 281→\n 282→ Args:\n 283→ issue (Dict[str, str]): The issue dictionary from parse_issues_csv.\n 284→ message (str): The processed \"message\" text to embed.\n 285→ snippet (str): The direct snippet from the code for the particular highlight.\n 286→ code (str): Additional code context (e.g. entire function).\n 287→\n 288→ Returns:\n 289→ str: A final prompt string with the template + hints + snippet + code.\n 290→ \n 291→ Raises:\n 292→ VulnhallaError: If template files cannot be read (not found, permission denied, etc.).\n 293→ \"\"\"\n 294→ # If language is 'c', many queries are stored under 'cpp'\n 295→ lang_folder = \"cpp\" if self.lang == \"c\" else self.lang\n 296→\n 297→ # Try to read an existing template specific to the issue name\n 298→ templates_base = Path(\"data/templates\") / lang_folder\n 299→ hints_path = templates_base / f\"{issue['name']}.template\"\n 300→ if not hints_path.exists():\n 301→ hints_path = templates_base / \"general.template\"\n 302→\n 303→ hints = read_file_utf8(str(hints_path))\n 304→\n 305→ # Read the larger general template\n 306→ template_path = templates_base / \"template.template\"\n 307→ template = read_file_utf8(str(template_path))\n 308→\n 309→ file_name = PurePosixPath(issue[\"file\"]).name\n 310→ location = f\"look at {file_name}:{int(issue['start_line'])} with '{snippet}'\"\n 311→\n 312→ # Special case for \"Use of object after its lifetime has ended\"\n 313→ if issue[\"name\"] == \"Use of object after its lifetime has ended\":\n 314→ message = message.replace(\"here\", f\"here ({location})\", 1)\n 315→\n 316→ prompt = template.format(\n 317→ name=issue[\"name\"],\n 318→ description=issue[\"help\"],\n 319→ message=message,\n 320→ location=location,\n 321→ hints=hints,\n 322→ code=code\n 323→ )\n 324→ return prompt\n 325→\n 326→ # ----------------------------------------------------------------------\n 327→ # 4. Saving LLM Results\n 328→ # ----------------------------------------------------------------------\n 329→\n 330→ def ensure_directories_exist(self, dirs: List[str]) -> None:\n 331→ \"\"\"\n 332→ Creates all directories in the given list if they do not already exist.\n 333→\n 334→ Args:\n 335→ dirs (List[str]): A list of directory paths to create if missing.\n 336→ \n 337→ Raises:\n 338→ VulnhallaError: If directory creation fails (permission denied, etc.).\n 339→ \"\"\"\n 340→ for d in dirs:\n 341→ dir_path = Path(d)\n 342→ if not dir_path.exists():\n 343→ try:\n 344→ dir_path.mkdir(parents=True, exist_ok=True)\n 345→ except PermissionError as e:\n 346→ raise VulnhallaError(f\"Permission denied creating directory: {d}\") from e\n 347→ except OSError as e:\n 348→ raise VulnhallaError(f\"OS error creating directory: {d}\") from e\n 349→\n 350→\n 351→ # ----------------------------------------------------------------------\n 352→ # 5. Main Analysis Routine\n 353→ # ----------------------------------------------------------------------\n 354→\n 355→ def save_raw_input_data(\n 356→ self,\n 357→ prompt: str,\n 358→ function_tree_file: str,\n 359→ current_function: Dict[str, str],\n 360→ results_folder: str,\n 361→ issue_id: int\n 362→ ) -> None:\n 363→ \"\"\"\n 364→ Saves the raw input data (prompt, function tree info, etc.) to a JSON file before\n 365→ sending it to the LLM.\n 366→\n 367→ Args:\n 368→ prompt (str): The final prompt text sent to the LLM.\n 369→ function_tree_file (str): Path to 'FunctionTree.csv'.\n 370→ current_function (Dict[str, str]): The currently found function dict.\n 371→ results_folder (str): Folder path where we store the result files.\n 372→ issue_id (int): The numeric ID of the current issue.\n 373→ \n 374→ Raises:\n 375→ VulnhallaError: If file cannot be written (permission denied, etc.).\n 376→ \"\"\"\n 377→ raw_data = json.dumps({\n 378→ \"function_tree_file\": function_tree_file,\n 379→ \"current_function\": current_function,\n 380→ \"db_path\": self.db_path,\n 381→ \"code_path\": self.code_path,\n 382→ \"prompt\": prompt\n 383→ }, ensure_ascii=False)\n 384→\n 385→ raw_output_file = Path(results_folder) / f\"{issue_id}_raw.json\"\n 386→ write_file_ascii(str(raw_output_file), raw_data)\n 387→\n 388→\n 389→ def format_llm_messages(self, messages: List[str]) -> str:\n 390→ \"\"\"\n 391→ Converts the list of messages returned by the LLM into a JSON-ish string to\n 392→ store as output.\n 393→\n 394→ Args:\n 395→ messages (List[str]): The messages from the LLM.\n 396→\n 397→ Returns:\n 398→ str: A string representation of LLM messages (somewhat JSON-formatted).\n 399→ \"\"\"\n 400→ gpt_result = \"[\\n \" + \",\\n \".join(\n 401→ f\"'''{item}'''\" if \"\\n\" in item else repr(item) for item in messages).replace(\"\\\\n\", \"\\n \").replace(\n 402→ \"\\\\t\", \" \") + \"\\n]\"\n 403→ return gpt_result\n 404→\n 405→\n 406→ def determine_issue_status(self, llm_content: str) -> str:\n 407→ \"\"\"\n 408→ Checks the content returned by the LLM to see if it includes certain\n 409→ status codes that classify the issue as 'true' or 'false' or 'more'.\n 410→\n 411→ Args:\n 412→ llm_content (str): The text content from the LLM's final response.\n 413→\n 414→ Returns:\n 415→ str: \"true\" if content has '1337', \"false\" if content has '1007',\n 416→ otherwise \"more\".\n 417→ \"\"\"\n 418→ if \"1337\" in llm_content:\n 419→ return \"true\"\n 420→ elif \"1007\" in llm_content:\n 421→ return \"false\"\n 422→ else:\n 423→ return \"more\"\n 424→\n 425→ def append_extra_functions(\n 426→ self,\n 427→ extra_lines: List[tuple[str, str, str]],\n 428→ function_tree_file: str,\n 429→ src_zip_path: str,\n 430→ code: str,\n 431→ current_function: Dict[str, str]\n 432→ ) -> Tuple[str, List[Dict[str, str]]]:\n 433→ \"\"\"\n 434→ Appends code from additional functions referenced outside the current function.\n 435→\n 436→ Algorithm:\n 437→ - Skip references within current function range\n 438→ - For external refs: find containing function via find_function_by_line(), dedupe by dict equality\n 439→ - Append extracted function code; return updated code and functions list\n 440→\n 441→ Args:\n 442→ extra_lines (List[tuple[str, str, str]]): References as (path_type, file_path, line_number).\n 443→ function_tree_file (str): Path to 'FunctionTree.csv'.\n 444→ src_zip_path (str): Path to the DB's src.zip file.\n 445→ code (str): The existing code snippet.\n 446→ current_function (Dict[str, str]): The currently found function dict.\n 447→\n 448→ Returns:\n 449→ Tuple[str, List[Dict[str, str]]]: Extended code snippet and list of all functions.\n 450→ \n 451→ Raises:\n 452→ CodeQLError: If function tree file or ZIP file cannot be read.\n 453→ \"\"\"\n 454→ functions = [current_function]\n 455→ for another_func_ref in extra_lines:\n 456→ # Unpack reference tuple: (path_type, file_path, line_number)\n 457→ path_type, file_ref, line_ref = another_func_ref\n 458→ file_ref = file_ref.strip()\n 459→\n 460→ # Resolve file path based on path type\n 461→ if path_type == \"relative://\":\n 462→ file_ref = self.code_path + file_ref\n 463→ else:\n 464→ # Remove leading slash for absolute paths (file://)\n 465→ file_ref = file_ref[1:] if file_ref.startswith(\"/\") else file_ref\n 466→\n 467→ # If it's within the same function's line range, skip\n 468→ start_line_func = int(current_function[\"start_line\"])\n 469→ end_line_func = int(current_function[\"end_line\"])\n 470→ if start_line_func <= int(line_ref) <= end_line_func:\n 471→ continue\n 472→\n 473→ # Find the function containing this reference using the greedy selection algorithm\n 474→ new_function = self.find_function_by_line(function_tree_file, \"/\" + file_ref, int(line_ref))\n 475→ # Deduplication: Only add if function was found and not already in the list\n 476→ if new_function and new_function not in functions:\n 477→ functions.append(new_function)\n 478→ # Read the function's source file and extract its code\n 479→ code_file2 = read_file_lines_from_zip(src_zip_path, file_ref).split(\"\\n\")\n 480→ code += (\n 481→ \"\\n\\nfile: \" + file_ref + \"\\n\" +\n 482→ self.extract_function_code(code_file2, new_function)\n 483→ )\n 484→\n 485→ return code, functions\n 486→\n 487→ def get_next_issue_id(self, issue_type: str) -> int:\n 488→ \"\"\"\n 489→ Gets the maximum issue ID currently in the results folder.\n 490→ Returns 0 if no files exist. The caller should add 1 to get the next ID.\n 491→ \"\"\"\n 492→ max_issue_id = 1\n 493→ results_folder = Path(\"output/results\") / self.lang / issue_type.replace(\" \", \"_\").replace(\"/\", \"-\")\n 494→ if not results_folder.exists() or len(list(results_folder.glob(\"*.json\"))) == 0:\n 495→ return 1\n 496→ \n 497→ for file in results_folder.glob(\"*.json\"):\n 498→ issue_id = int(file.stem.split(\"_\")[0])\n 499→ max_issue_id = max(issue_id, max_issue_id)\n 500→ return max_issue_id + 1\n 501→\n 502→\n 503→ def process_issue_type(\n 504→ self,\n 505→ issue_type: str,\n 506→ issues_of_type: List[Dict[str, str]],\n 507→ llm_analyzer: LLMAnalyzer\n 508→ ) -> None:\n 509→ \"\"\"\n 510→ Processes all issues of a single type. Builds file/folder paths, runs\n 511→ analysis, calls the LLM, and saves results.\n 512→\n 513→ Algorithm (per issue):\n 514→ - Normalize paths (Windows: ':'→'_', '\\'→'/'; Linux: strip leading '/')\n 515→ - Find function; extract snippet [start_offset-1:end_offset]\n 516→ - Replace bracket refs; append extra functions if needed\n 517→ - Build prompt; save raw/final; run LLM\n 518→ - Classify by '1337'/'1007'/else; log stats\n 519→\n 520→ Args:\n 521→ issue_type (str): The name of the issue type.\n 522→ issues_of_type (List[Dict[str, str]]): All issues belonging to that type.\n 523→ llm_analyzer (LLMAnalyzer): The LLM analyzer instance to use for queries.\n 524→ \n 525→ Raises:\n 526→ CodeQLError: If database files cannot be read (YAML, ZIP, CSV, etc.).\n 527→ VulnhallaError: If result files cannot be written.\n 528→ LLMError: If LLM analysis fails.\n 529→ \"\"\"\n 530→ results_folder = Path(\"output/results\") / self.lang / issue_type.replace(\" \", \"_\").replace(\"/\", \"-\")\n 531→ self.ensure_directories_exist([str(results_folder)])\n 532→\n 533→ issue_id = self.get_next_issue_id(issue_type)\n 534→ real_issues = []\n 535→ false_issues = []\n 536→ more_data = []\n 537→ skipped_issues = [] # Track issues skipped due to LLM errors (timeout, rate limit, etc.)\n 538→\n 539→ logger.info(\"Found %d issues of type %s\", len(issues_of_type), issue_type)\n 540→ logger.info(\"\")\n 541→ for issue in issues_of_type:\n 542→ self.db_path = issue[\"db_path\"]\n 543→ db_path_obj = Path(self.db_path)\n 544→ db_yml_path = db_path_obj / \"codeql-database.yml\"\n 545→ db_yml = read_yml(str(db_yml_path))\n 546→ self.code_path = db_yml[\"sourceLocationPrefix\"]\n 547→\n 548→ # Path normalization for cross-platform compatibility:\n 549→ # Windows paths contain \":\" (e.g., \"C:\\path\\to\\code\") which conflicts with\n 550→ # ZIP archive path handling. We normalize by:\n 551→ # - Replacing \":\" with \"_\" (e.g., \"C_\" instead of \"C:\")\n 552→ # - Converting backslashes to forward slashes\n 553→ # Linux paths are absolute (start with \"/\") which we remove for ZIP access\n 554→ if \":\" in self.code_path:\n 555→ # Windows path: normalize drive letter and separators\n 556→ self.code_path = self.code_path.replace(\":\", \"_\").replace(\"\\\\\", \"/\")\n 557→ else:\n 558→ # Linux path: remove leading slash\n 559→ self.code_path = self.code_path[1:]\n 560→\n 561→ function_tree_file = str(db_path_obj / \"FunctionTree.csv\")\n 562→ src_zip_path = str(db_path_obj / \"src.zip\")\n 563→\n 564→ full_file_path = self.code_path + issue[\"file\"]\n 565→ code_file_contents = read_file_lines_from_zip(src_zip_path, full_file_path).split(\"\\n\")\n 566→\n 567→ current_function = self.find_function_by_line(\n 568→ function_tree_file,\n 569→ \"/\" + self.code_path + issue[\"file\"],\n 570→ int(issue[\"start_line\"])\n 571→ )\n 572→ if not current_function:\n 573→ logger.warning(\"issue %s: Can't find the function or function is too big!\", issue_id)\n 574→ continue\n 575→\n 576→ snippet = code_file_contents[int(issue[\"start_line\"]) - 1][\n 577→ int(issue[\"start_offset\"]) - 1:int(issue[\"end_offset\"])\n 578→ ]\n 579→\n 580→ code = (\n 581→ \"file: \" + self.code_path + issue[\"file\"] + \"\\n\" +\n 582→ self.extract_function_code(code_file_contents, current_function)\n 583→ )\n 584→\n 585→ # Replace bracket refs in message\n 586→ bracket_pattern = r'\\[\\[\"(.*?)\"\\|\"((?:relative://|file://))?(/.*?):(\\d+):(\\d+):\\d+:(\\d+)\"\\]\\]'\n 587→ transform_func = self.create_bracket_reference_replacer(self.db_path, self.code_path)\n 588→ message = re.sub(bracket_pattern, transform_func, issue[\"message\"])\n 589→\n 590→ # Find extra refs for context expansion\n 591→ extra_lines_pattern = r'\\[\\[\".*?\"\\|\"((?:relative://|file://)?)(/.*?):(\\d+):\\d+:\\d+:\\d+\"\\]\\]'\n 592→ extra_lines = re.findall(extra_lines_pattern, issue[\"message\"])\n 593→ functions = [current_function]\n 594→\n 595→ if extra_lines:\n 596→ code, functions = self.append_extra_functions(\n 597→ extra_lines, function_tree_file, src_zip_path, code, current_function\n 598→ )\n 599→\n 600→ prompt = self.build_prompt_by_template(issue, message, snippet, code)\n 601→\n 602→ # Save raw input to the LLM\n 603→ self.save_raw_input_data(prompt, function_tree_file, current_function, results_folder, issue_id)\n 604→\n 605→ # Send to LLM (with error handling for timeouts and API errors)\n 606→ try:\n 607→ messages, content = llm_analyzer.run_llm_security_analysis(\n 608→ prompt,\n 609→ function_tree_file,\n 610→ current_function,\n 611→ functions,\n 612→ self.db_path\n 613→ )\n 614→ except LLMApiError as e:\n 615→ # Skip this issue on LLM errors (timeout, rate limit, etc.) and continue with others\n 616→ logger.warning(\"Issue ID: %s SKIPPED - LLM error: %s\", issue_id, e)\n 617→ skipped_issues.append(issue_id)\n 618→ issue_id += 1\n 619→ continue\n 620→\n 621→ gpt_result = self.format_llm_messages(messages)\n 622→ final_file = Path(results_folder) / f\"{issue_id}_final.json\"\n 623→ write_file_ascii(str(final_file), gpt_result)\n 624→\n 625→ # Check status code in LLM content\n 626→ status = self.determine_issue_status(content)\n 627→ if status == \"true\":\n 628→ real_issues.append(issue_id)\n 629→ status = \"True Positive\"\n 630→ elif status == \"false\":\n 631→ false_issues.append(issue_id)\n 632→ status = \"False Positive\"\n 633→ else:\n 634→ more_data.append(issue_id)\n 635→ status = \"LLM needs More Data\"\n 636→\n 637→ # Log issue status\n 638→ logger.info(\"Issue ID: %s, LLM decision: → %s\", issue_id, status)\n 639→ issue_id += 1\n 640→\n 641→ logger.info(\"\")\n 642→ logger.info(\"Issue type: %s\", issue_type)\n 643→ logger.info(\"Total issues: %d\", len(issues_of_type))\n 644→ logger.info(\"True Positive: %d\", len(real_issues))\n 645→ logger.info(\"False Positive: %d\", len(false_issues))\n 646→ logger.info(\"LLM needs More Data: %d\", len(more_data))\n 647→ if skipped_issues:\n 648→ logger.warning(\"Skipped (LLM errors): %d (IDs: %s)\", len(skipped_issues), skipped_issues)\n 649→ logger.info(\"\")\n 650→\n 651→\n 652→ def run(self, dbs_dir: str) -> None:\n 653→ \"\"\"\n 654→ Main analysis routine:\n 655→ 1. Initializes the LLM.\n 656→ 2. Finds all CodeQL DBs for the given language.\n 657→ 3. Parses each DB's issues.csv, aggregates them by issue type.\n 658→ 4. Asks the LLM for each issue's snippet context, saving final results\n 659→ in various directory structures.\n 660→ \n 661→ Args:\n 662→ dbs_dir (str): Path to the directory containing downloaded databases.\n 663→ \n 664→ Raises:\n 665→ CodeQLError: If database files cannot be accessed or read.\n 666→ VulnhallaError: If directory creation or file writing fails.\n 667→ LLMError: If LLM initialization or analysis fails.\n 668→ \"\"\"\n 669→ # Validate configuration before starting\n 670→ if self.config is None:\n 671→ validate_and_exit_on_error()\n 672→ \n 673→ llm_analyzer = LLMAnalyzer()\n 674→ llm_analyzer.init_llm_client(config=self.config)\n 675→\n 676→ # Gather issues from all DBs\n 677→ issues_statistics = self.collect_issues_from_databases(dbs_dir)\n 678→\n 679→ total_issues = 0\n 680→ for issue_type in issues_statistics:\n 681→ total_issues += len(issues_statistics[issue_type])\n 682→ logger.info(\"Total issues found: %d\", total_issues)\n 683→ logger.info(\"\")\n 684→\n 685→ # Process all issues, type by type\n 686→ for issue_type in issues_statistics.keys():\n 687→ self.process_issue_type(issue_type, issues_statistics[issue_type], llm_analyzer)\n 688→\n 689→if __name__ == '__main__':\n 690→ # Initialize logging\n 691→ from src.utils.logger import setup_logging\n 692→ setup_logging()\n 693→ \n 694→ # Loads configuration from .env file\n 695→ # Or use: analyzer = IssueAnalyzer(lang=\"c\", config={...})\n 696→ analyzer = IssueAnalyzer(lang=\"c\")\n 697→ analyzer.run()\n\n\nWhenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.\n\n"}]},"uuid":"c2d0386d-e671-4657-8334-e1de786bbe12","timestamp":"2026-02-11T13:25:09.898Z"},"normalizedMessages":[],"type":"agent_progress","prompt":"Explore how language affects the LLM analysis and UI layers in Vulnhalla:\n\n1. Read `src/llm/llm_analyzer.py` - how does it select templates? Are there language-specific tool calls or prompts?\n2. Read `src/vulnhalla.py` (IssueAnalyzer) - how does it handle language differences in code snippet extraction?\n3. Read `src/ui/ui_app.py` and `src/ui/components/controls_bar.py` - is there any language selection in the UI?\n4. Check the CLI entry points - look at `pyproject.toml` for script definitions and how args are parsed\n5. Look for any language constants, enums, or supported language lists in the codebase (grep for \"cpp\", \"go\", \"supported_lang\", \"LANGUAGES\" etc.)\n\nBe thorough in finding all places where language is referenced.","agentId":"a77e0c3"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01T7P5Gd5tzArGpoRoh4sVrf","uuid":"d016b856-e382-48d0-b98a-f1c2c7dea8ba","timestamp":"2026-02-11T13:25:10.055Z"}
{"parentUuid":"d016b856-e382-48d0-b98a-f1c2c7dea8ba","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"assistant","timestamp":"2026-02-11T13:25:10.186Z","message":{"model":"claude-haiku-4-5-20251001","id":"msg_01U9GcLr3utpKoqY7vdS9LPh","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_01Pyr8AbqXnX8xQ4qB5FDXrV","name":"Read","input":{"file_path":"/home/josie/development/personal/Vulnhalla/src/ui/components/controls_bar.py"}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":3,"cache_creation_input_tokens":6993,"cache_read_input_tokens":9758,"cache_creation":{"ephemeral_5m_input_tokens":0,"ephemeral_1h_input_tokens":6993},"output_tokens":3,"service_tier":"standard","inference_geo":"not_available"},"context_management":null},"requestId":"req_011CY2McgA6DYjmveUBt7CSt","uuid":"2abf4323-5197-4ec8-b353-093ba2e54ba4"},"normalizedMessages":[],"type":"agent_progress","prompt":"Explore how language affects the LLM analysis and UI layers in Vulnhalla:\n\n1. Read `src/llm/llm_analyzer.py` - how does it select templates? Are there language-specific tool calls or prompts?\n2. Read `src/vulnhalla.py` (IssueAnalyzer) - how does it handle language differences in code snippet extraction?\n3. Read `src/ui/ui_app.py` and `src/ui/components/controls_bar.py` - is there any language selection in the UI?\n4. Check the CLI entry points - look at `pyproject.toml` for script definitions and how args are parsed\n5. Look for any language constants, enums, or supported language lists in the codebase (grep for \"cpp\", \"go\", \"supported_lang\", \"LANGUAGES\" etc.)\n\nBe thorough in finding all places where language is referenced.","agentId":"a77e0c3"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01T7P5Gd5tzArGpoRoh4sVrf","uuid":"80bc35b8-d218-44da-9b97-d3a47bd124d2","timestamp":"2026-02-11T13:25:10.186Z"}
{"parentUuid":"80bc35b8-d218-44da-9b97-d3a47bd124d2","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"user","message":{"role":"user","content":[{"tool_use_id":"toolu_01FPx8tWy9Q3UnxQWPz3aSxn","type":"tool_result","content":" 1→#!/usr/bin/env python3\n 2→\"\"\"\n 3→Vulnhalla UI - User Interface for browsing analysis results.\n 4→\n 5→This module provides a three-panel UI for viewing and exploring\n 6→CodeQL analysis results processed by Vulnhalla.\n 7→\"\"\"\n 8→\n 9→import re\n 10→import sys\n 11→from pathlib import Path\n 12→from typing import Any, Dict, List, Optional, Tuple\n 13→\n 14→from rich.markup import escape as markup_escape\n 15→\n 16→from textual.app import App, ComposeResult\n 17→from textual.containers import Horizontal, Vertical\n 18→from textual.widgets import (\n 19→ DataTable, Static, Input, Select, Button, Label,\n 20→ Header, Footer\n 21→)\n 22→from textual.binding import Binding\n 23→\n 24→# Add project root to path for imports\n 25→PROJECT_ROOT = Path(__file__).parent.parent.parent\n 26→if str(PROJECT_ROOT) not in sys.path:\n 27→ sys.path.insert(0, str(PROJECT_ROOT))\n 28→\n 29→from src.ui.models import (\n 30→ Issue,\n 31→ format_status_display,\n 32→ format_manual_decision,\n 33→ get_default_sort_key,\n 34→ get_sort_key_for_column\n 35→)\n 36→from src.ui.results_loader import ResultsLoader\n 37→from src.ui.issue_parser import (\n 38→ extract_line_number_from_location,\n 39→ collect_all_code_snippets,\n 40→ extract_last_message\n 41→)\n 42→from src.ui.components.controls_bar import ControlsBar\n 43→from src.ui.components.splitter_divider import SplitterDivider\n 44→from src.ui.components.issues_list_panel import IssuesListPanel\n 45→from src.ui.components.details_panel import DetailsPanel\n 46→\n 47→\n 48→class VulnhallaUI(App):\n 49→ \"\"\"\n 50→ Main UI application for Vulnhalla.\n 51→ \"\"\"\n 52→ \n 53→ CSS = \"\"\"\n 54→ .panel-title { text-style: bold; margin: 1; }\n 55→ .help-text { margin: 1; }\n 56→ .control-label { margin: 0 1; }\n 57→ #issues-table { height: 1fr; }\n 58→ #details-content { padding: 1; }\n 59→ #issues-search { margin: 1; width: 100%; }\n 60→ #controls-bar { height: 11; border-top: solid $primary; }\n 61→ #details-scrollable { height: 1fr; }\n 62→ #manual-decision-container { height: 5; border-top: solid $primary; padding: 0 1; }\n 63→ #manual-decision-label { margin: 0; }\n 64→ #manual-decision-select { margin: 0; width: 100%; }\n 65→ #issues-list { width: 50%; }\n 66→ #details { width: 50%; }\n 67→ Select, Select:focus, SelectOverlay, SelectOverlay:focus { border: none; }\n 68→ Input, Input:focus { border: none; outline: none; }\n 69→ SplitterDivider { width: 1; background: transparent; color: $surface-lighten-2; }\n 70→ SplitterDivider:hover { background: $primary; color: $primary; }\n 71→ \"\"\"\n 72→ \n 73→ BINDINGS = [\n 74→ Binding(\"q\", \"quit\", \"Quit\"),\n 75→ Binding(\"r\", \"reload\", \"Reload\"),\n 76→ Binding(\"tab\", \"focus_next\", \"Next Panel\"),\n 77→ Binding(\"shift+tab\", \"focus_previous\", \"Previous Panel\"),\n 78→ Binding(\"/\", \"search\", \"Search\"),\n 79→ Binding(\"escape\", \"clear_search\", \"Clear Search\"),\n 80→ Binding(\"enter\", \"select_issue\", \"Show Details\"),\n 81→ Binding(\"[\", \"resize_left\", \"Resize Left\"),\n 82→ Binding(\"]\", \"resize_right\", \"Resize Right\"),\n 83→ ]\n 84→ \n 85→ def __init__(self) -> None:\n 86→ \"\"\"\n 87→ Initialize the VulnhallaUI application.\n 88→ \"\"\"\n 89→ super().__init__()\n 90→ self.loader = ResultsLoader()\n 91→ self.issues: List[Issue] = []\n 92→ self.filtered_issues: List[Issue] = []\n 93→ self.selected_issue: Optional[Issue] = None\n 94→ self.current_lang = \"c\"\n 95→ self.current_filter = \"all\"\n 96→ self.search_query = \"\"\n 97→ self.split_position = 0.5\n 98→ self.sort_column: Optional[str] = None\n 99→ self.sort_ascending: bool = True\n 100→ self._updating_manual_decision_select: bool = False\n 101→ \n 102→ def compose(self) -> ComposeResult:\n 103→ \"\"\"Compose the main application layout.\n 104→\n 105→ Builds the overall Textual UI, including the issues list panel,\n 106→ the details panel, and the bottom controls bar.\n 107→ \"\"\"\n 108→ yield Header()\n 109→ with Vertical():\n 110→ with Horizontal():\n 111→ yield IssuesListPanel(id=\"issues-list\")\n 112→ yield SplitterDivider(app_instance=self)\n 113→ yield DetailsPanel(id=\"details\")\n 114→ yield ControlsBar(id=\"controls-bar\")\n 115→ yield Footer()\n 116→\n 117→\n 118→ def on_mount(self) -> None:\n 119→ \"\"\"\n 120→ Initialize the UI when app starts.\n 121→ \"\"\"\n 122→ self.load_issues()\n 123→ self.update_issues_table()\n 124→ table = self.query_one(\"#issues-table\", DataTable)\n 125→ table.cursor_type = \"row\"\n 126→ table.show_header = True\n 127→ table.focus()\n 128→ # Set initial split position\n 129→ self._update_split_position()\n 130→ # Hide manual decision select initially (no issue selected)\n 131→ try:\n 132→ manual_decision_container = self.query_one(\"#manual-decision-container\", Vertical)\n 133→ manual_decision_container.styles.display = \"none\"\n 134→ except:\n 135→ pass\n 136→\n 137→\n 138→ def load_issues(self) -> None:\n 139→ \"\"\"\n 140→ Load issues from disk and update the UI.\n 141→ \n 142→ Displays error notifications if any files fail to load.\n 143→ \"\"\"\n 144→ all_issues: list = []\n 145→ all_errors: list = []\n 146→ results_path = Path(self.loader.results_root)\n 147→ if results_path.exists():\n 148→ for lang_dir in sorted(results_path.iterdir()):\n 149→ if lang_dir.is_dir():\n 150→ issues, errors_for_lang = self.loader.load_all_issues(lang_dir.name)\n 151→ all_issues.extend(issues)\n 152→ all_errors.extend(errors_for_lang)\n 153→ self.issues = all_issues\n 154→ errors = all_errors\n 155→ \n 156→ # Display errors to user if any occurred\n 157→ if errors:\n 158→ error_count = len(errors)\n 159→ if error_count == 1:\n 160→ self.notify(f\"Error loading file: {errors[0]}\", severity=\"error\")\n 161→ else:\n 162→ # Show summary for multiple errors\n 163→ self.notify(\n 164→ f\"Failed to load {error_count} file(s). Check logs for details.\",\n 165→ severity=\"warning\"\n 166→ )\n 167→ # Log all errors for debugging\n 168→ from src.utils.logger import get_logger\n 169→ logger = get_logger(__name__)\n 170→ for error in errors:\n 171→ logger.warning(error)\n 172→ \n 173→ # Load saved manual decisions from disk and apply to issues\n 174→ saved_decisions = self.loader.load_manual_decisions()\n 175→ for issue in self.issues:\n 176→ if issue.final_path in saved_decisions:\n 177→ issue.manual_decision = saved_decisions[issue.final_path]\n 178→ \n 179→ self.apply_filters()\n 180→\n 181→\n 182→ def apply_filters(self) -> None:\n 183→ \"\"\"\n 184→ Apply current filter and search to issues list.\n 185→ \"\"\"\n 186→ filter_select = self.query_one(\"#filter-select\", Select)\n 187→ self.current_filter = filter_select.value or \"all\"\n 188→ \n 189→ # Get search query from the persistent search input\n 190→ search_input = self.query_one(\"#issues-search\", Input)\n 191→ self.search_query = (search_input.value or \"\").strip()\n 192→ \n 193→ # Filter by status\n 194→ if self.current_filter == \"all\":\n 195→ filtered = self.issues\n 196→ else:\n 197→ filtered = [i for i in self.issues if i.status == self.current_filter]\n 198→ \n 199→ # Apply search filter\n 200→ if self.search_query:\n 201→ query_lower = self.search_query.lower()\n 202→ filtered = [\n 203→ i for i in filtered\n 204→ if query_lower in i.name.lower()\n 205→ or query_lower in i.file.lower()\n 206→ or query_lower in i.repo.lower()\n 207→ or query_lower in i.status.lower() or query_lower in i.id.lower()\n 208→ or (i.manual_decision and query_lower in i.manual_decision.lower())\n 209→ or (not i.manual_decision and query_lower in \"not set\")\n 210→ ]\n 211→ \n 212→ # Apply user-defined column sorting if set, otherwise use default ID sorting\n 213→ if self.sort_column:\n 214→ self._sort_filtered_issues(filtered)\n 215→ else:\n 216→ # Default: Sort by numeric ID\n 217→ filtered.sort(key=get_default_sort_key)\n 218→ \n 219→ self.filtered_issues = filtered\n 220→ self.update_issues_table()\n 221→\n 222→\n 223→ def _sort_filtered_issues(self, issues: List[Issue]) -> None:\n 224→ \"\"\"\n 225→ Sort filtered issues by the current sort column and direction.\n 226→\n 227→ Args:\n 228→ issues (List[Issue]): List of issues to sort (modified in-place).\n 229→ \"\"\"\n 230→ if not self.sort_column or not issues:\n 231→ return\n 232→ \n 233→ sort_key = get_sort_key_for_column(self.sort_column)\n 234→ if sort_key:\n 235→ issues.sort(key=sort_key, reverse=not self.sort_ascending)\n 236→\n 237→\n 238→ def update_issues_table(self, preserve_row_key: Optional[str] = None) -> None:\n 239→ \"\"\"\n 240→ Update the issues table with current filtered issues.\n 241→\n 242→ Args:\n 243→ preserve_row_key (Optional[str]): Optional row key (issue ID) to preserve \n 244→ cursor position after update.\n 245→ \"\"\"\n 246→ table = self.query_one(\"#issues-table\", DataTable)\n 247→ # Clear both rows and columns to prevent duplicates\n 248→ table.clear(columns=True)\n 249→ table.add_columns(\"ID\", \"LLM decision\", \"Manual decision\", \"Repo\", \"Issue name\", \"File\")\n 250→ \n 251→ for issue in self.filtered_issues:\n 252→ status_display = format_status_display(issue.status)\n 253→ manual_display = format_manual_decision(issue.manual_decision)\n 254→ \n 255→ # Normalize file name display format\n 256→ file_display = issue.file\n 257→ if file_display.endswith('\"') and not file_display.startswith('\"'):\n 258→ file_display = '\"' + file_display\n 259→ # Truncate if needed\n 260→ if len(file_display) > 30:\n 261→ file_display = file_display[:30] + \"...\"\n 262→ \n 263→ table.add_row(\n 264→ issue.id,\n 265→ status_display,\n 266→ manual_display,\n 267→ issue.repo,\n 268→ issue.name[:40] + \"...\" if len(issue.name) > 40 else issue.name,\n 269→ file_display,\n 270→ key=issue.id\n 271→ )\n 272→ \n 273→ # Restore cursor position if requested (immediately after adding all rows)\n 274→ if preserve_row_key is not None:\n 275→ # Find target row index and restore cursor\n 276→ for idx, issue in enumerate(self.filtered_issues):\n 277→ if issue.id == preserve_row_key and idx > 0:\n 278→ # Move cursor from row 0 (after clear) to target row\n 279→ for _ in range(idx):\n 280→ table.action_cursor_down()\n 281→ break\n 282→ \n 283→ # Refresh the table to ensure visual update\n 284→ table.refresh()\n 285→ \n 286→ # Update count with sort indicator\n 287→ count_widget = self.query_one(\"#issues-count\", Static)\n 288→ sort_indicator = \"\"\n 289→ if self.sort_column:\n 290→ direction = \"↑\" if self.sort_ascending else \"↓\"\n 291→ sort_indicator = f\" | Sorted by: {self.sort_column} {direction}\"\n 292→ count_widget.update(f\"Showing {len(self.filtered_issues)} of {len(self.issues)} issues{sort_indicator}\")\n 293→\n 294→\n 295→ def on_data_table_header_selected(self, event: DataTable.HeaderSelected) -> None:\n 296→ \"\"\"\n 297→ Handle column header click for sorting.\n 298→\n 299→ Args:\n 300→ event (DataTable.HeaderSelected): Event containing column index information.\n 301→ \"\"\"\n 302→ # Get column index from the event\n 303→ column_index = getattr(event, 'column_index', None)\n 304→ \n 305→ # Map column index to column name\n 306→ column_names = [\"ID\", \"LLM decision\", \"Manual decision\", \"Repo\", \"Issue name\", \"File\"]\n 307→ \n 308→ if column_index is None or not (0 <= column_index < len(column_names)):\n 309→ return\n 310→ \n 311→ column_key = column_names[column_index]\n 312→ \n 313→ # Toggle sort direction if clicking the same column, otherwise set new column\n 314→ if self.sort_column == column_key:\n 315→ self.sort_ascending = not self.sort_ascending\n 316→ else:\n 317→ self.sort_column = column_key\n 318→ self.sort_ascending = True\n 319→ \n 320→ # Re apply filters (which will apply sorting) and update table\n 321→ self.apply_filters()\n 322→\n 323→\n 324→ def on_data_table_row_selected(self, event: DataTable.RowSelected) -> None:\n 325→ \"\"\"\n 326→ Handle issue selection in the table.\n 327→\n 328→ Args:\n 329→ event (DataTable.RowSelected): Event containing row selection information.\n 330→ \"\"\"\n 331→ if event.cursor_row is None or event.cursor_row >= len(self.filtered_issues):\n 332→ return\n 333→ \n 334→ # Save current cursor position before updating\n 335→ table = self.query_one(\"#issues-table\", DataTable)\n 336→ current_cursor_row = event.cursor_row\n 337→ \n 338→ self.selected_issue = self.filtered_issues[event.cursor_row]\n 339→ self.update_details_panel()\n 340→ \n 341→ # Restore cursor position after update\n 342→ if current_cursor_row is not None and current_cursor_row < len(self.filtered_issues):\n 343→ try:\n 344→ table.cursor_row = current_cursor_row\n 345→ table.refresh()\n 346→ except:\n 347→ pass\n 348→\n 349→\n 350→ def action_select_issue(self) -> None:\n 351→ \"\"\"\n 352→ Action to select the currently highlighted issue and show details.\n 353→ \"\"\"\n 354→ table = self.query_one(\"#issues-table\", DataTable)\n 355→ # Get the current cursor row\n 356→ cursor_row = table.cursor_row\n 357→ if cursor_row is not None and 0 <= cursor_row < len(self.filtered_issues):\n 358→ self.selected_issue = self.filtered_issues[cursor_row]\n 359→ self.update_details_panel()\n 360→ # Trigger the row selection to highlight it\n 361→ table.action_select_cursor()\n 362→\n 363→\n 364→ def _escape_code_for_markup(self, code: str) -> str:\n 365→ \"\"\"\n 366→ Escape Rich markup characters in code to prevent interpretation.\n 367→\n 368→ Args:\n 369→ code (str): Code string to escape.\n 370→\n 371→ Returns:\n 372→ str: Escaped code string with Rich markup characters escaped.\n 373→ \"\"\"\n 374→ return code.replace('[', '\\\\[').replace(']', '\\\\]').replace('{', '\\\\{').replace('}', '\\\\}')\n 375→\n 376→\n 377→ def update_details_panel(self) -> None:\n 378→ \"\"\"\n 379→ Update the details panel with selected issue information.\n 380→ \"\"\"\n 381→ # Get widgets\n 382→ details_widget = self.query_one(\"#details-content\", Static)\n 383→ manual_decision_select = self.query_one(\"#manual-decision-select\", Select)\n 384→ manual_decision_label = self.query_one(\"#manual-decision-label\", Label)\n 385→ manual_decision_container = self.query_one(\"#manual-decision-container\", Vertical)\n 386→ \n 387→ if not self.selected_issue:\n 388→ details_widget.update(\"Select an issue to view details\")\n 389→ # Hide manual decision select when no issue is selected\n 390→ manual_decision_container.styles.display = \"none\"\n 391→ return\n 392→ \n 393→ # Show manual decision select when issue is selected\n 394→ manual_decision_container.styles.display = \"block\"\n 395→ \n 396→ issue = self.selected_issue\n 397→ \n 398→ # Build details text parts\n 399→ details_parts = []\n 400→ \n 401→ # ===== LLM DECISION SECTION =====\n 402→ # Map status to display text\n 403→ status_display = format_status_display(issue.status)\n 404→ details_parts.append(\"[bold cyan]LLM decision[/bold cyan]\")\n 405→ details_parts.append(markup_escape(status_display))\n 406→ details_parts.append(\"\")\n 407→ \n 408→ # ===== METADATA SECTION =====\n 409→ # Use Rich markup for styled metadata\n 410→ details_parts.append(\"[bold cyan]Metadata[/bold cyan]\")\n 411→ details_parts.append(f\"[bold]Issue name:[/bold] {markup_escape(issue.name)}\")\n 412→ details_parts.append(f\"[bold]Repo:[/bold] {markup_escape(issue.repo)}\")\n 413→ details_parts.append(f\"[bold]File:[/bold] {markup_escape(issue.file)}:{issue.line}\")\n 414→ details_parts.append(f\"[bold]Type:[/bold] {markup_escape(issue.issue_type)}\")\n 415→ \n 416→ # Add function name if available\n 417→ if issue.raw_data and \"current_function\" in issue.raw_data:\n 418→ func = issue.raw_data[\"current_function\"]\n 419→ func_name = func.get(\"function_name\", \"\").strip('\"')\n 420→ if func_name:\n 421→ details_parts.append(f\"[bold]Function:[/bold] {markup_escape(func_name)}\")\n 422→ \n 423→ details_parts.append(\"\")\n 424→ \n 425→ # ===== CODE SECTION =====\n 426→ initial_code, additional_code_list = collect_all_code_snippets(issue)\n 427→ \n 428→ details_parts.append(\"[bold cyan]Code[/bold cyan]\")\n 429→ details_parts.append(\"\")\n 430→ \n 431→ if not initial_code and not additional_code_list:\n 432→ details_parts.append(\"(No code available)\")\n 433→ else:\n 434→ # Helper function to render code with highlighting\n 435→ def render_code_block(code: str, to_highlight: bool = True) -> tuple[list[str], Optional[int]]:\n 436→ \"\"\"\n 437→ Render a code block with highlighting.\n 438→\n 439→ Args:\n 440→ code (str): Code block to render.\n 441→ to_highlight (bool): Whether to highlight the line number of the location.\n 442→ \n 443→ Returns:\n 444→ tuple[list[str], Optional[int]]: Tuple of (rendered_lines, highlight_index).\n 445→ \"\"\"\n 446→ if not code:\n 447→ return ([], None)\n 448→ \n 449→ location_line = extract_line_number_from_location(issue)\n 450→ code_lines = code.split('\\n')\n 451→ \n 452→ # Find highlight index within this block\n 453→ highlight_idx = None\n 454→ if location_line is not None:\n 455→ for idx, line in enumerate(code_lines):\n 456→ match = re.match(r'^\\s*(\\d+):', line)\n 457→ if match and int(match.group(1)) == location_line:\n 458→ highlight_idx = idx\n 459→ break\n 460→ \n 461→ # Process and escape lines\n 462→ rendered_lines = []\n 463→ for idx, line in enumerate(code_lines):\n 464→ escaped = self._escape_code_for_markup(line)\n 465→ if highlight_idx is not None and idx == highlight_idx and to_highlight:\n 466→ rendered_lines.append(f\"[bold red]{escaped}[/bold red]\")\n 467→ else:\n 468→ rendered_lines.append(escaped)\n 469→ \n 470→ return (rendered_lines, highlight_idx)\n 471→ \n 472→ if initial_code:\n 473→ details_parts.append(\"Initial Code Context:\")\n 474→ details_parts.append(\"\")\n 475→ initial_lines, _ = render_code_block(initial_code, to_highlight=True)\n 476→ details_parts.extend(initial_lines)\n 477→ details_parts.append(\"\")\n 478→ \n 479→ if additional_code_list:\n 480→ details_parts.append(\"\")\n 481→ details_parts.append(\"Additional Code (requested during analysis):\")\n 482→ details_parts.append(\"\")\n 483→ \n 484→ for additional_block in additional_code_list:\n 485→ additional_lines, _ = render_code_block(additional_block, to_highlight=False)\n 486→ details_parts.extend(additional_lines)\n 487→ # Add separator between code blocks\n 488→ if additional_block != additional_code_list[-1]:\n 489→ details_parts.append(\"\")\n 490→ details_parts.append(\"────────────────────────────────────────────────────────────────────────────────\")\n 491→ details_parts.append(\"\")\n 492→ \n 493→ details_parts.append(\"\")\n 494→ \n 495→ # ===== SUMMARY SECTION =====\n 496→ # Extract the last LLM message (final answer/decision)\n 497→ summary_content = extract_last_message(issue.final_data)\n 498→ \n 499→ details_parts.append(\"\")\n 500→ details_parts.append(\"[bold cyan]Summary (LLM final answer)[/bold cyan]\")\n 501→ details_parts.append(\"\")\n 502→ \n 503→ if summary_content:\n 504→ # Escape Rich markup and limit to 80 lines\n 505→ summary_lines = summary_content.split('\\n')\n 506→ MAX_SUMMARY_LINES = 80\n 507→ \n 508→ if len(summary_lines) > MAX_SUMMARY_LINES:\n 509→ summary_lines = summary_lines[:MAX_SUMMARY_LINES]\n 510→ summary_lines.append(\"\")\n 511→ summary_lines.append(\"... (truncated, showing first 80 lines)\")\n 512→ \n 513→ # Add each line, escaping markup\n 514→ for line in summary_lines:\n 515→ escaped_line = markup_escape(line)\n 516→ details_parts.append(escaped_line)\n 517→ else:\n 518→ details_parts.append(\"(No summary available)\")\n 519→ \n 520→ # Join all parts and update the widget\n 521→ details_text = \"\\n\".join(details_parts)\n 522→ details_widget = self.query_one(\"#details-content\", Static)\n 523→ details_widget.update(details_text)\n 524→ \n 525→ # Update manual decision select with current value\n 526→ manual_decision_select = self.query_one(\"#manual-decision-select\", Select)\n 527→ current_value = issue.manual_decision if issue.manual_decision else None\n 528→ # Set flag to prevent event when updating programmatically\n 529→ self._updating_manual_decision_select = True\n 530→ # Update the select value\n 531→ manual_decision_select.value = current_value\n 532→ # Reset flag after a brief moment\n 533→ self.set_timer(0.1, lambda: setattr(self, '_updating_manual_decision_select', False))\n 534→\n 535→\n 536→ def on_select_changed(self, event: Select.Changed) -> None:\n 537→ \"\"\"\n 538→ Handle filter selection change and manual decision selection.\n 539→\n 540→ Args:\n 541→ event (Select.Changed): Event containing select widget and new value.\n 542→ \"\"\"\n 543→ if event.select.id == \"filter-select\":\n 544→ self.apply_filters()\n 545→ elif event.select.id == \"manual-decision-select\":\n 546→ # Ignore if we're updating the select programmatically\n 547→ if self._updating_manual_decision_select:\n 548→ return\n 549→ # Update the selected issue's manual_decision\n 550→ if self.selected_issue:\n 551→ # Update the manual_decision\n 552→ self.selected_issue.manual_decision = event.value # Could be None for \"Not Set\"\n 553→ \n 554→ # Save to disk for persistence\n 555→ self.loader.save_manual_decision(self.selected_issue.final_path, event.value)\n 556→ \n 557→ # Update just the cell, not the whole table (avoids layout shifts)\n 558→ table = self.query_one(\"#issues-table\", DataTable)\n 559→ manual_display = format_manual_decision(event.value)\n 560→ row_index = table.get_row_index(self.selected_issue.id)\n 561→ # Column 2 is \"Manual decision\" (0=ID, 1=LLM decision, 2=Manual decision)\n 562→ table.update_cell_at((row_index, 2), manual_display)\n 563→\n 564→\n 565→ def on_button_pressed(self, event: Button.Pressed) -> None:\n 566→ \"\"\"\n 567→ Handle button clicks.\n 568→\n 569→ Args:\n 570→ event (Button.Pressed): Event containing button information.\n 571→ \"\"\"\n 572→ if event.button.id == \"refresh-btn\":\n 573→ self.load_issues()\n 574→ elif event.button.id == \"run-analysis-btn\":\n 575→ self.notify(\"Run analysis from command line: python examples/example.py\", severity=\"info\")\n 576→\n 577→\n 578→ def action_search(self) -> None:\n 579→ \"\"\"\n 580→ Focus the search input.\n 581→ \"\"\"\n 582→ search_input = self.query_one(\"#issues-search\", Input)\n 583→ search_input.focus()\n 584→\n 585→\n 586→ def action_clear_search(self) -> None:\n 587→ \"\"\"\n 588→ Clear search query and return focus to issues table.\n 589→ \"\"\"\n 590→ search_input = self.query_one(\"#issues-search\", Input)\n 591→ self.search_query = \"\"\n 592→ search_input.value = \"\"\n 593→ self.apply_filters()\n 594→ # Return focus to the issues table\n 595→ self.query_one(\"#issues-table\", DataTable).focus()\n 596→\n 597→\n 598→ def action_reload(self) -> None:\n 599→ \"\"\"\n 600→ Reload issues from disk.\n 601→ \"\"\"\n 602→ self.load_issues()\n 603→ self.notify(\"Reloaded issues\", severity=\"success\")\n 604→\n 605→\n 606→ def _update_split_position(self) -> None:\n 607→ \"\"\"\n 608→ Update CSS widths for both panels based on split_position.\n 609→ \"\"\"\n 610→ issues_panel = self.query_one(\"#issues-list\")\n 611→ details_panel = self.query_one(\"#details\")\n 612→ \n 613→ issues_width = int(self.split_position * 100)\n 614→ details_width = int((1 - self.split_position) * 100)\n 615→ \n 616→ issues_panel.styles.width = f\"{issues_width}%\"\n 617→ details_panel.styles.width = f\"{details_width}%\"\n 618→ \n 619→ def action_resize_left(self) -> None:\n 620→ \"\"\"\n 621→ Resize split to give more space to left panel (issues).\n 622→ \"\"\"\n 623→ self.split_position = max(0.2, self.split_position - 0.05) # Minimum 20% for right panel\n 624→ self._update_split_position()\n 625→\n 626→\n 627→ def action_resize_right(self) -> None:\n 628→ \"\"\"\n 629→ Resize split to give more space to right panel (details).\n 630→ \"\"\"\n 631→ self.split_position = min(0.8, self.split_position + 0.05) # Maximum 80% for right panel\n 632→ self._update_split_position()\n 633→\n 634→\n 635→ def on_input_changed(self, event: Input.Changed) -> None:\n 636→ \"\"\"\n 637→ Handle search input changes - update search in real-time.\n 638→\n 639→ Args:\n 640→ event (Input.Changed): Event containing input widget and new value.\n 641→ \"\"\"\n 642→ if event.input.id == \"issues-search\":\n 643→ self.search_query = event.value\n 644→ self.apply_filters()\n 645→\n 646→\n 647→ def get_actions(self) -> List[Any]:\n 648→ \"\"\"\n 649→ Override to filter out minimize and maximize from command palette.\n 650→\n 651→ Returns:\n 652→ List: Filtered list of actions excluding minimize and maximize.\n 653→ \"\"\"\n 654→ # Get all actions from parent class\n 655→ actions = super().get_actions()\n 656→ # Filter out minimize and maximize actions by their action ID\n 657→ if actions:\n 658→ return [\n 659→ action for action in actions\n 660→ if hasattr(action, 'id') and action.id not in (\"minimize\", \"maximize\")\n 661→ ]\n 662→ return actions or []\n 663→\n 664→\n 665→ def action_minimize(self) -> None:\n 666→ \"\"\"\n 667→ Override to prevent minimize from appearing in command palette.\n 668→ \"\"\"\n 669→ pass\n 670→\n 671→\n 672→ def action_maximize(self) -> None:\n 673→ \"\"\"\n 674→ Override to prevent maximize from appearing in command palette.\n 675→ \"\"\"\n 676→ pass\n 677→\n 678→\n 679→def main() -> None:\n 680→ \"\"\"\n 681→ Entry point for running the UI.\n 682→ \"\"\"\n 683→ app = VulnhallaUI()\n 684→ app.run()\n 685→\n 686→\n 687→if __name__ == \"__main__\":\n 688→ main()\n 689→\n\n\nWhenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.\n\n"}]},"uuid":"96d3fddb-8cf2-4235-8d50-18c6034a62f5","timestamp":"2026-02-11T13:25:10.140Z"},"normalizedMessages":[],"type":"agent_progress","prompt":"Explore how language affects the LLM analysis and UI layers in Vulnhalla:\n\n1. Read `src/llm/llm_analyzer.py` - how does it select templates? Are there language-specific tool calls or prompts?\n2. Read `src/vulnhalla.py` (IssueAnalyzer) - how does it handle language differences in code snippet extraction?\n3. Read `src/ui/ui_app.py` and `src/ui/components/controls_bar.py` - is there any language selection in the UI?\n4. Check the CLI entry points - look at `pyproject.toml` for script definitions and how args are parsed\n5. Look for any language constants, enums, or supported language lists in the codebase (grep for \"cpp\", \"go\", \"supported_lang\", \"LANGUAGES\" etc.)\n\nBe thorough in finding all places where language is referenced.","agentId":"a77e0c3"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01T7P5Gd5tzArGpoRoh4sVrf","uuid":"9d7574b7-cdaa-4d27-aabf-0de78368ca6f","timestamp":"2026-02-11T13:25:10.195Z"}
{"parentUuid":"9d7574b7-cdaa-4d27-aabf-0de78368ca6f","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"user","message":{"role":"user","content":[{"tool_use_id":"toolu_01Pyr8AbqXnX8xQ4qB5FDXrV","type":"tool_result","content":" 1→#!/usr/bin/env python3\n 2→\"\"\"\n 3→Controls bar component for Vulnhalla UI.\n 4→\"\"\"\n 5→\n 6→from textual.containers import Container, Horizontal, Vertical\n 7→from textual.widgets import Static, Label, Select, Button\n 8→from textual.app import ComposeResult\n 9→\n 10→\n 11→class ControlsBar(Container):\n 12→ \"\"\"\n 13→ Bottom horizontal bar with controls, filters, and actions.\n 14→ \"\"\"\n 15→ \n 16→ def compose(self) -> ComposeResult:\n 17→ \"\"\"Compose the controls bar layout.\n 18→\n 19→ Creates the bottom bar with language information, filters,\n 20→ action buttons and keyboard shortcut help text.\n 21→ \"\"\"\n 22→ with Vertical():\n 23→ # Language label only\n 24→ with Horizontal():\n 25→ yield Static(\"Languages: C/C++, Go\", classes=\"control-label\")\n 26→ # Filter and buttons\n 27→ with Horizontal():\n 28→ yield Label(\"Filter by llm decision:\", classes=\"control-label\")\n 29→ yield Select(\n 30→ [(\"All\", \"all\"), (\"True Positive\", \"true\"), (\"False Positive\", \"false\"), (\"Needs more Info to decide\", \"more\")],\n 31→ value=\"all\",\n 32→ id=\"filter-select\"\n 33→ )\n 34→ yield Button(\"Refresh\", id=\"refresh-btn\")\n 35→ yield Button(\"Run Analysis\", id=\"run-analysis-btn\")\n 36→ yield Static(\"\")\n 37→ # Key Bindings help text\n 38→ with Horizontal():\n 39→ yield Label(\"Key Bindings:\", classes=\"control-label\")\n 40→ yield Static(\"↑/↓: Navigate | Tab: Switch focus | Enter: Show details | /: Search | [: Resize left | ]: Resize right | r: Reload | q: Quit\", classes=\"help-text\")\n 41→\n 42→\n\n\nWhenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.\n\n"}]},"uuid":"030936d7-f2b2-4624-a140-73e8a6327b18","timestamp":"2026-02-11T13:25:10.231Z"},"normalizedMessages":[],"type":"agent_progress","prompt":"Explore how language affects the LLM analysis and UI layers in Vulnhalla:\n\n1. Read `src/llm/llm_analyzer.py` - how does it select templates? Are there language-specific tool calls or prompts?\n2. Read `src/vulnhalla.py` (IssueAnalyzer) - how does it handle language differences in code snippet extraction?\n3. Read `src/ui/ui_app.py` and `src/ui/components/controls_bar.py` - is there any language selection in the UI?\n4. Check the CLI entry points - look at `pyproject.toml` for script definitions and how args are parsed\n5. Look for any language constants, enums, or supported language lists in the codebase (grep for \"cpp\", \"go\", \"supported_lang\", \"LANGUAGES\" etc.)\n\nBe thorough in finding all places where language is referenced.","agentId":"a77e0c3"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01T7P5Gd5tzArGpoRoh4sVrf","uuid":"b30ae94a-0250-4b2d-b1e7-b7f60b33f8e1","timestamp":"2026-02-11T13:25:10.294Z"}
{"parentUuid":"b30ae94a-0250-4b2d-b1e7-b7f60b33f8e1","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"assistant","timestamp":"2026-02-11T13:25:10.349Z","message":{"model":"claude-haiku-4-5-20251001","id":"msg_01U9GcLr3utpKoqY7vdS9LPh","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_012oNwwLVDUsbxmiKeTQyC82","name":"Read","input":{"file_path":"/home/josie/development/personal/Vulnhalla/pyproject.toml"}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":3,"cache_creation_input_tokens":6993,"cache_read_input_tokens":9758,"cache_creation":{"ephemeral_5m_input_tokens":0,"ephemeral_1h_input_tokens":6993},"output_tokens":3,"service_tier":"standard","inference_geo":"not_available"},"context_management":null},"requestId":"req_011CY2McgA6DYjmveUBt7CSt","uuid":"05c5d817-7aa5-4e55-8d72-1f337d846114"},"normalizedMessages":[],"type":"agent_progress","prompt":"Explore how language affects the LLM analysis and UI layers in Vulnhalla:\n\n1. Read `src/llm/llm_analyzer.py` - how does it select templates? Are there language-specific tool calls or prompts?\n2. Read `src/vulnhalla.py` (IssueAnalyzer) - how does it handle language differences in code snippet extraction?\n3. Read `src/ui/ui_app.py` and `src/ui/components/controls_bar.py` - is there any language selection in the UI?\n4. Check the CLI entry points - look at `pyproject.toml` for script definitions and how args are parsed\n5. Look for any language constants, enums, or supported language lists in the codebase (grep for \"cpp\", \"go\", \"supported_lang\", \"LANGUAGES\" etc.)\n\nBe thorough in finding all places where language is referenced.","agentId":"a77e0c3"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01T7P5Gd5tzArGpoRoh4sVrf","uuid":"765b6afd-384e-412f-84df-1f0ddbb2f3dd","timestamp":"2026-02-11T13:25:10.349Z"}
{"parentUuid":"765b6afd-384e-412f-84df-1f0ddbb2f3dd","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"user","message":{"role":"user","content":[{"tool_use_id":"toolu_012oNwwLVDUsbxmiKeTQyC82","type":"tool_result","content":" 1→[tool.poetry]\n 2→name = \"vulnhalla\"\n 3→version = \"0.1.0\"\n 4→description = \"Automated CodeQL Analysis with LLM Classification\"\n 5→readme = \"README.md\"\n 6→license = \"Apache-2.0\"\n 7→authors = [\"CyberArk Software Ltd. \"]\n 8→repository = \"https://github.com/cyberark/Vulnhalla\"\n 9→\n 10→[tool.poetry.dependencies]\n 11→python = \">=3.10,<3.14\"\n 12→# Python version constraint: >=3.10,<3.14\n 13→# - Minimum 3.10\n 14→# - Maximum <3.14: Not supported due to grpcio wheels unavailable\n 15→\n 16→requests = \"^2.31.0\"\n 17→python-dotenv = \"^1.0.0\"\n 18→litellm = \"^1.0.0\"\n 19→PyYAML = \"^6.0\"\n 20→textual = \"^0.40.0\"\n 21→pySmartDL = \"^1.3.4\"\n 22→boto3 = \"^1.34.0\"\n 23→[tool.poetry.group.dev.dependencies]\n 24→pytest = \"^7.4.0\"\n 25→mypy = \"^1.11.0\"\n 26→types-requests = \"^2.31.0\"\n 27→types-PyYAML = \"^6.0\"\n 28→\n 29→[tool.poetry.scripts]\n 30→vulnhalla-setup = \"src.vulnhalla_setup:main\"\n 31→vulnhalla = \"src.pipeline:main_analyze\"\n 32→vulnhalla-ui = \"src.pipeline:main_ui\"\n 33→vulnhalla-validate = \"src.pipeline:main_validate\"\n 34→vulnhalla-list = \"src.pipeline:main_list\"\n 35→vulnhalla-example = \"src.pipeline:main_example\"\n 36→\n 37→[build-system]\n 38→requires = [\"poetry-core\"]\n 39→build-backend = \"poetry.core.masonry.api\"\n 40→\n 41→[tool.mypy]\n 42→# Mypy configuration - conservative baseline for gradual adoption\n 43→python_version = \"3.10\"\n 44→\n 45→# Handle namespace packages correctly (src/ is not a proper package)\n 46→namespace_packages = true\n 47→explicit_package_bases = true\n 48→\n 49→# Allow imports from third-party libraries without stubs\n 50→ignore_missing_imports = true\n 51→\n 52→# Useful warnings that catch common issues\n 53→warn_unused_ignores = true\n 54→warn_redundant_casts = true\n 55→no_implicit_optional = true\n 56→\n 57→# Exclude non-source directories from type checking\n 58→exclude = [\n 59→ \"^tests/\",\n 60→ \"^output/\",\n 61→ \"^data/\",\n 62→ \"^examples/\",\n 63→ \"__pycache__\",\n 64→ \"^build/\",\n 65→ \"^dist/\",\n 66→]\n 67→\n 68→# Per-module overrides for gradual adoption\n 69→# UI modules use Textual framework with complex typing; relax checks\n 70→[[tool.mypy.overrides]]\n 71→module = [\n 72→ \"src.ui.*\",\n 73→ \"src.ui.components.*\",\n 74→]\n 75→# Textual widgets have dynamic attributes and require gradual typing\n 76→disable_error_code = [\"attr-defined\", \"misc\", \"arg-type\", \"var-annotated\", \"assignment\"]\n 77→\n 78→# LLM module works with dynamic dict structures from API responses\n 79→[[tool.mypy.overrides]]\n 80→module = \"src.llm.*\"\n 81→disable_error_code = [\"attr-defined\"]\n 82→\n 83→# Main modules have some legacy typing issues to fix later\n 84→[[tool.mypy.overrides]]\n 85→module = [\n 86→ \"src.vulnhalla\",\n 87→ \"src.pipeline\",\n 88→]\n 89→disable_error_code = [\"arg-type\", \"call-arg\", \"operator\"]\n 90→\n 91→# Utils and setup modules with some Optional handling to fix later\n 92→[[tool.mypy.overrides]]\n 93→module = [\n 94→ \"src.utils.logger\",\n 95→ \"src.vulnhalla_setup\",\n 96→]\n 97→disable_error_code = [\"union-attr\"]\n 98→\n 99→# CodeQL modules have some type annotation and return type issues\n 100→[[tool.mypy.overrides]]\n 101→module = \"src.codeql.*\"\n 102→disable_error_code = [\"var-annotated\", \"return-value\", \"union-attr\", \"arg-type\", \"assignment\"]\n 103→\n\n\nWhenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.\n\n"}]},"uuid":"2928c1e0-fb16-44a4-a5fc-ec19b9018585","timestamp":"2026-02-11T13:25:10.387Z"},"normalizedMessages":[],"type":"agent_progress","prompt":"Explore how language affects the LLM analysis and UI layers in Vulnhalla:\n\n1. Read `src/llm/llm_analyzer.py` - how does it select templates? Are there language-specific tool calls or prompts?\n2. Read `src/vulnhalla.py` (IssueAnalyzer) - how does it handle language differences in code snippet extraction?\n3. Read `src/ui/ui_app.py` and `src/ui/components/controls_bar.py` - is there any language selection in the UI?\n4. Check the CLI entry points - look at `pyproject.toml` for script definitions and how args are parsed\n5. Look for any language constants, enums, or supported language lists in the codebase (grep for \"cpp\", \"go\", \"supported_lang\", \"LANGUAGES\" etc.)\n\nBe thorough in finding all places where language is referenced.","agentId":"a77e0c3"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01T7P5Gd5tzArGpoRoh4sVrf","uuid":"acc6de01-0084-4833-92c2-c9e16d323918","timestamp":"2026-02-11T13:25:10.427Z"}
{"parentUuid":"acc6de01-0084-4833-92c2-c9e16d323918","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"assistant","timestamp":"2026-02-11T13:25:10.444Z","message":{"model":"claude-haiku-4-5-20251001","id":"msg_01NDPiiqc34oqdAd6mnhZoz2","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_01T2R4dR7M3Nc65FEYo5Fxnw","name":"Read","input":{"file_path":"/home/josie/development/personal/Vulnhalla/src/vulnhalla.py","limit":100}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":7,"cache_creation_input_tokens":20013,"cache_read_input_tokens":26446,"cache_creation":{"ephemeral_5m_input_tokens":0,"ephemeral_1h_input_tokens":20013},"output_tokens":4,"service_tier":"standard","inference_geo":"not_available"},"context_management":null},"requestId":"req_011CY2Mcbjvw31yWvFzpsHU8","uuid":"7676349f-98d0-4ed4-8b19-22d389e324c3"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"af56aab9-6aa6-4190-8ef4-39c10259b175","timestamp":"2026-02-11T13:25:10.445Z"}
{"parentUuid":"af56aab9-6aa6-4190-8ef4-39c10259b175","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"assistant","timestamp":"2026-02-11T13:25:10.641Z","message":{"model":"claude-haiku-4-5-20251001","id":"msg_016LwKDMheYhStFpeQtLXfkq","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_0197vrfKrXa69z5XPftJSZaq","name":"Bash","input":{"command":"ls -la /home/josie/development/personal/Vulnhalla/data/queries/go/ && echo \"---\" && ls -la /home/josie/development/personal/Vulnhalla/data/queries/go/issues/ && echo \"---\" && ls -la /home/josie/development/personal/Vulnhalla/data/queries/go/tools/"}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":2,"cache_creation_input_tokens":965,"cache_read_input_tokens":18356,"cache_creation":{"ephemeral_5m_input_tokens":0,"ephemeral_1h_input_tokens":965},"output_tokens":25,"service_tier":"standard","inference_geo":"not_available"},"context_management":null},"requestId":"req_011CY2McntesmPCPaRkap1n8","uuid":"9fe60ea5-7be6-4f6e-9eaf-7b3770f5fa87"},"normalizedMessages":[],"type":"agent_progress","prompt":"Explore the data directory structure for existing language support in Vulnhalla:\n\n1. List and read files in `data/queries/cpp/` - understand the query structure (issues/ and tools/ subdirs)\n2. List and read files in `data/queries/go/` - see how Go queries differ from C++\n3. List and read files in `data/templates/cpp/` - understand LLM prompt templates\n4. List and read files in `data/templates/go/` - see how Go templates differ\n5. Check if there are any qlpack.yml or similar CodeQL pack config files\n\nI need to understand the full pattern for adding a new language's queries and templates.","agentId":"affd883"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01SBzXiYDFMSMi3vxEqQAeQd","uuid":"7a65e9bb-25fd-4059-bc1a-768f81b1d8c7","timestamp":"2026-02-11T13:25:10.641Z"}
{"parentUuid":"7a65e9bb-25fd-4059-bc1a-768f81b1d8c7","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"user","message":{"role":"user","content":[{"tool_use_id":"toolu_0197vrfKrXa69z5XPftJSZaq","type":"tool_result","content":"total 16\ndrwxr-xr-x 4 josie wheel 4096 Feb 11 13:44 .\ndrwxr-xr-x 4 josie wheel 4096 Feb 11 13:44 ..\ndrwxr-xr-x 3 josie wheel 4096 Feb 11 14:23 issues\ndrwxr-xr-x 3 josie wheel 4096 Feb 11 14:23 tools\n---\ntotal 468\ndrwxr-xr-x 3 josie wheel 4096 Feb 11 14:23 .\ndrwxr-xr-x 4 josie wheel 4096 Feb 11 13:44 ..\ndrwxr-xr-x 3 josie wheel 4096 Feb 11 14:23 .codeql\n-rw-r--r-- 1 josie wheel 438 Feb 11 13:51 codeql-pack.lock.yml\n-rw-r--r-- 1 josie wheel 743 Feb 11 13:45 Command injection.ql\n-rw-r--r-- 1 josie wheel 134577 Feb 11 14:23 Command injection.qlx\n-rw-r--r-- 1 josie wheel 701 Feb 11 13:45 Path traversal.ql\n-rw-r--r-- 1 josie wheel 177461 Feb 11 14:23 Path traversal.qlx\n-rw-r--r-- 1 josie wheel 69 Feb 11 13:45 qlpack.yml\n-rw-r--r-- 1 josie wheel 704 Feb 11 13:45 SQL injection.ql\n-rw-r--r-- 1 josie wheel 129759 Feb 11 14:23 SQL injection.qlx\n---\ntotal 48\ndrwxr-xr-x 3 josie wheel 4096 Feb 11 14:23 .\ndrwxr-xr-x 4 josie wheel 4096 Feb 11 13:44 ..\ndrwxr-xr-x 3 josie wheel 4096 Feb 11 14:23 .codeql\n-rw-r--r-- 1 josie wheel 438 Feb 11 13:50 codeql-pack.lock.yml\n-rw-r--r-- 1 josie wheel 689 Feb 11 14:17 FunctionTree.ql\n-rw-r--r-- 1 josie wheel 5664 Feb 11 14:23 FunctionTree.qlx\n-rw-r--r-- 1 josie wheel 319 Feb 11 14:17 GlobalVars.ql\n-rw-r--r-- 1 josie wheel 3411 Feb 11 14:23 GlobalVars.qlx\n-rw-r--r-- 1 josie wheel 75 Feb 11 13:45 qlpack.yml\n-rw-r--r-- 1 josie wheel 598 Feb 11 14:17 Types.ql\n-rw-r--r-- 1 josie wheel 3628 Feb 11 14:23 Types.qlx","is_error":false}]},"uuid":"37a5fee3-8e5e-4dd4-ae40-d3bc653422b4","timestamp":"2026-02-11T13:25:10.702Z"},"normalizedMessages":[],"type":"agent_progress","prompt":"Explore the data directory structure for existing language support in Vulnhalla:\n\n1. List and read files in `data/queries/cpp/` - understand the query structure (issues/ and tools/ subdirs)\n2. List and read files in `data/queries/go/` - see how Go queries differ from C++\n3. List and read files in `data/templates/cpp/` - understand LLM prompt templates\n4. List and read files in `data/templates/go/` - see how Go templates differ\n5. Check if there are any qlpack.yml or similar CodeQL pack config files\n\nI need to understand the full pattern for adding a new language's queries and templates.","agentId":"affd883"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01SBzXiYDFMSMi3vxEqQAeQd","uuid":"92b3b021-e6a4-448a-ba39-cf1cde63415c","timestamp":"2026-02-11T13:25:10.736Z"}
{"parentUuid":"92b3b021-e6a4-448a-ba39-cf1cde63415c","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"user","message":{"role":"user","content":[{"tool_use_id":"toolu_01T2R4dR7M3Nc65FEYo5Fxnw","type":"tool_result","content":" 1→#!/usr/bin/env python3\n 2→\"\"\"\n 3→Core analysis engine for Vulnhalla.\n 4→\n 5→This module coordinates the aggregation of raw CodeQL findings and their\n 6→classification by an LLM. It loads issues from CodeQL result files,\n 7→groups them by issue type, runs LLM-based analysis to decide whether\n 8→each finding is a true positive, false positive, or needs more data,\n 9→and writes structured result files for further inspection (e.g. in the UI).\n 10→\n 11→Analysis Pipeline Algorithm:\n 12→ 1. Collect DBs via get_all_dbs(dbs_folder), parse issues.csv, group by issue['name'].\n 13→ 2. For each issue: find containing function via find_function_by_line() (smallest line range).\n 14→ 3. Extract snippet and full function code.\n 15→ 4. Replace bracket references in the message; if references point outside current function, append those functions' code.\n 16→ 5. Build prompt; save *_raw.json; run LLM analysis; save *_final.json.\n 17→ 6. Classify by substring: \"1337\" → true, \"1007\" → false, else → more; log stats.\n 18→\"\"\"\n 19→\n 20→from pathlib import Path, PurePosixPath\n 21→import csv\n 22→import re\n 23→import json\n 24→from typing import Any, Callable, Dict, List, Optional, Tuple\n 25→from src.utils.common_functions import (\n 26→ get_all_dbs,\n 27→ read_file_lines_from_zip,\n 28→ read_file as read_file_utf8,\n 29→ write_file_ascii,\n 30→ read_yml\n 31→)\n 32→\n 33→# LLM analyzer for security analysis\n 34→from src.llm.llm_analyzer import LLMAnalyzer\n 35→from src.utils.config_validator import validate_and_exit_on_error\n 36→from src.utils.logger import get_logger\n 37→from src.utils.exceptions import VulnhallaError, CodeQLError, LLMApiError\n 38→\n 39→logger = get_logger(__name__)\n 40→\n 41→\n 42→class IssueAnalyzer:\n 43→ \"\"\"\n 44→ Analyzes all issues in CodeQL databases, fetches relevant code snippets,\n 45→ and forwards them to an LLM (via llm_analyzer) for triage.\n 46→ \"\"\"\n 47→\n 48→ def __init__(self, lang: str = \"c\", config: Optional[Dict[str, Any]] = None) -> None:\n 49→ \"\"\"\n 50→ Initialize the IssueAnalyzer with default parameters.\n 51→\n 52→ Args:\n 53→ lang (str, optional): The language code. Defaults to 'c'.\n 54→ config (Dict, optional): Full LLM configuration dictionary. If not provided, loads from .env file.\n 55→ \"\"\"\n 56→ self.lang = lang\n 57→ self.db_path: Optional[str] = None\n 58→ self.code_path: Optional[str] = None\n 59→ self.config = config\n 60→\n 61→ # ----------------------------------------------------------------------\n 62→ # 1. CSV Parsing and Data Gathering\n 63→ # ----------------------------------------------------------------------\n 64→\n 65→ def parse_issues_csv(self, file_name: str) -> List[Dict[str, str]]:\n 66→ \"\"\"\n 67→ Reads the issues.csv file produced by CodeQL (with a custom or default\n 68→ set of columns) and returns a list of dicts.\n 69→\n 70→ Args:\n 71→ file_name (str): The path to 'issues.csv'.\n 72→\n 73→ Returns:\n 74→ List[Dict[str, str]]: A list of issue objects parsed from CSV rows.\n 75→ \n 76→ Raises:\n 77→ CodeQLError: If file cannot be read (not found, permission denied, etc.).\n 78→ \"\"\"\n 79→ field_names = [\n 80→ \"name\", \"help\", \"type\", \"message\",\n 81→ \"file\", \"start_line\", \"start_offset\",\n 82→ \"end_line\", \"end_offset\"\n 83→ ]\n 84→ issues = []\n 85→ try:\n 86→ with Path(file_name).open(\"r\", encoding=\"utf-8\") as f:\n 87→ csv_reader = csv.DictReader(f, fieldnames=field_names)\n 88→ for row in csv_reader:\n 89→ issues.append(row)\n 90→ except FileNotFoundError as e:\n 91→ raise CodeQLError(f\"Issues CSV file not found: {file_name}\") from e\n 92→ except PermissionError as e:\n 93→ raise CodeQLError(f\"Permission denied reading issues CSV: {file_name}\") from e\n 94→ except OSError as e:\n 95→ raise CodeQLError(f\"OS error while reading issues CSV: {file_name}\") from e\n 96→ return issues\n 97→\n 98→ def collect_issues_from_databases(self, dbs_dir: str) -> Dict[str, List[Dict[str, str]]]:\n 99→ \"\"\"\n 100→ Searches through all CodeQL databases in `dbs_folder`, collects issues\n\n\nWhenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.\n\n"}]},"uuid":"e3970609-2eec-4efa-9e21-df61f4c35790","timestamp":"2026-02-11T13:25:10.487Z"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"13e76292-2251-415d-933e-2b21a1721dff","timestamp":"2026-02-11T13:25:10.880Z"}
{"parentUuid":"13e76292-2251-415d-933e-2b21a1721dff","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"assistant","timestamp":"2026-02-11T13:25:10.963Z","message":{"model":"claude-haiku-4-5-20251001","id":"msg_01NDPiiqc34oqdAd6mnhZoz2","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_016Rfy1a95KF7WSxCs4SfZMD","name":"Bash","input":{"command":"find /home/josie/development/personal/Vulnhalla/data/queries -type d -maxdepth 2 | sort"}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":7,"cache_creation_input_tokens":20013,"cache_read_input_tokens":26446,"cache_creation":{"ephemeral_5m_input_tokens":0,"ephemeral_1h_input_tokens":20013},"output_tokens":4,"service_tier":"standard","inference_geo":"not_available"},"context_management":null},"requestId":"req_011CY2Mcbjvw31yWvFzpsHU8","uuid":"816f9e3f-7ff7-4cf6-ac3c-cbcccc4b7c72"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"337f2cc9-3e89-48eb-bfc2-c235d6fca148","timestamp":"2026-02-11T13:25:10.963Z"}
{"parentUuid":"337f2cc9-3e89-48eb-bfc2-c235d6fca148","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"assistant","timestamp":"2026-02-11T13:25:11.031Z","message":{"model":"claude-haiku-4-5-20251001","id":"msg_01NDPiiqc34oqdAd6mnhZoz2","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_01FjtEHW9YEZqf4WSdck7rKY","name":"Bash","input":{"command":"find /home/josie/development/personal/Vulnhalla/data/templates -type d -maxdepth 2 | sort"}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":7,"cache_creation_input_tokens":20013,"cache_read_input_tokens":26446,"cache_creation":{"ephemeral_5m_input_tokens":0,"ephemeral_1h_input_tokens":20013},"output_tokens":4,"service_tier":"standard","inference_geo":"not_available"},"context_management":null},"requestId":"req_011CY2Mcbjvw31yWvFzpsHU8","uuid":"dbe37787-327f-405f-9eb3-47c0b77c40e2"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"800ffadf-db3c-4d59-851f-3d21e4587d0b","timestamp":"2026-02-11T13:25:11.031Z"}
{"parentUuid":"800ffadf-db3c-4d59-851f-3d21e4587d0b","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"user","message":{"role":"user","content":[{"tool_use_id":"toolu_016Rfy1a95KF7WSxCs4SfZMD","type":"tool_result","content":"/home/josie/development/personal/Vulnhalla/data/queries\n/home/josie/development/personal/Vulnhalla/data/queries/cpp\n/home/josie/development/personal/Vulnhalla/data/queries/cpp/issues\n/home/josie/development/personal/Vulnhalla/data/queries/cpp/tools\n/home/josie/development/personal/Vulnhalla/data/queries/go\n/home/josie/development/personal/Vulnhalla/data/queries/go/issues\n/home/josie/development/personal/Vulnhalla/data/queries/go/tools","is_error":false}]},"uuid":"7a37ce77-3d40-421a-b8ac-be372cbe5a31","timestamp":"2026-02-11T13:25:11.021Z"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"0bb5b76c-5349-4cfa-b86d-b531ba92f061","timestamp":"2026-02-11T13:25:11.067Z"}
{"parentUuid":"0bb5b76c-5349-4cfa-b86d-b531ba92f061","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"user","message":{"role":"user","content":[{"tool_use_id":"toolu_01FjtEHW9YEZqf4WSdck7rKY","type":"tool_result","content":"/home/josie/development/personal/Vulnhalla/data/templates\n/home/josie/development/personal/Vulnhalla/data/templates/cpp\n/home/josie/development/personal/Vulnhalla/data/templates/go","is_error":false}]},"uuid":"247f0cd6-742e-4fa5-9db4-78ea523823ca","timestamp":"2026-02-11T13:25:11.091Z"},"normalizedMessages":[],"type":"agent_progress","prompt":"I need to understand how Vulnhalla supports multiple languages (currently cpp and go). Explore:\n\n1. How language selection works in the pipeline (`src/pipeline.py`) - look for `--lang` flag handling, language-related conditionals\n2. How `src/codeql/` modules handle language differences - especially `fetch_repos.py`, `run_codeql_queries.py`, `db_lookup.py`\n3. How language config is stored/validated in `src/utils/config.py` and any related config files\n4. The `src/vulnhalla_setup.py` file - how CodeQL packs are initialized per language\n\nBe very thorough - trace through the full flow of how a language parameter affects the pipeline from CLI entry to query execution.","agentId":"ae9ead7"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01FkocvKbEziSuWKxNShtsub","uuid":"92d717d2-af2f-4c74-a3c9-51f3ed2c66ed","timestamp":"2026-02-11T13:25:11.137Z"}
{"parentUuid":"92d717d2-af2f-4c74-a3c9-51f3ed2c66ed","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"assistant","timestamp":"2026-02-11T13:25:12.096Z","message":{"model":"claude-haiku-4-5-20251001","id":"msg_01KnA3apg9CJciME7YnMDgig","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_017PtHmQL8uMktzpFiWuwsYD","name":"Bash","input":{"command":"ls -la /home/josie/development/personal/Vulnhalla/data/templates/cpp/ && echo \"---\" && ls -la /home/josie/development/personal/Vulnhalla/data/templates/go/"}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":1,"cache_creation_input_tokens":1265,"cache_read_input_tokens":19321,"cache_creation":{"ephemeral_5m_input_tokens":0,"ephemeral_1h_input_tokens":1265},"output_tokens":26,"service_tier":"standard","inference_geo":"not_available"},"context_management":null},"requestId":"req_011CY2MctP49NCmAYpEXKaPo","uuid":"5c15c0a2-de58-4e62-93c8-2e535a01c03c"},"normalizedMessages":[],"type":"agent_progress","prompt":"Explore the data directory structure for existing language support in Vulnhalla:\n\n1. List and read files in `data/queries/cpp/` - understand the query structure (issues/ and tools/ subdirs)\n2. List and read files in `data/queries/go/` - see how Go queries differ from C++\n3. List and read files in `data/templates/cpp/` - understand LLM prompt templates\n4. List and read files in `data/templates/go/` - see how Go templates differ\n5. Check if there are any qlpack.yml or similar CodeQL pack config files\n\nI need to understand the full pattern for adding a new language's queries and templates.","agentId":"affd883"},"toolUseID":"agent_msg_014rwsuJq2Vy4RedbBfZrLmL","parentToolUseID":"toolu_01SBzXiYDFMSMi3vxEqQAeQd","uuid":"198889cf-4fb1-498a-b788-e628c2ec0c65","timestamp":"2026-02-11T13:25:12.096Z"}
{"parentUuid":"198889cf-4fb1-498a-b788-e628c2ec0c65","isSidechain":false,"userType":"external","cwd":"/home/josie/development/personal/Vulnhalla","sessionId":"237b90d4-76fb-400e-9223-3a3754e071ff","version":"2.1.38","gitBranch":"main","slug":"cozy-snacking-plum","type":"progress","data":{"message":{"type":"user","message":{"role":"user","content":[{"tool_use_id":"toolu_017PtHmQL8uMktzpFiWuwsYD","type":"tool_result","content":"total 20\ndrwxr-xr-x 2 josie wheel 4096 Feb 11 12:14 .\ndrwxr-xr-x 4 josie wheel 4096 Feb 11 13:44 ..\n-rw-r--r-- 1 josie wheel 787 Feb 11 12:14 Copy function using source size.template\n-rw-r--r-- 1 josie wheel 54 Feb