LearningCircuit/local-deep-research

48.0

Adjusted Score

48.0

Raw Score

100%

Time Factor

2026-07-14

Last Push

8.7K

Stars

Python

Language

1.1M

Lines of Code

3.0K

Files

36.2K

Pattern Hits

2026-07-14

Scan Date

0.11

HC Hit Rate

What These Metrics Mean

Adjusted Score: Primary synthetic code indicator. Raw score normalised per 1,000 lines of code and multiplied by the temporal discount factor. This is the definitive comparative metric — use it to rank repositories by AI authorship density.
Raw Score: The unmodified sum of all severity-weighted, context-multiplied pattern match scores before temporal discounting. Reflects the absolute signal strength independent of when the repository was last active.
Time Factor: The temporal discount multiplier (0–100%) applied to the raw score. Repositories last updated before ChatGPT's launch (Nov 2022) receive a 5% factor. Full signal is only assigned to repositories active in the post-adoption era (Jan 2024+).
Pattern Hits: Total count of individual pattern matches across all files and categories. A high hit count with a low score may indicate a very large codebase with isolated AI snippets; a low count with a high score indicates dense, concentrated AI signatures.
HC Hit Rate: High+Critical pattern hits per file, averaged across the repository. This orthogonal signal catches repositories where a few files are densely packed with high-severity AI tells — a strong indicator even when the normalised score appears moderate due to codebase size.
Lines of Code / Files: Total lines and files analysed. The scanner examines 94 file extensions. These denominators are used to normalise the score, enabling fair comparison between repositories of vastly different sizes.

Score History

This chart maps the temporal evolution of the adjusted synthetic code score across successive scan runs. An upward trajectory indicates ongoing incorporation of AI-generated code or expanding LLM-assisted scaffolding; a stable or declining trajectory may reflect active human refactoring, code removal, or the adoption of stricter authorship policies. The dashed secondary line (right axis) independently tracks total raw pattern hit count, which can diverge from the normalised score when codebase size changes significantly between scans.

Severity Breakdown

Classifies detected patterns by their diagnostic confidence and structural impact. CRITICAL patterns (coefficient 10) represent definitive synthetic signatures — hallucinated imports, explicit LLM attribution metadata — virtually never produced by human authors. HIGH (5) indicates strong structural tells such as cross-file repetition or cross-linguistic idioms. MEDIUM (2) covers recognisable conversational padding and AI-specific vocabulary. LOW (1) captures subtle indicators like tautological comments and generic boilerplate that require density to carry independent signal.

CRITICAL 18HIGH 303MEDIUM 5762LOW 30167

Directory Score Breakdown

This horizontal bar chart decomposes the repository's raw synthetic code score by top-level directory, allowing you to pinpoint precisely which modules or components carry the highest AI authorship density. Directories with disproportionately high scores relative to their size warrant targeted manual review: concentrated AI signatures often trace back to mass-generated configuration layers, auto-ported test suites, LLM-scaffolded boilerplate classes, or entire subsystems authored under heavy copilot assistance. Use this view to prioritise your human code-review effort.

Pattern Findings

The scanner identified 36250 distinct pattern matches across 26 syntactic categories. Each entry below represents a discrete location in the source code where the engine recorded a statistically significant AI authorship indicator. Expand any category row to inspect the individual file paths, line numbers, code snippets, and the lexical context (CODE, COMMENT, or STRING) in which each match was detected.

Reading the findings table: The Severity column indicates the diagnostic confidence level (CRITICAL / HIGH / MEDIUM / LOW). The Context column identifies whether the match occurred inside executable code, an inline comment, or a string literal — comment-context matches receive a ×1.5 weight because LLMs systematically over-annotate. The ⚡ bolt icon marks clustered matches: three or more patterns within a 10-line window, each receiving an additional ×1.5 density multiplier as dense clusters constitute far stronger evidence of synthetic authorship than isolated hits.

Hyper-Verbose Identifiers26244 hits · 24426 pts

Severity	File	Line	Snippet	Context
LOW	.pre-commit-hooks/custom-checks.py	156	def _format_string_references_exception(self, node):	CODE
LOW	.pre-commit-hooks/custom-checks.py	180	def _string_concat_references_exception(self, node):	CODE
LOW	.pre-commit-hooks/check-bearer-disable.py	112	def _classify_js_line_comment(	CODE
LOW	.pre-commit-hooks/check-fixture-duplication.py	78	def find_module_level_fixture_redefinitions(	CODE
LOW	…e-commit-hooks/check-settings-manager-thread-safety.py	81	def _check_body_for_unsafe_calls(self, node) -> None:	CODE
LOW	…e-commit-hooks/check-settings-manager-thread-safety.py	117	def _is_get_settings_manager_call(call_node: ast.Call) -> bool:	CODE
LOW	.pre-commit-hooks/check-sensitive-logging.py	268	def _is_literal_dynamic_import(node: ast.AST, module: str) -> bool:	CODE
LOW	.pre-commit-hooks/check-sensitive-logging.py	360	def _check_import_from_secure_dir(self, node: ast.ImportFrom) -> None:	CODE
LOW	.pre-commit-hooks/check-sensitive-logging.py	815	def _check_exc_info_on_warning(self, node: ast.Call) -> None:	CODE
LOW	.pre-commit-hooks/check-sensitive-logging.py	837	def _check_exception_var_in_log(self, node: ast.Call) -> None:	CODE
LOW	.pre-commit-hooks/check-sensitive-logging.py	972	def _check_expression_for_sensitive_data(	CODE
LOW	.pre-commit-hooks/check-service-context-managers.py	229	def _check_statements_recursive(	CODE
LOW	.pre-commit-hooks/check-session-context-manager.py	34	def _check_function_for_pattern(self, func_node) -> None:	CODE
LOW	.pre-commit-hooks/check-session-context-manager.py	62	def _get_session_var_from_assign(self, assign_node: ast.Assign) -> str:	CODE
LOW	.pre-commit-hooks/check-session-context-manager.py	93	def _has_session_close_in_finally(	CODE
LOW	.pre-commit-hooks/check-settings-key-namespace.py	88	def _extract_frozenset_strings(node):	CODE
LOW	tests/test_api_settings_validation.py	16	def test_temperature_validation(self):	CODE
LOW	tests/test_api_settings_validation.py	48	def test_provider_name_normalization(self):	CODE
LOW	tests/test_api_settings_validation.py	65	def test_search_results_validation(self):	CODE
LOW	tests/test_api_settings_validation.py	84	def test_quick_summary_with_invalid_provider(self, mock_init):	CODE
LOW	tests/test_api_settings_validation.py	96	def test_quick_summary_with_missing_api_key(self, mock_init):	CODE
LOW	tests/test_api_settings_validation.py	118	def test_settings_with_circular_references(self):	CODE
LOW	tests/test_api_settings_validation.py	141	def test_environment_variable_type_conversion(self, monkeypatch):	CODE
LOW	tests/test_api_settings_validation.py	159	def test_invalid_environment_variable_values(self, monkeypatch):	CODE
LOW	tests/test_api_settings_validation.py	171	def test_environment_variable_precedence(self, monkeypatch):	CODE
LOW	tests/test_api_settings_validation.py	195	def test_minimal_configuration(self):	CODE
LOW	tests/test_api_settings_validation.py	208	def test_common_research_presets(self):	CODE
LOW	tests/test_api_settings_validation.py	292	def test_legacy_setting_names(self):	CODE
LOW	tests/test_context_overflow_detection.py	58	def test_context_overflow_detection_no_overflow(self, token_callback):	CODE
LOW	tests/test_context_overflow_detection.py	87	def test_context_overflow_detection_with_overflow(self, token_callback):	CODE
LOW	tests/test_context_overflow_detection.py	117	def test_ollama_raw_metrics_capture(self, token_callback):	CODE
LOW	tests/test_context_overflow_detection.py	150	def test_context_limit_from_research_context(self):	CODE
LOW	tests/test_context_overflow_detection.py	168	def test_prompt_size_estimation(self, token_callback):	CODE
LOW	tests/test_context_overflow_detection.py	192	def test_overflow_warning_logged(self, mock_logger, token_callback):	CODE
LOW	tests/test_context_overflow_detection.py	223	def test_estimated_overflow_for_non_ollama_provider(	CODE
LOW	tests/test_context_overflow_detection.py	259	def test_provider_confirmed_total_context_overflow(	CODE
LOW	tests/test_context_overflow_detection.py	295	def test_estimated_total_context_overflow_for_non_ollama(	CODE
LOW	tests/test_context_overflow_detection.py	335	def test_estimated_total_context_overflow_via_llm_output(	CODE
LOW	tests/test_context_overflow_detection.py	386	def test_estimated_path_fires_on_subsequent_calls_after_first_truncation(	CODE
LOW	tests/test_context_overflow_detection.py	399	def llm_output_overflow_response():	CODE
LOW	tests/test_context_overflow_detection.py	428	def test_estimated_overflow_skipped_when_context_limit_none(	CODE
LOW	tests/test_context_overflow_detection.py	456	def test_estimated_overflow_zero_prompt_estimate(	CODE
LOW	tests/test_context_overflow_detection.py	481	def test_estimated_overflow_without_on_llm_start(	CODE
LOW	tests/test_context_overflow_detection.py	510	def test_ollama_context_overflow_real(self):	CODE
LOW	tests/TESTING_PROPOSAL.md	263	def test_create_documents_empty(citation_handler):	CODE
LOW	tests/TESTING_PROPOSAL.md	269	def test_create_documents_string(citation_handler):	CODE
LOW	tests/test_utils.py	62	def assert_search_result_format(result: Dict[str, Any]):	CODE
LOW	tests/test_utils.py	112	def create_test_research_context(query: str = "test query") -> Dict[str, Any]:	CODE
LOW	tests/test_utils.py	157	def assert_progress_callback_called(	CODE
LOW⚡	tests/test_search_system_factory_high_value.py	25	def test_all_entries_are_dicts(self):	CODE
LOW⚡	tests/test_search_system_factory_high_value.py	29	def test_all_entries_have_name_key(self):	CODE
LOW⚡	tests/test_search_system_factory_high_value.py	33	def test_all_entries_have_description_key(self):	CODE
LOW⚡	tests/test_search_system_factory_high_value.py	37	def test_all_names_are_nonempty_strings(self):	CODE
LOW⚡	tests/test_search_system_factory_high_value.py	42	def test_all_descriptions_are_nonempty_strings(self):	CODE
LOW⚡	tests/test_search_system_factory_high_value.py	77	def test_returns_copy_not_original(self):	CODE
LOW⚡	tests/test_search_system_factory_high_value.py	81	def test_copy_has_same_length(self):	CODE
LOW⚡	tests/test_search_system_factory_high_value.py	85	def test_copy_has_same_content(self):	CODE
LOW⚡	tests/test_search_system_factory_high_value.py	89	def test_modifying_returned_list_does_not_affect_original(self):	CODE
LOW⚡	tests/test_search_system_factory_high_value.py	95	def test_removing_from_returned_list_does_not_affect_original(self):	CODE
LOW⚡	tests/test_search_system_factory_high_value.py	105	def test_returns_default_when_snapshot_is_none(self):	CODE
26184 more matches not shown…

Decorative Section Separators5041 hits · 18504 pts

Severity	File	Line	Snippet	Context
MEDIUM⚡	docker-compose.gpu.override.yml	1	# ============================================================================	COMMENT
MEDIUM⚡	docker-compose.gpu.override.yml	3	# ============================================================================	COMMENT
MEDIUM⚡	docker-compose.gpu.override.yml	21	# ============================================================================	COMMENT
MEDIUM	docker-compose.unraid.yml	1	# ============================================================================	COMMENT
MEDIUM	docker-compose.unraid.yml	3	# ============================================================================	COMMENT
MEDIUM	docker-compose.unraid.yml	16	# ============================================================================	COMMENT
MEDIUM⚡	.file-whitelist.txt	1	# ============================================================================	COMMENT
MEDIUM⚡	.file-whitelist.txt	11	# ============================================================================	COMMENT
MEDIUM⚡	.file-whitelist.txt	13	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	.file-whitelist.txt	15	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	.file-whitelist.txt	23	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	.file-whitelist.txt	25	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	.file-whitelist.txt	40	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	.file-whitelist.txt	42	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	.file-whitelist.txt	56	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	.file-whitelist.txt	58	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	.file-whitelist.txt	66	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	.file-whitelist.txt	68	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	.file-whitelist.txt	77	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	.file-whitelist.txt	79	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	.file-whitelist.txt	97	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	.file-whitelist.txt	100	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	pyproject.toml	419	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	pyproject.toml	421	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	.grype.yaml	9	# ==========================================================================	COMMENT
MEDIUM	.grype.yaml	11	# ==========================================================================	COMMENT
MEDIUM	.grype.yaml	32	# ==========================================================================	COMMENT
MEDIUM	.grype.yaml	34	# ==========================================================================	COMMENT
MEDIUM	.grype.yaml	88	# ==========================================================================	COMMENT
MEDIUM	.grype.yaml	93	# ==========================================================================	COMMENT
MEDIUM	.grype.yaml	143	# ==========================================================================	COMMENT
MEDIUM	.grype.yaml	164	# ==========================================================================	COMMENT
MEDIUM⚡	.grype.yaml	199	# ==========================================================================	COMMENT
MEDIUM⚡	.grype.yaml	207	# ==========================================================================	COMMENT
MEDIUM⚡	.grype.yaml	215	# ==========================================================================	COMMENT
MEDIUM⚡	.grype.yaml	217	# ==========================================================================	COMMENT
MEDIUM⚡	docker-compose.yml	34	# ============================================================================	COMMENT
MEDIUM⚡	docker-compose.yml	36	# ============================================================================	COMMENT
MEDIUM⚡	docker-compose.yml	46	# ============================================================================	COMMENT
MEDIUM⚡	docker-compose.yml	48	# ============================================================================	COMMENT
MEDIUM⚡	docker-compose.yml	54	# ============================================================================	COMMENT
MEDIUM⚡	docker-compose.yml	59	# ============================================================================	COMMENT
MEDIUM⚡	docker-compose.yml	66	# ============================================================================	COMMENT
MEDIUM⚡	docker-compose.yml	68	# ============================================================================	COMMENT
MEDIUM⚡	docker-compose.yml	74	# ============================================================================	COMMENT
MEDIUM⚡	docker-compose.yml	78	# ============================================================================	COMMENT
MEDIUM⚡	docker-compose.yml	82	# ============================================================================	COMMENT
MEDIUM⚡	docker-compose.yml	85	# ============================================================================	COMMENT
MEDIUM⚡	docker-compose.yml	88	# ============================================================================	COMMENT
MEDIUM⚡	docker-compose.yml	94	# ============================================================================	COMMENT
MEDIUM⚡	docker-compose.yml	99	# ============================================================================	COMMENT
MEDIUM⚡	docker-compose.yml	105	# ============================================================================	COMMENT
MEDIUM⚡	docker-compose.yml	108	# ============================================================================	COMMENT
MEDIUM⚡	docker-compose.yml	114	# ============================================================================	COMMENT
MEDIUM⚡	docker-compose.yml	118	# ============================================================================	COMMENT
MEDIUM⚡	docker-compose.yml	126	# ============================================================================	COMMENT
MEDIUM⚡	docker-compose.yml	130	# ============================================================================	COMMENT
MEDIUM⚡	docker-compose.yml	133	# ============================================================================	COMMENT
MEDIUM⚡	docker-compose.yml	139	# ============================================================================	COMMENT
MEDIUM⚡	docker-compose.yml	141	# ============================================================================	COMMENT
4981 more matches not shown…

Excessive Try-Catch Wrapping1708 hits · 1687 pts

Severity	File	Line	Snippet	Context
LOW	.pre-commit-hooks/check-css-class-prefix.py	177	except Exception as e:	CODE
MEDIUM	.pre-commit-hooks/check-css-class-prefix.py	178	print(f"Error reading {file_path}: {e}", file=sys.stderr)	CODE
LOW	.pre-commit-hooks/check-css-class-prefix.py	331	except Exception as e:	CODE
MEDIUM	.pre-commit-hooks/check-css-class-prefix.py	332	print(f"Error reading {file_path}: {e}", file=sys.stderr)	CODE
LOW	.pre-commit-hooks/check-css-class-prefix.py	450	except Exception as e:	CODE
MEDIUM	.pre-commit-hooks/check-css-class-prefix.py	451	print(f"Error reading {file_path}: {e}", file=sys.stderr)	CODE
LOW	.pre-commit-hooks/check-absolute-module-paths.py	115	except Exception as e:	CODE
MEDIUM	.pre-commit-hooks/check-absolute-module-paths.py	116	print(f"Error reading {filename}: {e}")	CODE
LOW	.pre-commit-hooks/check-absolute-module-paths.py	133	except Exception as e:	CODE
MEDIUM	.pre-commit-hooks/check-absolute-module-paths.py	134	print(f"Error parsing {filename}: {e}")	CODE
LOW	.pre-commit-hooks/check-absolute-module-paths.py	148	except Exception as e:	CODE
MEDIUM	.pre-commit-hooks/check-absolute-module-paths.py	149	print(f"Error reading {filename}: {e}")	CODE
LOW	.pre-commit-hooks/check-env-vars.py	279	except Exception as e:	CODE
MEDIUM	.pre-commit-hooks/check-env-vars.py	280	print(f"Error reading {filename}: {e}")	CODE
LOW	.pre-commit-hooks/check-env-vars.py	297	except Exception as e:	CODE
MEDIUM	.pre-commit-hooks/check-env-vars.py	298	print(f"Error parsing {filename}: {e}")	CODE
LOW	.pre-commit-hooks/check-pathlib-usage.py	147	except Exception as e:	CODE
MEDIUM	.pre-commit-hooks/check-pathlib-usage.py	148	print(f"Error reading {filepath}: {e}", file=sys.stderr)	CODE
LOW	.pre-commit-hooks/check-utcnow-parens.py	34	except Exception:	CODE
LOW	.pre-commit-hooks/check-double-escaping.py	130	except Exception as e:	CODE
MEDIUM	.pre-commit-hooks/check-double-escaping.py	131	print(f"Error checking {file_path}: {e}")	CODE
LOW	.pre-commit-hooks/check-url-security.py	143	except Exception as e:	CODE
MEDIUM	.pre-commit-hooks/check-url-security.py	144	print(f"Error checking {file_path}: {e}")	CODE
LOW⚡	.pre-commit-hooks/fix-exception-logging.py	234	except Exception:	CODE
LOW	.pre-commit-hooks/check-silent-cleanup.py	187	except Exception as e:	CODE
MEDIUM	.pre-commit-hooks/check-silent-cleanup.py	188	print(f"Error reading {filename}: {e}")	CODE
LOW	.pre-commit-hooks/check-silent-cleanup.py	209	except Exception as e:	CODE
MEDIUM	.pre-commit-hooks/check-silent-cleanup.py	210	print(f"Error parsing {filename}: {e}")	CODE
LOW	.pre-commit-hooks/custom-checks.py	535	except Exception as e:	CODE
MEDIUM	.pre-commit-hooks/custom-checks.py	536	print(f"Error reading {filename}: {e}")	CODE
LOW	.pre-commit-hooks/custom-checks.py	562	except Exception as e:	CODE
MEDIUM	.pre-commit-hooks/custom-checks.py	563	print(f"Error parsing {filename}: {e}")	CODE
LOW	.pre-commit-hooks/check-weak-tests.py	59	except Exception: # pragma: no cover - unparse is stable on 3.9+	CODE
LOW	…e-commit-hooks/check-settings-manager-thread-safety.py	149	except Exception as e:	CODE
MEDIUM	…e-commit-hooks/check-settings-manager-thread-safety.py	150	print(f"Error checking {filepath}: {e}", file=sys.stderr)	CODE
LOW	.pre-commit-hooks/check-sensitive-logging.py	1128	except Exception as e:	CODE
LOW	.pre-commit-hooks/check-open-encoding.py	140	except Exception:	CODE
LOW	.pre-commit-hooks/check-safe-requests.py	99	except Exception as e:	CODE
MEDIUM	.pre-commit-hooks/check-safe-requests.py	100	print(f"Error reading {filename}: {e}")	CODE
LOW	.pre-commit-hooks/check-safe-requests.py	117	except Exception as e:	CODE
MEDIUM	.pre-commit-hooks/check-safe-requests.py	118	print(f"Error parsing {filename}: {e}")	CODE
LOW	.pre-commit-hooks/check-service-context-managers.py	408	except Exception as e:	CODE
MEDIUM	.pre-commit-hooks/check-service-context-managers.py	409	print(f"Error reading {filename}: {e}")	CODE
LOW	.pre-commit-hooks/check-service-context-managers.py	428	except Exception as e:	CODE
MEDIUM	.pre-commit-hooks/check-service-context-managers.py	429	print(f"Error parsing {filename}: {e}")	CODE
LOW	.pre-commit-hooks/check-deprecated-settings-wrapper.py	63	except Exception as e:	CODE
MEDIUM	.pre-commit-hooks/check-deprecated-settings-wrapper.py	64	print(f"Error checking {filepath}: {e}", file=sys.stderr)	CODE
LOW	.pre-commit-hooks/check-session-context-manager.py	130	except Exception as e:	CODE
MEDIUM	.pre-commit-hooks/check-session-context-manager.py	131	print(f"Error checking {filepath}: {e}", file=sys.stderr)	CODE
LOW	.pre-commit-hooks/check-settings-key-namespace.py	197	except Exception:	CODE
LOW	.pre-commit-hooks/check-settings-key-namespace.py	216	except Exception:	CODE
LOW	.pre-commit-hooks/check-unmarked-sleep.py	155	except Exception as exc:	CODE
LOW	.pre-commit-hooks/check-loguru-formatting.py	119	except Exception as exc:	CODE
LOW	.pre-commit-hooks/check-golden-master-settings.py	45	except Exception:	CODE
LOW	.pre-commit-hooks/check-silent-exceptions.py	75	except Exception as exc:	CODE
LOW	tests/test_api_settings_validation.py	133	except Exception as e:	CODE
LOW	tests/test_context_overflow_detection.py	546	except Exception as e:	CODE
LOW	tests/conftest.py	87	except Exception:	CODE
LOW	tests/conftest.py	115	except Exception:	CODE
LOW	tests/conftest.py	327	except Exception as e:	CODE
1648 more matches not shown…

Self-Referential Comments330 hits · 1016 pts

Severity	File	Line	Snippet	Context
MEDIUM	.pre-commit-hooks/check-service-context-managers.py	195	# Create a fake function body from module-level statements	COMMENT
MEDIUM	tests/conftest.py	330	# Create a test client	COMMENT
MEDIUM	tests/conftest.py	592	# Create a mock module	COMMENT
MEDIUM	tests/test_openai_api_key_usage.py	110	# Create a mock LLM instance	COMMENT
MEDIUM	tests/test_reexport_modules.py	80	# Create a fake config.config_files module	COMMENT
MEDIUM⚡	tests/test_report_generator.py	306	# Define a structure with multiple sections	COMMENT
MEDIUM	tests/test_report_generator.py	354	# Define a structure with 5 sections	COMMENT
MEDIUM	tests/test_settings_manager.py	226	session = SessionLocal() # Create a new session instance for this test	CODE
MEDIUM	tests/test_settings_manager.py	262	# Create a new session for this test	COMMENT
MEDIUM	tests/test_search_engines_enhanced.py	159	# Create a mock paper object	COMMENT
MEDIUM	tests/test_search_engines_enhanced.py	274	# Create a minimal settings snapshot for the factory	COMMENT
MEDIUM	tests/test_api_key_configuration.py	159	# Create a mock LLM instance	COMMENT
MEDIUM	tests/test_api_key_configuration.py	182	# Create a mock LLM instance	COMMENT
MEDIUM	tests/test_api_key_configuration.py	217	# Create a mock LLM instance	COMMENT
MEDIUM	tests/test_api_key_configuration.py	240	# Create a mock LLM instance with invoke method	COMMENT
MEDIUM	tests/test_search_system.py	41	# Create a mock strategy class and instance	COMMENT
MEDIUM	tests/test_search_system.py	64	# Create the search system (will use default source-based strategy)	COMMENT
MEDIUM	tests/test_search_system.py	67	# Create a mock progress callback	COMMENT
MEDIUM	tests/test_search_system.py	196	# Create a mock callback	COMMENT
MEDIUM	tests/test_search_system.py	216	# Create a mock strategy class and instance	COMMENT
MEDIUM	tests/test_search_system.py	271	# Create the search system (uses source-based strategy by default)	COMMENT
MEDIUM	tests/metrics/test_query_utils.py	15	# Create a model for SQLAlchemy column testing	COMMENT
MEDIUM⚡	tests/settings/test_generate_config_docs.py	294	# Create a minimal project structure with a bad JSON file	COMMENT
MEDIUM	tests/database/test_database_init.py	223	# Create a research record	COMMENT
MEDIUM	tests/database/test_database_init.py	268	# Create a benchmark run with results	COMMENT
MEDIUM	tests/database/test_benchmark_models.py	100	# Create a benchmark run first	COMMENT
MEDIUM	tests/database/test_benchmark_models.py	210	# Create a benchmark run	COMMENT
MEDIUM	tests/database/test_benchmark_models.py	273	# Create a run	COMMENT
MEDIUM	tests/database/test_benchmark_models.py	399	# Create a completed run	COMMENT
MEDIUM⚡	tests/database/test_sqlcipher_integration.py	1309	# Create main database	COMMENT
MEDIUM	tests/database/test_sqlcipher_integration.py	960	# Create a regular (unencrypted) SQLite database	COMMENT
MEDIUM	tests/database/test_sqlcipher_integration.py	2465	# Create main database	COMMENT
MEDIUM	tests/database/test_sqlcipher_integration.py	2827	# Create main database	COMMENT
MEDIUM	tests/database/test_sqlcipher_integration.py	3135	# Create main database	COMMENT
MEDIUM	tests/database/test_sqlcipher_integration.py	4224	# Create an encrypted database first	COMMENT
MEDIUM	tests/database/test_sqlcipher_integration.py	4286	# Create an encrypted database with a table	COMMENT
MEDIUM	tests/database/test_orm_conversions.py	80	# Create a research entry first with UUID	COMMENT
MEDIUM⚡	tests/database/test_alembic_migrations.py	525	# Create a corrupted alembic_version table	COMMENT
MEDIUM⚡	tests/database/test_alembic_migrations.py	3682	# Create an engine with invalid credentials in URL	COMMENT
MEDIUM⚡	tests/database/test_alembic_migrations.py	4020	# Create a mock migrations directory structure	COMMENT
MEDIUM⚡	tests/database/test_alembic_migrations.py	4025	# Create a world-writable migration file	COMMENT
MEDIUM	tests/database/test_alembic_migrations.py	318	# Create a few more tables to simulate existing database	COMMENT
MEDIUM	tests/database/test_alembic_migrations.py	1114	# Create a conflicting table structure	COMMENT
MEDIUM	tests/database/test_alembic_migrations.py	2257	# Create a partial state - some tables but not all	COMMENT
MEDIUM	tests/database/test_alembic_migrations.py	2759	# Create a very long string	COMMENT
MEDIUM	tests/database/test_alembic_migrations.py	3646	# Create a read-only directory scenario	COMMENT
MEDIUM	tests/database/test_alembic_migrations.py	3817	# Create a scenario that will cause a migration error	COMMENT
MEDIUM	tests/database/test_alembic_migrations.py	3963	# Create a mock symlinked path scenario	COMMENT
MEDIUM	tests/database/test_alembic_migrations.py	4046	# Create a mock migrations directory with secure files	COMMENT
MEDIUM	tests/database/test_alembic_migrations.py	4070	# Create a mock migrations directory (permissions don't matter)	COMMENT
MEDIUM⚡	tests/database/test_alembic_migrations.py	4437	# Create a fresh Alembic database	STRING
MEDIUM⚡	tests/database/test_alembic_migrations.py	4442	# Create a pre-Alembic database and upgrade it	STRING
MEDIUM	tests/database/test_auth_db.py	90	# Create the file	COMMENT
MEDIUM	tests/database/test_auth_db.py	153	# Create the file so init is skipped	COMMENT
MEDIUM	tests/database/test_auth_db.py	362	# Create an engine	COMMENT
MEDIUM	tests/database/test_auth_db.py	390	# Create an engine	COMMENT
MEDIUM	tests/database/test_encrypted_db_manager.py	106	# Create the database file	COMMENT
MEDIUM	tests/database/test_encrypted_db_manager.py	911	# Create a plain SQLite database (no encryption needed for this test)	COMMENT
MEDIUM⚡	tests/database/backup/test_backup_service.py	2294	# Create a fake database file	COMMENT
MEDIUM⚡	tests/database/backup/test_backup_service.py	2302	# Create a backup directory with a double quote in the path	COMMENT
270 more matches not shown…

Cross-File Repetition159 hits · 795 pts

Severity	File	Line	Snippet	Context
HIGH	tests/test_report_generator_edge_cases.py	0	create a report generator with mocked dependencies.	STRING
HIGH	tests/report/test_report_structure_parsing.py	0	create a report generator with mocked dependencies.	STRING
HIGH	tests/report/test_report_section_generation.py	0	create a report generator with mocked dependencies.	STRING
HIGH	tests/metrics/test_token_counter_high_value.py	0	create a tokencountingcallback with sensible defaults.	STRING
HIGH	tests/metrics/test_token_counter_logic.py	0	create a tokencountingcallback with sensible defaults.	STRING
HIGH	tests/metrics/test_token_counter_coverage.py	0	create a tokencountingcallback with sensible defaults.	STRING
HIGH	…dvanced_search_system/strategies/test_base_strategy.py	0	concrete implementation for testing abstract class.	STRING
HIGH	tests/news/test_rating_system_behavior.py	0	concrete implementation for testing abstract class.	STRING
HIGH	tests/news/test_base_recommender_behavior.py	0	concrete implementation for testing abstract class.	STRING
HIGH	tests/citation_handlers/test_base_citation_handler.py	0	concrete implementation for testing abstract class.	STRING
HIGH	tests/news/test_preference_manager_behavior.py	0	concrete implementation for testing abstract class.	STRING
HIGH	tests/benchmarks/evaluators/test_base.py	0	concrete implementation for testing abstract class.	STRING
HIGH	tests/news/test_preference_manager_extended.py	0	concrete implementation for testing abstract class.	STRING
HIGH	tests/llm/providers/test_openai_base.py	0	raises valueerror when no model name is provided (no silent default).	STRING
HIGH	tests/llm/providers/test_openai_base_deep_coverage.py	0	raises valueerror when no model name is provided (no silent default).	STRING
HIGH	tests/llm_providers/test_openai_base.py	0	raises valueerror when no model name is provided (no silent default).	STRING
HIGH	…_providers/implementations/test_orcarouter_provider.py	0	raises valueerror when no model name is provided (no silent default).	STRING
HIGH	…sts/llm_providers/implementations/test_xai_provider.py	0	raises valueerror when no model name is provided (no silent default).	STRING
HIGH	…/llm_providers/implementations/test_openai_provider.py	0	raises valueerror when no model name is provided (no silent default).	STRING
HIGH	…m_providers/implementations/test_anthropic_provider.py	0	raises valueerror when no model name is provided (no silent default).	STRING
HIGH	…/llm_providers/implementations/test_google_provider.py	0	raises valueerror when no model name is provided (no silent default).	STRING
HIGH	…s/llm_providers/implementations/test_ionos_provider.py	0	raises valueerror when no model name is provided (no silent default).	STRING
HIGH	…_providers/implementations/test_openrouter_provider.py	0	raises valueerror when no model name is provided (no silent default).	STRING
HIGH	…h_library/routes/test_library_routes_extra_coverage.py	0	return a magicmock that satisfies the login_required db_manager check.	STRING
HIGH	tests/web/routes/test_settings_routes_deep_coverage2.py	0	return a magicmock that satisfies the login_required db_manager check.	STRING
HIGH	tests/web/routes/test_api_routes_coverage.py	0	return a magicmock that satisfies the login_required db_manager check.	STRING
HIGH	tests/followup_research/test_routes_coverage.py	0	return a magicmock that satisfies the login_required db_manager check.	STRING
HIGH	tests/web/routes/test_history_routes_extended.py	0	return a magicmock that satisfies the login_required db_manager check.	STRING
HIGH	…h_library/routes/test_library_routes_extra_coverage.py	0	build a mock context-manager for get_user_db_session.	STRING
HIGH	tests/web/routes/test_history_routes_extended.py	0	build a mock context-manager for get_user_db_session.	STRING
HIGH	tests/web/routes/test_settings_routes_deep_coverage2.py	0	build a mock context-manager for get_user_db_session.	STRING
HIGH	tests/web/routes/test_api_routes_coverage.py	0	build a mock context-manager for get_user_db_session.	STRING
HIGH	tests/followup_research/test_routes_coverage.py	0	build a mock context-manager for get_user_db_session.	STRING
HIGH	…h_library/routes/test_library_routes_extra_coverage.py	0	issue an authenticated post request and return the response.	STRING
HIGH	tests/web/routes/test_api_routes_coverage.py	0	issue an authenticated post request and return the response.	STRING
HIGH	tests/followup_research/test_routes_coverage.py	0	issue an authenticated post request and return the response.	STRING
HIGH	…ary/services/test_library_service_collections_stats.py	0	patch get_user_db_session as a proper context manager.	STRING
HIGH	…arch_library/services/test_library_service_coverage.py	0	patch get_user_db_session as a proper context manager.	STRING
HIGH	…rch_library/services/test_library_service_crud_deep.py	0	patch get_user_db_session as a proper context manager.	STRING
HIGH	tests/exporters/test_latex_exporter.py	0	test handling of markdown with tables, code, lists.	STRING
HIGH	tests/exporters/test_pdf_exporter.py	0	test handling of markdown with tables, code, lists.	STRING
HIGH	tests/exporters/test_quarto_exporter.py	0	test handling of markdown with tables, code, lists.	STRING
HIGH	tests/web_services/test_pdf_service.py	0	test handling of markdown with tables, code, lists.	STRING
HIGH	tests/exporters/test_latex_exporter.py	0	test that valueerror is raised for content exceeding size limit.	STRING
HIGH	tests/exporters/test_pdf_exporter.py	0	test that valueerror is raised for content exceeding size limit.	STRING
HIGH	tests/exporters/test_odt_exporter.py	0	test that valueerror is raised for content exceeding size limit.	STRING
HIGH	tests/exporters/test_ris_exporter.py	0	test that valueerror is raised for content exceeding size limit.	STRING
HIGH	tests/exporters/test_quarto_exporter.py	0	test that valueerror is raised for content exceeding size limit.	STRING
HIGH	tests/exporters/test_latex_exporter.py	0	test that content at exactly the limit is accepted.	STRING
HIGH	tests/exporters/test_pdf_exporter.py	0	test that content at exactly the limit is accepted.	STRING
HIGH	tests/exporters/test_ris_exporter.py	0	test that content at exactly the limit is accepted.	STRING
HIGH	tests/exporters/test_quarto_exporter.py	0	test that content at exactly the limit is accepted.	STRING
HIGH	tests/exporters/test_latex_exporter.py	0	test that filename is truncated when title exceeds 50 chars.	STRING
HIGH	tests/exporters/test_pdf_exporter.py	0	test that filename is truncated when title exceeds 50 chars.	STRING
HIGH	tests/exporters/test_odt_exporter.py	0	test that filename is truncated when title exceeds 50 chars.	STRING
HIGH	tests/exporters/test_ris_exporter.py	0	test that filename is truncated when title exceeds 50 chars.	STRING
HIGH	tests/exporters/test_quarto_exporter.py	0	test that filename is truncated when title exceeds 50 chars.	STRING
HIGH	tests/exporters/test_latex_exporter.py	0	test that filename is not truncated when under 50 chars.	STRING
HIGH	tests/exporters/test_pdf_exporter.py	0	test that filename is not truncated when under 50 chars.	STRING
HIGH	tests/exporters/test_odt_exporter.py	0	test that filename is not truncated when under 50 chars.	STRING
99 more matches not shown…

Deep Nesting684 hits · 522 pts

Severity	File	Line	Context
LOW	.pre-commit-hooks/check-css-class-prefix.py	136	CODE
LOW	.pre-commit-hooks/check-css-class-prefix.py	183	CODE
LOW	.pre-commit-hooks/check-css-class-prefix.py	337	CODE
LOW	.pre-commit-hooks/check-css-class-prefix.py	456	CODE
LOW	.pre-commit-hooks/check-absolute-module-paths.py	140	CODE
LOW	.pre-commit-hooks/check-absolute-module-paths.py	187	CODE
LOW	.pre-commit-hooks/check-absolute-module-paths.py	154	CODE
LOW	.pre-commit-hooks/check-env-vars.py	109	CODE
LOW	.pre-commit-hooks/check-env-vars.py	188	CODE
LOW	.pre-commit-hooks/check-env-vars.py	230	CODE
LOW	.pre-commit-hooks/check-double-escaping.py	30	CODE
LOW	.pre-commit-hooks/fix-exception-logging.py	200	CODE
LOW	.pre-commit-hooks/check-layer-imports.py	53	CODE
LOW	.pre-commit-hooks/check-silent-cleanup.py	70	CODE
LOW	.pre-commit-hooks/custom-checks.py	469	CODE
LOW	.pre-commit-hooks/custom-checks.py	68	CODE
LOW	.pre-commit-hooks/custom-checks.py	207	CODE
LOW	.pre-commit-hooks/custom-checks.py	307	CODE
LOW	.pre-commit-hooks/check-external-resources.py	57	CODE
LOW	.pre-commit-hooks/check-bearer-disable.py	82	CODE
LOW	.pre-commit-hooks/check-bearer-disable.py	126	CODE
LOW	…e-commit-hooks/check-settings-manager-thread-safety.py	55	CODE
LOW	.pre-commit-hooks/check-sensitive-logging.py	292	CODE
LOW	.pre-commit-hooks/check-sensitive-logging.py	360	CODE
LOW	.pre-commit-hooks/check-sensitive-logging.py	631	CODE
LOW	.pre-commit-hooks/check-sensitive-logging.py	684	CODE
LOW	.pre-commit-hooks/check-sensitive-logging.py	972	CODE
LOW	.pre-commit-hooks/check-service-context-managers.py	117	CODE
LOW	.pre-commit-hooks/check-service-context-managers.py	229	CODE
LOW	.pre-commit-hooks/check-session-context-manager.py	34	CODE
LOW	.pre-commit-hooks/check-session-context-manager.py	93	CODE
LOW	.pre-commit-hooks/check-settings-key-namespace.py	51	CODE
LOW	.pre-commit-hooks/_commit_analysis.py	199	CODE
LOW	tests/test_openai_api_key_e2e.py	44	CODE
LOW	tests/test_llm_provider_integration.py	207	CODE
LOW	tests/test_llm_provider_integration.py	343	CODE
LOW	tests/run_all_tests.py	530	CODE
LOW	tests/run_all_tests.py	77	CODE
LOW	tests/run_all_tests.py	250	CODE
LOW	tests/settings/test_settings_manager.py	599	CODE
LOW	tests/settings/test_settings_defaults_integrity.py	328	CODE
LOW	tests/database/test_sqlcipher_integration.py	564	CODE
LOW	tests/database/test_sqlcipher_integration.py	3632	CODE
LOW	tests/database/test_sqlcipher_integration.py	3719	CODE
LOW	tests/database/test_sqlcipher_integration.py	4040	CODE
LOW	tests/database/test_sqlcipher_integration.py	4683	CODE
LOW	tests/database/test_sqlcipher_integration.py	4717	CODE
LOW	tests/database/test_db_file_permissions.py	70	CODE
LOW	tests/database/test_alembic_migrations.py	4167	CODE
LOW	tests/database/test_alembic_migrations.py	6491	CODE
LOW	tests/database/test_auth_db.py	147	CODE
LOW	tests/database/test_auth_db.py	180	CODE
LOW	tests/database/test_auth_db.py	220	CODE
LOW	tests/database/test_encryption_threads.py	112	CODE
LOW	tests/database/test_encryption_threads.py	155	CODE
LOW	tests/database/test_no_raw_sql.py	16	CODE
LOW	tests/database/test_no_raw_sql.py	182	CODE
LOW	tests/database/test_encrypted_db_manager.py	27	CODE
LOW	tests/database/test_encrypted_db_manager.py	123	CODE
LOW	tests/database/test_encrypted_db_manager.py	193	CODE
624 more matches not shown…

Redundant / Tautological Comments344 hits · 520 pts

Severity	File	Line	Snippet	Context
LOW	.pre-commit-hooks/check-env-vars.py	240	# Check if the left side is a system var	COMMENT
LOW	.pre-commit-hooks/check-image-pinning.sh	61	# Check if any image lines lack @sha256	COMMENT
LOW	.pre-commit-hooks/check-url-security.py	29	# Check if the file imports or includes URL validation	COMMENT
LOW	.pre-commit-hooks/check-url-security.py	82	# Check if it's preceded by validation	COMMENT
LOW	.pre-commit-hooks/fix-exception-logging.py	210	# Check if the variable is still used anywhere in nearby lines	COMMENT
LOW	.pre-commit-hooks/check-silent-cleanup.py	48	# Check if the handler is "except Exception:" or bare "except:"	COMMENT
LOW	.pre-commit-hooks/check-silent-cleanup.py	55	# Check if handler body is only `pass` (no logging, no raise)	COMMENT
LOW	.pre-commit-hooks/custom-checks.py	308	# Check if this class inherits from Base (SQLAlchemy model)	COMMENT
LOW	.pre-commit-hooks/custom-checks.py	437	# Check if line has allowed patterns first	COMMENT
LOW	.pre-commit-hooks/custom-checks.py	495	# Check if this file is allowed to use datetime.now()	COMMENT
LOW	.pre-commit-hooks/custom-checks.py	514	# Check if it's already using UTC	COMMENT
LOW	.pre-commit-hooks/check-external-resources.py	73	# Check if line contains external patterns	COMMENT
LOW	.pre-commit-hooks/check-external-resources.py	76	# Check if it's an allowed exception	COMMENT
LOW	.pre-commit-hooks/check-pdm-lock.sh	2	# Check if pdm.lock is in sync with pyproject.toml	COMMENT
LOW	.pre-commit-hooks/check-sensitive-logging.py	767	# Check if it's a logger call	COMMENT
LOW	.pre-commit-hooks/check-service-context-managers.py	89	# Check if it's a service class	COMMENT
LOW	.pre-commit-hooks/check-service-context-managers.py	93	# Check if it's a function returning a resource	COMMENT
LOW	.pre-commit-hooks/check-service-context-managers.py	359	# Check if this is a safe instantiation	COMMENT
LOW	.pre-commit-hooks/check-session-context-manager.py	38	# Check if this is a session assignment	COMMENT
LOW	.pre-commit-hooks/check-session-context-manager.py	50	# Check if finally has session.close()	COMMENT
LOW	.pre-commit-hooks/check-session-context-manager.py	104	# Check if it's our session variable	COMMENT
LOW	.pre-commit-hooks/check-unmarked-sleep.py	89	# Check if enclosing function or class has @pytest.mark.slow	COMMENT
LOW	.pre-commit-hooks/check-golden-master-settings.py	34	# Check if regeneration changed the file	COMMENT
LOW	tests/test_context_overflow_detection.py	538	# Check if overflow was detected	COMMENT
LOW	tests/run_followup_tests.sh	13	# Check if server is running	COMMENT
LOW	tests/test_openai_api_key_e2e.py	84	# Check if API key exists in settings or environment	COMMENT
LOW⚡	tests/test_database_initialization.py	130	# Check if settings table is queryable	COMMENT
LOW⚡	tests/test_citation_handler.py	61	# Check if the correct number of documents was created	COMMENT
LOW	tests/test_citation_handler.py	86	# Check if indexes were correctly offset	COMMENT
LOW	tests/test_citation_handler.py	106	# Check if sources are correctly formatted with citation numbers	COMMENT
LOW	tests/test_citation_handler.py	119	# Check if LLM was called with the correct prompt	COMMENT
LOW	tests/test_citation_handler.py	123	# Check if prompt contains expected elements	COMMENT
LOW	tests/run_all_tests.py	444	# Check if we're in a headless environment (CI)	COMMENT
LOW	tests/test_search_system.py	117	# Check if the correct strategy type was created	COMMENT
LOW	tests/metrics/test_research_metrics_extended.py	378	# Check if current is better than baseline	COMMENT
LOW	tests/metrics/test_token_counter_extended.py	151	# Set usage_metadata to None to force response_metadata path	COMMENT
LOW	tests/settings/env_vars/test_env_var_usage.py	155	# Check if file is allowed to use os.environ	COMMENT
LOW⚡	tests/database/test_sqlcipher_integration.py	805	# Check if it changed (it shouldn't for an already-initialized DB)	COMMENT
LOW⚡	tests/database/test_sqlcipher_integration.py	2304	# Check if encryption is actually applied	COMMENT
LOW	tests/database/test_sqlcipher_integration.py	4183	# Check if salt was actually applied	COMMENT
LOW	tests/database/test_alembic_migrations.py	2432	# Check if 'key' has unique constraint	COMMENT
LOW	tests/database/test_no_raw_sql.py	68	# Check if it's in a comment or docstring	COMMENT
LOW	tests/database/test_no_raw_sql.py	77	# Check if it's an allowed pattern	COMMENT
LOW	tests/database/test_no_raw_sql.py	144	# Check if file has database operations	COMMENT
LOW	tests/database/test_no_raw_sql.py	155	# Check if it has ORM imports	COMMENT
LOW	tests/database/test_schema_stability.py	143	# Check if there are new tables that might be renames	COMMENT
LOW	tests/deletion/test_document_deletion.py	209	# Check if document is in any collection	COMMENT
LOW	tests/test_llm/test_llm_benchmarks.py	24	# Check if we have a predefined answer	COMMENT
LOW	…i_tests_with_login/pytest_tests/test_start_research.py	70	# Check if model appears in logs	COMMENT
LOW	tests/infrastructure_tests/test_urls_js.py	118	# Check if the URL exists in backend (with some flexibility for parameter names)	COMMENT
LOW	tests/infrastructure_tests/test_urls_js.py	343	# Check if this is an allowed duplicate	COMMENT
LOW	tests/accessibility_tests/test_accessibility_backend.py	87	# Check if there are any fieldsets	COMMENT
LOW	tests/security/test_xss_prevention.py	280	# Check if CSP header is present (it's a good security practice)	COMMENT
LOW	tests/security/test_repo_guardrails.py	162	# Check if this pattern matches a binary extension	COMMENT
LOW	tests/security/test_csrf_protection.py	116	# Check if it's a CSRF error specifically	COMMENT
LOW	tests/exporters/test_odt_exporter.py	6	# Check if pandoc is available (required by pypandoc)	COMMENT
LOW⚡	tests/web/auth/test_auth_coverage.py	622	# Set last_access to 2 hours ago (would expire normal session)	COMMENT
LOW	tests/web/services/test_research_service.py	830	# Check if pandoc is available	COMMENT
LOW⚡	tests/web/services/test_research_service_core.py	79	# Check if research is terminated	COMMENT
LOW⚡	tests/strategies/test_strategy_imports.py	64	# Check if at least some strategies are exported	COMMENT
284 more matches not shown…

Modern AI Meta-Vocabulary163 hits · 504 pts

Severity	File	Line	Snippet	Context
MEDIUM⚡	.gitleaks.toml	146	# RAG routes and services use db_password variable names (not actual secrets)	COMMENT
MEDIUM⚡	.gitleaks.toml	149	# RAG service factory passes db_password variable names (not actual secrets)	COMMENT
MEDIUM⚡	.gitleaks.toml	152	# the RAG factory (not actual secrets)	COMMENT
MEDIUM	docker-compose.yml	231	# digest are the meaningful guardrails. See #3874.	COMMENT
MEDIUM	.pre-commit-hooks/check-service-context-managers.py	373	# Variable is passed to another function (dependency injection) - receiver responsible	COMMENT
MEDIUM	tests/test_context_overflow_detection.py	520	# Create LLM with small context window	COMMENT
MEDIUM	tests/database/test_alembic_migrations.py	6050	# 0018: restoring 'mcp'/'agentic' strategy references would recreate	COMMENT
MEDIUM	tests/embeddings/test_openai_embeddings.py	618	"""The headline regression for #4195: a Nomic embedding model	STRING
MEDIUM	tests/deletion/test_cascade_integration.py	317	# Add RAG index	COMMENT
MEDIUM⚡	tests/deletion/test_cascade_integration.py	411	# Step 2: Delete RAG index	COMMENT
MEDIUM⚡	tests/deletion/test_collection_deletion.py	250	# Verify RAG index exists	COMMENT
MEDIUM⚡	tests/deletion/test_collection_deletion.py	258	# Manually delete RAG index (should be done by service)	COMMENT
MEDIUM⚡	tests/deletion/test_collection_deletion.py	266	# Verify RAG index is deleted	COMMENT
MEDIUM	tests/deletion/test_collection_deletion.py	290	# Delete RAG index	COMMENT
MEDIUM⚡	tests/security/test_egress_run_classification.py	294	# A RAG run over a collection embeds, so a cloud embedder is an exposing	COMMENT
MEDIUM⚡	tests/security/test_egress_run_classification.py	295	# sink for the sensitive source -> refused even with a local LLM. The RAG	COMMENT
MEDIUM	tests/security/test_egress_pep_coverage.py	290	# `both` is retired (ADR-0007): it coerces to ADAPTIVE, and the RAG gate	COMMENT
MEDIUM	tests/research_library/zotero/test_sync_service.py	637	) # spy: collection isn't RAG-indexed, so only assert calls	CODE
MEDIUM⚡	…ts/research_library/routes/test_rag_routes_coverage.py	325	# No more "try a dedicated embedding model" guessing.	COMMENT
MEDIUM	…ts/research_library/routes/test_rag_routes_coverage.py	1187	q.first.return_value = None # No RAG index	CODE
MEDIUM	…ts/research_library/routes/test_rag_routes_coverage.py	1233	q.first.return_value = None # No RAG index	CODE
MEDIUM	…search_library/routes/test_rag_routes_deep_coverage.py	1100	q.first.return_value = None # No RAG index	CODE
MEDIUM	…arch_library/services/test_library_rag_service_info.py	47	# Collection found, but no RAG index	COMMENT
MEDIUM	…arch_library/services/test_library_rag_service_info.py	75	# RAG index found	COMMENT
MEDIUM	…arch_library/services/test_library_rag_service_info.py	119	# No RAG index	COMMENT
MEDIUM⚡	…rch_library/services/test_download_service_3827_fix.py	936	# (RAG, last_run commit) sees a clean session.	COMMENT
MEDIUM⚡	…rch_library/services/test_download_service_3827_fix.py	944	# Change 3 (continued): RAG indexing of research downloads has been RETIRED from	COMMENT
MEDIUM⚡	…rch_library/services/test_download_service_3827_fix.py	947	# assert the inline RAG block is gone: generate_rag no longer drives any RAG	COMMENT
MEDIUM	…/research_library/services/test_library_rag_service.py	735	# Mock RAG index record	COMMENT
MEDIUM	…/research_library/services/test_library_rag_service.py	800	# Mock RAG index that will fail integrity check	COMMENT
MEDIUM	…/research_library/services/test_library_rag_service.py	853	# Mock RAG index with different dimension	COMMENT
MEDIUM	tests/research_library/services/test_faiss_safe_load.py	38	# Metadata mirrors what the RAG service attaches: plain scalars + lists.	COMMENT
MEDIUM	tests/web/test_startup_import_weight.py	96	# scheduler -> RAG service -> splitter chain, so a regression in	STRING
MEDIUM⚡	tests/web/routes/test_metrics_routes_coverage.py	220	# 5 strategies after the 'mcp'/'agentic' strategy was removed (#4548):	COMMENT
MEDIUM⚡	tests/web/services/test_research_service_core.py	387	# Use 80% of context window	COMMENT
MEDIUM⚡	tests/text_optimization/test_citation_formatter.py	1891	# /library/document/<uuid> from RAG / library sources). The three	COMMENT
MEDIUM⚡	tests/feature_tests/IMPLEMENTATION_GUIDE_241.md	46	# Get context window size from settings	COMMENT
MEDIUM⚡	tests/feature_tests/IMPLEMENTATION_GUIDE_241.md	49	# Ensure max_tokens doesn't exceed context window size	COMMENT
MEDIUM⚡	tests/feature_tests/IMPLEMENTATION_GUIDE_241.md	51	# Use 80% of context window to leave room for prompts	COMMENT
MEDIUM	tests/feature_tests/IMPLEMENTATION_GUIDE_241.md	70	n_ctx=context_window_size, # Set context window size	CODE
MEDIUM	tests/ui_tests/test_context_overflow_ci.js	19	// The page-specific scaffold is server-rendered (pages/context_overflow.html):	COMMENT
MEDIUM	tests/ui_tests/test_context_overflow_ci.js	185	// assert on the overflow-specific chart scaffold: the #context-overflow-section	COMMENT
MEDIUM	tests/ui_tests/test_context_overflow_ci.js	219	// wrong page or the overflow scaffold did not load.	COMMENT
MEDIUM	tests/ui_tests/test_context_overflow_ci.js	223	? 'No token data: #context-overflow-section scaffold present and #empty-no-data shown (no #context-chart	CODE
MEDIUM⚡	tests/news/test_base_recommender.py	1964	# Tests for dependency injection patterns	COMMENT
MEDIUM	tests/news/test_library_sweep.py	146	# One RAG service built per distinct collection (A, B). No orphans here so	COMMENT
MEDIUM	tests/news/test_library_sweep.py	186	# The RAG service for the orphan path was built for the default library.	COMMENT
MEDIUM	tests/news/test_library_sweep.py	1229	# No work to do, so no RAG service was built.	COMMENT
MEDIUM⚡	tests/news/test_topic_generator_coverage.py	259	# generate_topics – orchestration (uses real _validate_topics)	COMMENT
MEDIUM⚡	…s/news/subscription_manager/test_scheduler_coverage.py	56	# NOTE: RAG indexing moved out of _process_user_documents into the unified	COMMENT
MEDIUM	tests/performance/relevance_filter/eval_prompt.py	48	# The shared scaffolding around the guidance block. The variants below only	COMMENT
MEDIUM⚡	…_search_engines/test_search_engine_library_settings.py	40	# search.rag.max_results — cap local RAG retrieval (vector search returns many	COMMENT
MEDIUM⚡	…_search_engines/test_search_engine_library_settings.py	42	# search.rag.enable_relevance_filter — opt-in LLM relevance filter for RAG.	COMMENT
MEDIUM⚡	tests/web_search_engines/test_engine_groups.py	29	# A collection is still "collections" even though it is Local RAG.	COMMENT
MEDIUM	…engines/engines/test_search_engine_library_coverage.py	135	# col1 fails when its RAG service is created; col2 succeeds	COMMENT
MEDIUM⚡	…b_search_engines/engines/test_local_search_coverage.py	744	# No RAG index -> skip	COMMENT
MEDIUM	…b_search_engines/engines/test_local_search_coverage.py	160	# RAG index lookup	COMMENT
MEDIUM	…b_search_engines/engines/test_local_search_coverage.py	163	# RAG service context manager	COMMENT
MEDIUM	…b_search_engines/engines/test_local_search_coverage.py	436	# RAG service	COMMENT
MEDIUM	…b_search_engines/engines/test_local_search_coverage.py	528	# 1) For RAG index lookup (inside collection loop)	COMMENT
103 more matches not shown…

Docstring Block Structure99 hits · 495 pts

Severity	File	Line	Snippet	Context
HIGH	tests/mock_modules.py	16	Create a mock module with specified attributes. Args: module_name: Name of the module to create	STRING
HIGH	examples/optimization/run_gemini_benchmark.py	87	Run benchmarks with Gemini Flash via OpenRouter. Args: examples: Number of examples to evaluate for ea	STRING
HIGH	examples/benchmarks/run_browsecomp.py	62	Run BrowseComp benchmark with proper decryption using canary field. Args: num_examples: Number of exam	STRING
HIGH	src/local_deep_research/database/sqlcipher_utils.py	78	Create and store a new random salt for a database. This should be called when creating a new database. The	STRING
HIGH	src/local_deep_research/database/sqlcipher_utils.py	599	Create a properly configured SQLCipher connection. Implements the full PRAGMA sequence with proper error clean	STRING
HIGH	src/local_deep_research/database/session_context.py	84	Context manager that ensures proper database session with encryption. Now uses thread-local sessions for better	STRING
HIGH	src/local_deep_research/database/library_init.py	294	Get the ID of a source type by name. Args: username: User to query for type_name: Name of sour	STRING
HIGH	src/local_deep_research/database/encrypted_db.py	410	Create a properly initialized SQLCipher connection. Follows the canonical SQLCipher initialization order: set k	STRING
HIGH	…ced_search_system/filters/journal_reputation_filter.py	709	Analyze journal reputation via 1 SearXNG search + 1 LLM call. This is Tier 4 — the last-resort scoring path. On	STRING
HIGH	…ced_search_system/filters/followup_relevance_filter.py	26	Filter search results by relevance to the follow-up query. Args: results: List of source d	STRING
HIGH	src/local_deep_research/llm/providers/openai_base.py	35	Factory function for OpenAI-compatible LLMs. Args: model_name: Name of the model to use	STRING
HIGH	src/local_deep_research/llm/providers/base.py	82	Create and return a LangChain chat model instance. Subclasses MUST override this method. The returned LLM is BA	STRING
HIGH	…_deep_research/llm/providers/implementations/openai.py	36	Factory function for OpenAI LLMs. Args: model_name: Name of the model to use temperatur	STRING
HIGH	…ep_research/llm/providers/implementations/anthropic.py	37	Factory function for Anthropic LLMs. Args: model_name: Name of the model to use tempera	STRING
HIGH	…_deep_research/llm/providers/implementations/ollama.py	106	Factory function for Ollama LLMs. Args: model_name: Name of the model to use temperatur	STRING
HIGH	src/local_deep_research/embeddings/embeddings_config.py	132	Get embeddings instance based on provider and model. Args: provider: Embedding provider to use (if Non	STRING
HIGH	src/local_deep_research/embeddings/providers/base.py	41	Create an embeddings instance for this provider. Args: model: Name of the embedding model	STRING
HIGH	…esearch/embeddings/providers/implementations/openai.py	49	Create OpenAI embeddings instance. Args: model: Model name (defaults to text-embedding-3-s	STRING
HIGH	…esearch/embeddings/splitters/text_splitter_registry.py	61	Get text splitter based on type. Args: splitter_type: Type of splitter ('recursive', 'token', 'sentenc	STRING
HIGH	src/local_deep_research/chat/service.py	249	Add a durable message (query/followup/response) to a chat session. Content is required and stored inli	STRING
HIGH	src/local_deep_research/chat/service.py	448	Get a chat session by ID. Args: session_id: ID of the session Returns:	STRING
HIGH	src/local_deep_research/chat/service.py	813	Archive a chat session. Refuses to archive while a research is still in_progress for the sessi	STRING
HIGH	src/local_deep_research/chat/service.py	922	Permanently delete one chat attempt (research + its messages + steps). An "attempt" is the user message that tr	STRING
HIGH	src/local_deep_research/chat/service.py	1128	Return the original user message content for a chat research. Used by the retry route to re-submit the same que	STRING
HIGH	src/local_deep_research/config/thread_settings.py	77	Get setting from context only - no database access from threads. Args: key: Setting key to retrieve	STRING
HIGH	src/local_deep_research/security/safe_requests.py	149	Make a safe HTTP GET request with SSRF protection. Args: url: URL to request params: URL param	STRING
HIGH	src/local_deep_research/security/safe_requests.py	285	Make a safe HTTP POST request with SSRF protection. Args: url: URL to request data: Data to se	STRING
HIGH	src/local_deep_research/security/safe_requests.py	590	`safe_get` plus exponential-backoff retry on transient errors. Retries on: * ``requests.ConnectionError``	STRING
HIGH	…local_deep_research/security/notification_validator.py	202	Validate a notification service URL for security issues. This function prevents SSRF attacks by valida	STRING
HIGH	…local_deep_research/security/notification_validator.py	393	Strict validation that raises an exception on invalid URLs. Args: url: Service URL to vali	STRING
HIGH	src/local_deep_research/security/url_builder.py	44	Build a base URL from application settings with intelligent fallbacks. This function handles the common patter	STRING
HIGH	src/local_deep_research/security/url_builder.py	98	Build a complete URL from base URL and path. Args: base_url: Base URL (e.g., "https://myapp.com")	STRING
HIGH	src/local_deep_research/security/url_builder.py	136	Validate a constructed URL. Args: url: URL to validate allowed_schemes: List of allowed scheme	STRING
HIGH	src/local_deep_research/security/path_validator.py	94	Validate and sanitize a user-provided path. Args: user_input: The user-provided path strin	STRING
HIGH	src/local_deep_research/security/path_validator.py	176	Validate a user-provided absolute filesystem path for local indexing. This is for features like local	STRING
HIGH	src/local_deep_research/security/path_validator.py	299	Re-sanitize a validated path for static analyzer recognition. This method takes an already-validated P	STRING
HIGH	src/local_deep_research/security/path_validator.py	340	Validate a model file path specifically. Args: model_path: Path to the model file	STRING
HIGH	src/local_deep_research/security/path_validator.py	383	Validate a path within the data directory. Args: file_path: Path relative to data root	STRING
HIGH	src/local_deep_research/security/path_validator.py	412	Validate a configuration file path. Args: config_path: Path to config file con	STRING
HIGH	src/local_deep_research/security/module_whitelist.py	181	Safely import a class from a module, validating against both whitelists. This function provides secure dynamic	STRING
HIGH	src/local_deep_research/security/filename_sanitizer.py	28	Sanitize an uploaded filename for safe filesystem storage. Args: filename: Raw filename from the upload.	STRING
HIGH	src/local_deep_research/security/url_validator.py	287	Validate that a callback URL is well-formed and safe for HTTP/HTTPS use. This is stricter than is_safe	STRING
HIGH	src/local_deep_research/security/network_utils.py	11	Check if hostname is a private/local IP address. Recognizes: - Localhost values (127.0.0.1, localhost, [::1], 0	STRING
HIGH	…_research/security/file_integrity/integrity_manager.py	116	Create or update integrity record for a file. Args: file_path: Path to file to record	STRING
HIGH	…deep_research/security/file_integrity/base_verifier.py	67	Calculate SHA256 checksum of file. Can be overridden by subclasses for different algorithms.	STRING
HIGH	…eep_research/research_library/routes/library_routes.py	74	Get authenticated user password from session store with fallback to g.user_password. Args: username: T	STRING
HIGH	…_research/research_library/services/faiss_safe_load.py	106	Load a FAISS index from disk without dangerous deserialization. Drop-in replacement for ``FAISS.load_local(...,	STRING
HIGH	…research/research_library/services/download_service.py	428	Queue all downloadable PDFs from a research session. Args: research_id: The research sessi	STRING
HIGH	src/local_deep_research/exporters/odt_exporter.py	61	Convert markdown content to ODT using Pandoc. The conversion runs entirely in memory: markdown is piped to	STRING
HIGH	src/local_deep_research/exporters/quarto_exporter.py	57	Convert markdown content to Quarto format. Args: markdown_content: The markdown text to convert	STRING
HIGH	src/local_deep_research/exporters/ris_exporter.py	50	Extract references from markdown and convert to RIS format. Args: markdown_content: The markdown te	STRING
HIGH	src/local_deep_research/exporters/latex_exporter.py	49	Convert markdown content to LaTeX. Args: markdown_content: The markdown text to convert	STRING
HIGH	src/local_deep_research/exporters/pdf_exporter.py	53	Convert markdown content to PDF using existing PDFService. Args: markdown_content: The markdown tex	STRING
HIGH	…l_deep_research/web/services/pdf_extraction_service.py	24	Extract text and metadata from PDF in a single pass. This method opens the PDF only once and extracts	STRING
HIGH	…c/local_deep_research/web/services/resource_service.py	95	Delete a resource from the database Args: resource_id (int): The ID of the resource to delete Ret	STRING
HIGH	src/local_deep_research/storage/factory.py	20	Get a report storage instance that always uses database with optional file backup. Args: session: Database	STRING
HIGH	src/local_deep_research/utilities/type_utils.py	13	Convert a value to boolean, handling string representations. This is a standalone utility for converting any v	STRING
HIGH	src/local_deep_research/utilities/url_utils.py	42	Normalize a URL to ensure it has a proper scheme and format. Args: raw_url: The raw URL string to norm	STRING
HIGH	src/local_deep_research/news/core/card_factory.py	60	Get or create the storage instance. Args: session: SQLAlchemy session. If not provided, attempts to	STRING
HIGH	src/local_deep_research/news/core/card_factory.py	104	Create a new card of the specified type. Args: card_type: Type of card to create ('news',	STRING
39 more matches not shown…

Unused Imports516 hits · 464 pts

Severity	File	Line	Context
LOW	.pre-commit-hooks/check-target-blank-rel.py	19	CODE
LOW	.pre-commit-hooks/check-bearer-disable.py	30	CODE
LOW	.pre-commit-hooks/check-journal-quality-readonly.py	15	CODE
LOW	.pre-commit-hooks/check-author-identity.py	26	CODE
LOW	tests/database/test_schema_index_completeness.py	13	CODE
LOW	tests/database/test_journal_migrations_encrypted.py	14	CODE
LOW	tests/database/test_research_strategy_fk_regression.py	14	CODE
LOW	tests/database/test_fk_targets_resolve.py	9	CODE
LOW	…sts/database/test_journal_rebuild_data_preservation.py	20	CODE
LOW	tests/advanced_search_system/filters/conftest.py	12	CODE
LOW	tests/advanced_search_system/tools/test_fetch_modes.py	8	CODE
LOW	tests/content_fetcher/test_lazy_content_fetcher.py	16	CODE
LOW	tests/security/test_collection_agent_enabled.py	14	CODE
LOW	tests/security/test_egress_threadpool_propagation.py	27	CODE
LOW	tests/security/test_egress_guidance.py	4	CODE
LOW	…ts/security/test_egress_pep_llm_embeddings_callsite.py	26	CODE
LOW	tests/security/test_egress_policy.py	3	CODE
LOW	tests/security/test_egress_pep_factory_callsite.py	19	CODE
LOW	tests/security/test_egress_notifications_callsite.py	20	CODE
LOW	tests/security/test_egress_langgraph_tool_filter.py	31	CODE
LOW	tests/security/test_egress_e2e_private_only_tripwire.py	27	CODE
LOW	tests/security/test_egress_inference_gates_followup.py	20	CODE
LOW	tests/security/test_egress_run_classification.py	8	CODE
LOW	tests/security/test_egress_audit_hook.py	20	CODE
LOW	…ts/security/test_egress_pep_fetch_download_callsite.py	24	CODE
LOW	tests/security/test_egress_fullsearch.py	15	CODE
LOW	tests/security/test_egress_url_edgecases_followup.py	28	CODE
LOW	tests/security/test_egress_backstop_rearm_followup.py	22	CODE
LOW	…s/security/test_egress_adaptive_resolution_followup.py	21	CODE
LOW	…/security/test_egress_collection_semantics_followup.py	18	CODE
LOW	…/security/test_egress_downloader_threading_followup.py	26	CODE
LOW	…sts/security/test_egress_news_subscription_callsite.py	24	CODE
LOW	tests/security/test_egress_classification.py	7	CODE
LOW	tests/security/test_egress_unprotected.py	8	CODE
LOW	tests/integration/test_journal_quality_release_gate.py	49	CODE
LOW	tests/journal_quality/test_lookup_institution_keys.py	8	CODE
LOW	tests/journal_quality/test_openalex_common.py	9	CODE
LOW	tests/journal_quality/test_openalex_schema_drift.py	11	CODE
LOW	…s/journal_quality/test_institutions_malformed_lines.py	11	CODE
LOW	tests/journal_quality/test_predatory_min_floor.py	10	CODE
LOW	tests/mcp/test_server_coverage.py	19	CODE
LOW	tests/mcp/test_validation.py	11	CODE
LOW	tests/mcp/test_server_validators.py	9	CODE
LOW	tests/mcp/test_egress_audit_net.py	20	CODE
LOW	tests/mcp/test_server.py	14	CODE
LOW	tests/mcp/test_edge_cases.py	13	CODE
LOW	tests/mcp/test_integration.py	13	CODE
LOW	tests/error_handling/test_openai_compat_errors.py	9	CODE
LOW	tests/performance/_shared/build_eval_dataset.py	25	CODE
LOW	tests/performance/_shared/run_full_search.py	19	CODE
LOW	tests/performance/relevance_filter/eval_prompt.py	17	CODE
LOW	tests/performance/relevance_filter/test_live.py	19	CODE
LOW	tests/performance/relevance_filter/eval_models.py	20	CODE
LOW	src/local_deep_research/__init__.py	10	CODE
LOW	src/local_deep_research/search_system_factory.py	14	CODE
LOW	src/local_deep_research/search_system_factory.py	14	CODE
LOW	src/local_deep_research/metrics/__init__.py	3	CODE
LOW	src/local_deep_research/metrics/__init__.py	3	CODE
LOW	src/local_deep_research/metrics/__init__.py	4	CODE
LOW	src/local_deep_research/metrics/__init__.py	4	CODE
456 more matches not shown…

Structural Annotation Overuse146 hits · 269 pts

Severity	File	Line	Snippet	Context
LOW⚡	README.md	52	# Step 1: Pull and run Ollama	COMMENT
LOW⚡	README.md	56	# Step 2: Pull and run SearXNG for optimal search results	COMMENT
LOW⚡	README.md	59	# Step 3: Pull and run Local Deep Research	COMMENT
LOW⚡	docker-compose.yml	87	# WARNING: This will disable UI configuration for these settings!	COMMENT
LOW⚡	tests/test_openai_api_key_e2e.py	64	# Step 1: Authenticate	COMMENT
LOW⚡	tests/test_openai_api_key_e2e.py	71	# Step 2: Configure settings	COMMENT
LOW⚡	tests/test_openai_api_key_e2e.py	109	# Step 3: Test LLM initialization	COMMENT
LOW⚡	tests/test_openai_api_key_e2e.py	120	# Step 4: Test simple LLM call	COMMENT
LOW⚡	tests/test_openai_api_key_e2e.py	143	# Step 5: Test research functionality	COMMENT
LOW⚡	tests/database/test_alembic_migrations.py	4533	# Step 1: Migrate to 0001 only	STRING
LOW⚡	tests/database/test_alembic_migrations.py	4537	# Step 2: Insert data	STRING
LOW⚡	tests/database/test_alembic_migrations.py	4564	# Step 3: Upgrade to head (0005)	STRING
LOW⚡	tests/database/test_alembic_migrations.py	4568	# Step 4: Verify data survived	STRING
LOW	tests/database/test_alembic_migrations.py	4581	# Step 5: Verify new columns exist	STRING
LOW	tests/database/test_alembic_migrations.py	4613	# Step 6: Another run_migrations should be no-op	STRING
LOW⚡	tests/deletion/test_cascade_integration.py	241	# Step 1: Delete chunks (no FK, manual cleanup required)	COMMENT
LOW⚡	tests/deletion/test_cascade_integration.py	247	# Step 2: Delete document (CASCADE handles blob and collection links)	COMMENT
LOW⚡	tests/deletion/test_cascade_integration.py	406	# Step 1: Delete chunks (no FK, manual cleanup)	COMMENT
LOW⚡	tests/deletion/test_cascade_integration.py	411	# Step 2: Delete RAG index	COMMENT
LOW⚡	tests/deletion/test_cascade_integration.py	416	# Step 3: Delete collection (CASCADE handles folders, links)	COMMENT
LOW⚡	tests/chat/test_chat_e2e_flows.py	19	# Step 1: Create session	COMMENT
LOW	tests/chat/test_chat_e2e_flows.py	30	# Step 2: Send a message	COMMENT
LOW	tests/chat/test_chat_e2e_flows.py	44	# Step 3: Get messages	COMMENT
LOW⚡	tests/security/test_csrf_e2e_flow.py	31	# Step 1: GET /auth/login to get a CSRF token for registration	COMMENT
LOW	tests/security/test_csrf_e2e_flow.py	43	# Step 2: Register (auto-logs in the user)	COMMENT
LOW⚡	tests/security/test_csrf_e2e_flow.py	62	# Step 3: Get API CSRF token from /auth/csrf-token	COMMENT
LOW⚡	tests/security/test_csrf_e2e_flow.py	69	# Step 4: POST /api/start_research WITH CSRF token — should pass CSRF	COMMENT
LOW	tests/security/test_csrf_e2e_flow.py	89	# Step 5: POST /api/start_research WITHOUT CSRF token — should be rejected	COMMENT
LOW	tests/research_library/zotero/test_sync_service.py	1738	# Step 1: first contact — byte-identical, so the item adopts the upload.	COMMENT
LOW	tests/research_library/zotero/test_sync_service.py	1753	# Step 2: the PDF is replaced in Zotero — content now differs.	COMMENT
LOW⚡	tests/web/routes/test_search_favorites.py	458	# Step 1: Get empty favorites	COMMENT
LOW⚡	tests/web/routes/test_search_favorites.py	465	# Step 2: Add searxng to favorites	COMMENT
LOW⚡	tests/web/routes/test_search_favorites.py	474	# Step 3: Add arxiv to favorites	COMMENT
LOW⚡	tests/web/routes/test_search_favorites.py	484	# Step 4: Remove searxng from favorites	COMMENT
LOW⚡	tests/ui_tests/test_research_diagnosis.js	75	// Step 1: Authenticate	COMMENT
LOW⚡	tests/ui_tests/test_research_diagnosis.js	80	// Step 2: Go to home page	COMMENT
LOW⚡	tests/ui_tests/test_research_diagnosis.js	86	// Step 3: Check what's on the page	COMMENT
LOW	tests/ui_tests/test_research_diagnosis.js	151	// Step 4: Fill the form	COMMENT
LOW	tests/ui_tests/test_research_diagnosis.js	190	// Step 5: Check JavaScript state	COMMENT
LOW	tests/ui_tests/test_research_diagnosis.js	235	// Step 6: Submit the form	COMMENT
LOW	tests/ui_tests/test_research_diagnosis.js	279	// Step 7: Summary	COMMENT
LOW	…ts/ui_tests/NO_CI_executes_research_followup_simple.js	41	// Step 1: Login	COMMENT
LOW⚡	…ts/ui_tests/NO_CI_executes_research_followup_simple.js	55	// Step 2: Navigate to parent research	COMMENT
LOW⚡	…ts/ui_tests/NO_CI_executes_research_followup_simple.js	65	// Step 3: Test direct API call for follow-up	COMMENT
LOW⚡	…sts/ui_tests/NO_CI_executes_research_fixed_research.js	27	// Step 1: Authenticate	COMMENT
LOW⚡	…sts/ui_tests/NO_CI_executes_research_fixed_research.js	32	// Step 2: Navigate to home	COMMENT
LOW⚡	…sts/ui_tests/NO_CI_executes_research_fixed_research.js	39	// Step 3: Configure model	COMMENT
LOW⚡	…sts/ui_tests/NO_CI_executes_research_fixed_research.js	47	// Step 4: Enter query	COMMENT
LOW⚡	…sts/ui_tests/NO_CI_executes_research_fixed_research.js	53	// Step 5: Submit research	COMMENT
LOW	…sts/ui_tests/NO_CI_executes_research_fixed_research.js	69	// Step 6: Verify research started	COMMENT
LOW⚡	tests/ui_tests/test_metrics_display.js	17	// Step 1: Create and authenticate user	COMMENT
LOW⚡	tests/ui_tests/test_metrics_display.js	27	// Step 2: Start a simple research	COMMENT
LOW⚡	tests/ui_tests/test_metrics_display.js	54	// Step 3: Wait a bit for metrics to be generated	COMMENT
LOW⚡	tests/ui_tests/test_metrics_display.js	58	// Step 4: Go to metrics page	COMMENT
LOW⚡	tests/ui_tests/test_metrics_display.js	63	// Step 5: Check what's on the page (with error handling)	COMMENT
LOW	tests/ui_tests/DEBUG_research_submit_debug.js	49	// Step 1: Login	COMMENT
LOW	tests/ui_tests/DEBUG_research_submit_debug.js	73	// Step 2: Wait for form to load	COMMENT
LOW	tests/ui_tests/DEBUG_research_submit_debug.js	98	// Step 3: Fill the form	COMMENT
LOW	tests/ui_tests/DEBUG_research_submit_debug.js	148	// Step 4: Check form values	COMMENT
LOW	tests/ui_tests/DEBUG_research_submit_debug.js	166	// Step 5: Submit the form	COMMENT
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Over-Commented Block289 hits · 240 pts

Severity	File	Line	Snippet	Context
LOW	docker-compose.gpu.override.yml	1	# ============================================================================	COMMENT
LOW	docker-compose.unraid.yml	1	# ============================================================================	COMMENT
LOW	.pre-commit-config.yaml	461	#	COMMENT
LOW	.hadolint.yaml	1	# Hadolint configuration file	COMMENT
LOW	.hadolint.yaml	21	# caching. npm ci, npm run build, and pdm install have different change	COMMENT
LOW	.file-whitelist.txt	1	# ============================================================================	COMMENT
LOW	pyproject.toml	421	# ---------------------------------------------------------------------------	COMMENT
LOW	pyproject.toml	441	# would fail with ModuleNotFoundError. `package`/`package_dir` are	COMMENT
LOW	.grype.yaml	1	# Grype vulnerability ignore file	COMMENT
LOW	.grype.yaml	21	# fixability only, not by severity.	COMMENT
LOW	.grype.yaml	141	reason: "Heap overflow in Media. Playwright 1.58 bundles pre-fix Chromium. Headless scraping only."	COMMENT
LOW	.grype.yaml	201	# The binary-cataloged CPython is matched via NVD CPE data, which carries	COMMENT
LOW	.grype.yaml	421		COMMENT
LOW	docker-compose.yml	1	# ============================================================================	COMMENT
LOW	docker-compose.yml	41	# Only use environment variables if you want to enforce specific settings	COMMENT
LOW	docker-compose.yml	61	# Example - to expose on port 8080 instead of 5000:	COMMENT
LOW	docker-compose.yml	81	# Register your initial account FIRST, then set this to false.	COMMENT
LOW	docker-compose.yml	101	# - LDR_LLM_OPENAI_ENDPOINT_URL=https://openrouter.ai/api/v1	COMMENT
LOW	docker-compose.yml	121	# - LDR_LLM_LMSTUDIO_API_KEY=<api-key-if-required> # optional; leave out for unauth instances	COMMENT
LOW	docker-compose.yml	141	# ============================================================================	COMMENT
LOW	docker-compose.yml	181	image: ollama/ollama:latest@sha256:8850b8b33936b9fb246e7b3e02849941f1151ea847e5fb15511f17de9589aea1	COMMENT
LOW	eslint.config.js	241	"chai-friendly/no-unused-expressions": "error",	COMMENT
LOW	eslint.config.js	301	confirm: "readonly",	COMMENT
LOW	bearer.yml	1	# Bearer SAST Scanner Configuration	COMMENT
LOW	bearer.yml	21		COMMENT
LOW	bearer.yml	41	# - validate_config_path(): Validates config file paths	COMMENT
LOW	bearer.yml	61	# SAFE TO SKIP: Same rationale as python_lang_insecure_random above.	COMMENT
LOW	bearer.yml	81	# - All user data in HTML templates is escaped	COMMENT
LOW	bearer.yml	101	# ------------------------------------------------------------	COMMENT
LOW	community_benchmark_results/benchmark_template.yaml	61	test_details:	COMMENT
LOW	tests/settings/test_settings_defaults_integrity.py	61	# 'dark' was a legacy theme name; dynamic options from theme_registry	COMMENT
LOW	tests/database/test_alembic_migrations.py	6041	# data migrations that delete stale keys with no consumers).	COMMENT
LOW	tests/database/test_settings_models.py	421	# Note: onupdate might not trigger in SQLite without proper configuration	COMMENT
LOW	tests/database/test_encrypted_db_manager.py	1561		COMMENT
LOW	tests/database/test_migration_0010.py	221	# Relies on 0010 using server_default="0" (SQL-side, applied by	COMMENT
LOW	tests/database/test_paper_dedup_integration.py	461	assert len(all_papers) == 1, (	COMMENT
LOW	tests/database/test_paper_dedup_integration.py	481	# dedup coverage above (test_same_doi_deduped_across_two_sources,	COMMENT
LOW	tests/database/test_sqlcipher_connection_factory.py	341	# the inline SQLCipher creator inside create_thread_safe_session_for_metrics.	COMMENT
LOW	tests/database/backup/test_backup_service.py	4121	username="testuser", password="testpass", max_backups=3	COMMENT
LOW	tests/chat/test_chat_send_message_followups.py	181	session_a = _create_session(authenticated_client)	COMMENT
LOW	tests/chat/test_chat_send_message_followups.py	201	# thread is dead, gated only by a 30s grace window on	COMMENT
LOW	tests/chat/test_chat_research_history_integration.py	101	# stored inline (snapshot semantics). The "fetch from	COMMENT
LOW	tests/security/test_xss_prevention.py	221	# DOM-based XSS happens when client-side JavaScript uses untrusted data	COMMENT
LOW	tests/security/test_xss_prevention.py	241	@pytest.mark.skip(reason="documentation/placeholder test - not implemented")	COMMENT
LOW	tests/security/test_egress_langgraph_tool_filter.py	221	assert _specialized(names) == set()	COMMENT
LOW	tests/security/test_egress_langgraph_tool_filter.py	281		COMMENT
LOW	tests/security/test_auth_security.py	21	LDR uses SQLCipher encryption for user databases.	COMMENT
LOW	tests/security/test_auth_security.py	121	"""Test that logout completely invalidates the session."""	COMMENT
LOW	tests/security/test_api_key_leakage.py	861	# call fails — its message embeds the assembled URL with the	COMMENT
LOW	tests/security/test_sql_injection.py	281	# - session.query() - ✓ Safe (parameterized)	COMMENT
LOW	tests/security/test_csrf_protection.py	161		COMMENT
LOW	tests/security/test_csrf_protection.py	201	# - Request headers (X-CSRFToken)	COMMENT
LOW	tests/js/components/logpanel.test.js	321	});	COMMENT
LOW	tests/js/components/logpanel.test.js	421	'live-A',	COMMENT
LOW	tests/js/components/logpanel.test.js	901	if (!el) return null;	COMMENT
LOW	tests/js/components/logpanel.test.js	981	// Explicit timeout + faked timers: this test fills the DOM to the real	COMMENT
LOW	tests/js/services/ui.test.js	361	});	COMMENT
LOW	tests/web/test_api_coverage.py	1661		COMMENT
LOW	tests/web/test_api_coverage.py	1821	f"This bug class — endpoint passes kwargs the function "	COMMENT
LOW	tests/web/queue/test_processor_v2_real.py	921	# that distinguishes this branch from the generic spawn-failure	COMMENT
229 more matches not shown…

Verbosity Indicators125 hits · 230 pts

Severity	File	Line	Snippet	Context
LOW⚡	tests/test_openai_api_key_e2e.py	64	# Step 1: Authenticate	COMMENT
LOW⚡	tests/test_openai_api_key_e2e.py	71	# Step 2: Configure settings	COMMENT
LOW⚡	tests/test_openai_api_key_e2e.py	109	# Step 3: Test LLM initialization	COMMENT
LOW⚡	tests/test_openai_api_key_e2e.py	120	# Step 4: Test simple LLM call	COMMENT
LOW⚡	tests/test_openai_api_key_e2e.py	143	# Step 5: Test research functionality	COMMENT
LOW⚡	tests/database/test_alembic_migrations.py	4533	# Step 1: Migrate to 0001 only	STRING
LOW⚡	tests/database/test_alembic_migrations.py	4537	# Step 2: Insert data	STRING
LOW⚡	tests/database/test_alembic_migrations.py	4564	# Step 3: Upgrade to head (0005)	STRING
LOW⚡	tests/database/test_alembic_migrations.py	4568	# Step 4: Verify data survived	STRING
LOW	tests/database/test_alembic_migrations.py	4581	# Step 5: Verify new columns exist	STRING
LOW	tests/database/test_alembic_migrations.py	4613	# Step 6: Another run_migrations should be no-op	STRING
LOW⚡	tests/deletion/test_cascade_integration.py	241	# Step 1: Delete chunks (no FK, manual cleanup required)	COMMENT
LOW⚡	tests/deletion/test_cascade_integration.py	247	# Step 2: Delete document (CASCADE handles blob and collection links)	COMMENT
LOW⚡	tests/deletion/test_cascade_integration.py	406	# Step 1: Delete chunks (no FK, manual cleanup)	COMMENT
LOW⚡	tests/deletion/test_cascade_integration.py	411	# Step 2: Delete RAG index	COMMENT
LOW⚡	tests/deletion/test_cascade_integration.py	416	# Step 3: Delete collection (CASCADE handles folders, links)	COMMENT
LOW⚡	tests/chat/test_chat_e2e_flows.py	19	# Step 1: Create session	COMMENT
LOW	tests/chat/test_chat_e2e_flows.py	30	# Step 2: Send a message	COMMENT
LOW	tests/chat/test_chat_e2e_flows.py	44	# Step 3: Get messages	COMMENT
LOW⚡	tests/security/test_csrf_e2e_flow.py	31	# Step 1: GET /auth/login to get a CSRF token for registration	COMMENT
LOW	tests/security/test_csrf_e2e_flow.py	43	# Step 2: Register (auto-logs in the user)	COMMENT
LOW⚡	tests/security/test_csrf_e2e_flow.py	62	# Step 3: Get API CSRF token from /auth/csrf-token	COMMENT
LOW⚡	tests/security/test_csrf_e2e_flow.py	69	# Step 4: POST /api/start_research WITH CSRF token — should pass CSRF	COMMENT
LOW	tests/security/test_csrf_e2e_flow.py	89	# Step 5: POST /api/start_research WITHOUT CSRF token — should be rejected	COMMENT
LOW	tests/research_library/zotero/test_sync_service.py	1738	# Step 1: first contact — byte-identical, so the item adopts the upload.	COMMENT
LOW	tests/research_library/zotero/test_sync_service.py	1753	# Step 2: the PDF is replaced in Zotero — content now differs.	COMMENT
LOW⚡	tests/web/routes/test_search_favorites.py	458	# Step 1: Get empty favorites	COMMENT
LOW⚡	tests/web/routes/test_search_favorites.py	465	# Step 2: Add searxng to favorites	COMMENT
LOW⚡	tests/web/routes/test_search_favorites.py	474	# Step 3: Add arxiv to favorites	COMMENT
LOW⚡	tests/web/routes/test_search_favorites.py	484	# Step 4: Remove searxng from favorites	COMMENT
LOW⚡	tests/ui_tests/test_research_diagnosis.js	75	// Step 1: Authenticate	COMMENT
LOW⚡	tests/ui_tests/test_research_diagnosis.js	80	// Step 2: Go to home page	COMMENT
LOW⚡	tests/ui_tests/test_research_diagnosis.js	86	// Step 3: Check what's on the page	COMMENT
LOW	tests/ui_tests/test_research_diagnosis.js	151	// Step 4: Fill the form	COMMENT
LOW	tests/ui_tests/test_research_diagnosis.js	190	// Step 5: Check JavaScript state	COMMENT
LOW	tests/ui_tests/test_research_diagnosis.js	235	// Step 6: Submit the form	COMMENT
LOW	tests/ui_tests/test_research_diagnosis.js	279	// Step 7: Summary	COMMENT
LOW	…ts/ui_tests/NO_CI_executes_research_followup_simple.js	41	// Step 1: Login	COMMENT
LOW⚡	…ts/ui_tests/NO_CI_executes_research_followup_simple.js	55	// Step 2: Navigate to parent research	COMMENT
LOW⚡	…ts/ui_tests/NO_CI_executes_research_followup_simple.js	65	// Step 3: Test direct API call for follow-up	COMMENT
LOW⚡	…sts/ui_tests/NO_CI_executes_research_fixed_research.js	27	// Step 1: Authenticate	COMMENT
LOW⚡	…sts/ui_tests/NO_CI_executes_research_fixed_research.js	32	// Step 2: Navigate to home	COMMENT
LOW⚡	…sts/ui_tests/NO_CI_executes_research_fixed_research.js	39	// Step 3: Configure model	COMMENT
LOW⚡	…sts/ui_tests/NO_CI_executes_research_fixed_research.js	47	// Step 4: Enter query	COMMENT
LOW⚡	…sts/ui_tests/NO_CI_executes_research_fixed_research.js	53	// Step 5: Submit research	COMMENT
LOW	…sts/ui_tests/NO_CI_executes_research_fixed_research.js	69	// Step 6: Verify research started	COMMENT
LOW⚡	tests/ui_tests/test_metrics_display.js	17	// Step 1: Create and authenticate user	COMMENT
LOW⚡	tests/ui_tests/test_metrics_display.js	27	// Step 2: Start a simple research	COMMENT
LOW⚡	tests/ui_tests/test_metrics_display.js	54	// Step 3: Wait a bit for metrics to be generated	COMMENT
LOW⚡	tests/ui_tests/test_metrics_display.js	58	// Step 4: Go to metrics page	COMMENT
LOW⚡	tests/ui_tests/test_metrics_display.js	63	// Step 5: Check what's on the page (with error handling)	COMMENT
LOW	tests/ui_tests/DEBUG_research_submit_debug.js	49	// Step 1: Login	COMMENT
LOW	tests/ui_tests/DEBUG_research_submit_debug.js	73	// Step 2: Wait for form to load	COMMENT
LOW	tests/ui_tests/DEBUG_research_submit_debug.js	98	// Step 3: Fill the form	COMMENT
LOW	tests/ui_tests/DEBUG_research_submit_debug.js	148	// Step 4: Check form values	COMMENT
LOW	tests/ui_tests/DEBUG_research_submit_debug.js	166	// Step 5: Submit the form	COMMENT
LOW⚡	tests/ui_tests/test_research_search_analysis.js	42	// Step 1: Authentication	COMMENT
LOW⚡	tests/ui_tests/test_research_search_analysis.js	47	// Step 2: Navigate to research page	COMMENT
LOW	tests/ui_tests/test_research_search_analysis.js	58	// Step 3: Fill in research question	COMMENT
LOW	tests/ui_tests/test_research_search_analysis.js	172	// Step 4: Submit research	COMMENT
65 more matches not shown…

Hallucination Indicators18 hits · 200 pts

Severity	File	Line	Snippet	Context
CRITICAL⚡	tests/security/test_file_integrity_manager_coverage.py	927	session.query.return_value.filter_by.return_value.order_by.return_value.limit.assert_called()	CODE
CRITICAL	tests/js/deletion/delete-modules.test.js	115	const deleteCall = window.api.fetchWithErrorHandling.mock.calls.find(	CODE
CRITICAL	tests/research_library/zotero/test_client.py	420	assert client.session.get.call_args.kwargs.get("allow_redirects") is False	CODE
CRITICAL	…s/research_library/routes/test_rag_indexing_helpers.py	185	db.query.return_value.filter_by.return_value.update.assert_called_once()	CODE
CRITICAL	tests/web/auth/test_cleanup_middleware.py	332	mock_db_session.query.return_value.filter_by.return_value.limit.assert_called_with(	CODE
CRITICAL	tests/web/routes/test_history_routes_coverage.py	252	chain.group_by.return_value.order_by.return_value.limit.assert_called_with(	CODE
CRITICAL	tests/web/routes/test_history_routes_coverage.py	255	chain.group_by.return_value.order_by.return_value.limit.return_value.offset.assert_called_with(	CODE
CRITICAL	tests/web/routes/test_history_routes_coverage.py	275	chain.group_by.return_value.order_by.return_value.limit.assert_called_with(	CODE
CRITICAL	tests/web/routes/test_settings_routes_rate_limiting.py	171	session.query.return_value.filter_by.return_value.delete.assert_called_once()	CODE
CRITICAL⚡	tests/web/routes/test_settings_routes_rate_limiting.py	197	session.query.return_value.filter.return_value.delete.assert_called_once()	CODE
CRITICAL	tests/web/routes/test_settings_routes_rate_limiting.py	208	session.query.return_value.filter.return_value.delete.assert_called_once()	CODE
CRITICAL	tests/news/test_rating_storage_extended.py	529	mock_query.filter_by.return_value.order_by.return_value.limit.assert_called_with(	CODE
CRITICAL⚡	tests/news/test_folder_manager_behavior.py	268	session.query.return_value.filter_by.return_value.update.assert_called()	CODE
CRITICAL⚡	tests/news/test_folder_manager_behavior.py	277	session.query.return_value.filter_by.return_value.update.assert_called()	CODE
CRITICAL	tests/news/test_folder_manager_extended.py	255	mock_session.query.return_value.filter_by.return_value.update.assert_called_once_with(	CODE
CRITICAL	tests/news/test_folder_manager_extended.py	271	mock_session.query.return_value.filter_by.return_value.update.assert_called_once_with(	CODE
CRITICAL	tests/news/rating_system/test_storage.py	373	mock_query.order_by.return_value.limit.return_value.offset.assert_called_once_with(	CODE
CRITICAL	.github/workflows/welcome-first-time.yml	59	const opts = github.rest.issues.listForRepo.endpoint.merge({	CODE

AI Slop Vocabulary79 hits · 183 pts

Severity	File	Line	Snippet	Context
MEDIUM	tests/test_api_settings_e2e.py	80	"""Test detailed_research with comprehensive settings.	STRING
MEDIUM	tests/test_openai_api_key_e2e.py	247	# diagnose=False: this e2e harness passes args.api_key and	STRING
MEDIUM	tests/run_all_tests.py	593	# Legacy comprehensive testing - runs some tests multiple times (< 15min)	COMMENT
MEDIUM	tests/database/test_sqlcipher_utils.py	1243	# robust if that min_value is ever raised.	COMMENT
MEDIUM	…earch_system/filters/test_followup_relevance_filter.py	349	assert call_args.count("A") < 200 # Definitely truncated from original	CODE
MEDIUM	…_system/strategies/test_topic_organization_strategy.py	783	"""Format topic findings creates comprehensive output."""	STRING
LOW	…ed_search_system/questions/test_browsecomp_question.py	692	# Should not raise, just return False	COMMENT
MEDIUM	…_system/questions/test_flexible_browsecomp_question.py	257	assert call_args.count("A") < 500 # Definitely truncated from original	CODE
MEDIUM	tests/infrastructure_tests/test_urls_js.py	39	# More robust extraction pattern that handles multiline and comments	COMMENT
LOW	tests/content_fetcher/test_html_content_extraction.py	155	# Should not crash, just return minimal/empty output	COMMENT
LOW⚡	tests/security/test_safe_requests_hook.py	224	# Should not raise, just return True (let other tools handle syntax)	COMMENT
MEDIUM⚡	tests/security/test_url_validator_extended.py	96	# is_safe_url -- comprehensive scheme / option / pattern tests	COMMENT
MEDIUM	tests/security/test_safe_requests_retries.py	186	# 30s band absorbs clock jitter and test-harness latency.	COMMENT
LOW	tests/research_library/test_utils.py	457	# Should not raise an error, just return False	COMMENT
LOW	…esearch_library/downloaders/test_biorxiv_downloader.py	70	# Should not raise, just return False	COMMENT
MEDIUM	tests/research_library/routes/test_rag_routes.py	2558	# Create comprehensive mock for SettingsManager	COMMENT
MEDIUM	tests/web/routes/test_research_routes.py	365	# call (not a positional index) so the guard stays robust if queries	COMMENT
LOW⚡	tests/web/routes/test_settings_policy_validators.py	34	# Should simply return (not raise) for any well-formed input.	COMMENT
MEDIUM	tests/error_handling/test_error_categorization.py	301	"""Tests for comprehensive error analysis."""	STRING
MEDIUM	tests/ui_tests/run_api_key_test.sh	38	# Run the comprehensive test	COMMENT
MEDIUM	tests/ui_tests/test_register_full_flow.js	350	// Uses AuthHelper for robust CI-compatible registration with proper timeouts	COMMENT
MEDIUM	tests/ui_tests/test_register_full_flow.js	372	// Use AuthHelper which has robust CI-compatible registration logic	COMMENT
MEDIUM	tests/ui_tests/test_checkbox_settings.js	342	// Toggle checkbox using robust method	COMMENT
MEDIUM	tests/ui_tests/test_checkbox_settings.js	384	// Toggle using robust method	COMMENT
MEDIUM	tests/ui_tests/test_checkbox_settings.js	485	// Toggle the checkbox using robust method	COMMENT
MEDIUM	tests/ui_tests/test_research_submit.js	88	// Submit the form with robust retry logic	COMMENT
LOW⚡	tests/news/test_card_factory_extended.py	777	# This should not raise, just return None	COMMENT
LOW	…citation_handlers/test_precision_extraction_handler.py	817	# Should just return the LLM response without extraction modifications	COMMENT
MEDIUM⚡	tests/document_loaders/test_loader_registry_coverage.py	314	# get_loader_for_path - comprehensive coverage	COMMENT
MEDIUM	tests/pdf_tests/test_file_validator.py	242	"""Tests for validate_upload comprehensive method."""	STRING
MEDIUM	tests/health_check/test_endpoints_health.py	67	"""Run comprehensive health check and print summary"""	STRING
LOW⚡	…ch_engines/rate_limiting/test_tracker_quality_stats.py	512	# Should not raise, just return early	COMMENT
MEDIUM	…web_search_engines/engines/test_search_engine_sofya.py	530	# distinct class objects; only `.value` (or `.name`) is robust.	COMMENT
MEDIUM	examples/optimization/strategy_benchmark_plan.py	141	num_examples=NUM_EXAMPLES, # Use 500 examples for robust evaluation	CODE
MEDIUM	examples/optimization/strategy_benchmark_plan.py	185	num_examples=NUM_EXAMPLES, # Use 500 examples for robust evaluation	CODE
MEDIUM	examples/optimization/strategy_benchmark_plan.py	229	num_examples=NUM_EXAMPLES, # Use 500 examples for robust evaluation	CODE
MEDIUM	examples/optimization/strategy_benchmark_plan.py	274	num_examples=NUM_EXAMPLES, # Use 500 examples for robust evaluation	CODE
LOW	examples/api_usage/simple_client_example.py	37	# Now just use it - no more CSRF hassles!	COMMENT
MEDIUM	…es/api_usage/programmatic/advanced_features_example.py	54	# Generate a comprehensive report	STRING
MEDIUM	…/api_usage/programmatic/simple_programmatic_example.py	75	# Generate a comprehensive report	COMMENT
MEDIUM	…pi_usage/programmatic/api_public_contract_guardrail.py	32	# DO NOT MODIFY this function — it is the test harness for the guardrail	COMMENT
MEDIUM	examples/benchmarks/claude_grading/run_benchmark.sh	26	# Use a long timeout for comprehensive benchmarks	COMMENT
MEDIUM	.github/workflows/ai-code-reviewer.yml	144	# spaces — model ids shouldn't have either, but this is robust.)	COMMENT
MEDIUM	.github/workflows/file-whitelist-check.yml	2	# Enhanced security checks with comprehensive file type detection	COMMENT
MEDIUM	.github/workflows/gitleaks.yml	37	fetch-depth: 0 # Fetch full history for comprehensive secret scanning	CODE
MEDIUM	.github/workflows/playwright-webkit-tests.yml	154	# - mobile-ui-audit: comprehensive mobile UI quality checks	COMMENT
MEDIUM	.github/workflows/playwright-webkit-tests.yml	324	# - mobile-ui-audit: comprehensive mobile UI quality checks	COMMENT
MEDIUM	.github/scripts/file-whitelist-check.sh	4	# Enhanced security checks with comprehensive file type detection	COMMENT
MEDIUM	.github/scripts/file-whitelist-check.sh	57	# Use a more robust approach that handles edge cases	COMMENT
MEDIUM	src/local_deep_research/report_generator.py	422	# Section-level prompt - more comprehensive	STRING
MEDIUM	src/local_deep_research/search_system.py	62	strategy_name: str = "source-based", # Default to comprehensive research strategy	CODE
MEDIUM	…ced_search_system/filters/journal_reputation_filter.py	93	# controls — the comprehensive pattern audited in log_sanitizer,	COMMENT
MEDIUM	…earch_system/strategies/topic_organization_strategy.py	1675	# Part 2: Generate comprehensive summary based on the topic sections	COMMENT
MEDIUM	…em/strategies/followup/enhanced_contextual_followup.py	69	# Build comprehensive context	COMMENT
MEDIUM	…research/advanced_search_system/findings/repository.py	275	prompt = f"""Use IEEE style citations [1], [2], etc. Never make up your own citations. Synthesize the follow	CODE
LOW	src/local_deep_research/security/url_builder.py	213	# If parsing fails, just return generic mask	COMMENT
MEDIUM	src/local_deep_research/security/security_headers.py	159	"""Add comprehensive security headers to Flask response.	STRING
MEDIUM	…earch/research_library/downloaders/semantic_scholar.py	101	# Use urlparse for more robust URL handling (handles query strings, fragments)	COMMENT
MEDIUM	…deep_research/research_library/downloaders/openalex.py	104	# Use urlparse for more robust URL handling (handles query strings, fragments)	COMMENT
LOW	…_deep_research/research_library/zotero/sync_service.py	1125	# document just add the collection link — never clobber the user's	COMMENT
19 more matches not shown…

Magic Placeholder Names27 hits · 158 pts

Severity	File	Line	Snippet	Context
HIGH	.gitleaks.toml	212	'''your-api-key-here''',	STRING
HIGH⚡	docker-compose.yml	91	# - LDR_LLM_OPENAI_API_KEY=<your-api-key> # Lock OpenAI API key	COMMENT
HIGH⚡	docker-compose.yml	92	# - LDR_LLM_ANTHROPIC_API_KEY=<your-api-key> # Lock Anthropic API key	COMMENT
HIGH⚡	docker-compose.yml	102	# - LDR_LLM_OPENAI_ENDPOINT_API_KEY=<your-api-key>	COMMENT
HIGH⚡	docker-compose.yml	111	# - LDR_LLM_OPENAI_ENDPOINT_API_KEY=<your-api-key>	COMMENT
HIGH	tests/test_openai_api_key_e2e.py	18	export LDR_LLM_OPENAI_API_KEY=your_api_key	STRING
HIGH	docs/faq.md	359	export LDR_LLM_OPENAI_ENDPOINT_API_KEY="<your-api-key>"	CODE
HIGH	docs/faq.md	370	- LDR_LLM_OPENAI_ENDPOINT_API_KEY=<your-api-key>	CODE
HIGH	docs/docker-compose-guide.md	140	- LDR_LLM_OPENAI_ENDPOINT_API_KEY=<your-api-key>	CODE
HIGH	docs/troubleshooting-openai-api-key.md	19	export OPENAI_API_KEY=sk-your-api-key	CODE
HIGH	docs/troubleshooting-openai-api-key.md	42	export OPENAI_API_KEY=sk-your-api-key	CODE
HIGH	docs/troubleshooting-openai-api-key.md	54	settings_manager.set_setting("llm.openai.api_key", "sk-your-api-key")	CODE
HIGH	docs/troubleshooting-openai-api-key.md	74	-H "Authorization: Bearer YOUR_API_KEY"	CODE
HIGH	docs/troubleshooting-openai-api-key.md	218	settings_manager.set_setting("llm.openai.api_key", "your-api-key")	CODE
HIGH	docs/env_configuration.md	75	export LDR_LLM_OPENAI_ENDPOINT_API_KEY="<your-api-key>"	CODE
HIGH	docs/env_configuration.md	89	- LDR_LLM_OPENAI_ENDPOINT_API_KEY=<your-api-key>	CODE
HIGH	docs/env_configuration.md	105	export LDR_LLM_OPENAI_ENDPOINT_API_KEY="<your-api-key>"	CODE
HIGH	docs/env_configuration.md	115	-e LDR_LLM_OPENAI_API_KEY=your-api-key-here \	CODE
HIGH	docs/env_configuration.md	153	export LDR_LLM_ANTHROPIC_API_KEY=your-api-key-here	CODE
HIGH	docs/env_configuration.md	156	set LDR_LLM_ANTHROPIC_API_KEY=your-api-key-here	CODE
HIGH	examples/optimization/README.md	47	python update_llm_config.py --model "google/gemini-2.0-flash" --provider "openai_endpoint" --endpoint "https://openrou	CODE
HIGH	examples/optimization/README.md	52	python run_gemini_benchmark.py --api-key "your-api-key" --examples 10	CODE
HIGH	examples/optimization/update_llm_config.py	14	pdm run python examples/optimization/update_llm_config.py --model "google/gemini-2.0-flash" --provider "openai_endpo	STRING
HIGH	examples/benchmarks/run_gemini_benchmark.py	13	pdm run python examples/benchmarks/run_gemini_benchmark.py --api-key YOUR_API_KEY	STRING
HIGH⚡	…deep_research/web_search_engines/search_engine_base.py	45	"YOUR_API_KEY",	CODE
HIGH⚡	…deep_research/web_search_engines/search_engine_base.py	47	"your_api_key",	CODE
HIGH⚡	…deep_research/web_search_engines/search_engine_base.py	48	"your-api-key",	CODE

Modern Structural Boilerplate98 hits · 98 pts

Severity	File	Line	Snippet	Context
LOW	src/local_deep_research/__init__.py	15	__all__ = [	CODE
LOW	src/local_deep_research/metrics/__init__.py	6	__all__ = [	CODE
LOW	src/local_deep_research/metrics/pricing/__init__.py	12	__all__ = ["CostCalculator", "PricingCache", "PricingFetcher"]	CODE
LOW	src/local_deep_research/settings/env_settings.py	376	__all__ = [	CODE
LOW	src/local_deep_research/settings/__init__.py	18	__all__ = [	CODE
LOW	src/local_deep_research/settings/env_registry.py	147	__all__ = [	CODE
LOW	src/local_deep_research/settings/manager.py	1255	def update_db_version(self, commit: bool = True) -> None:	CODE
LOW	…cal_deep_research/settings/env_definitions/__init__.py	27	__all__ = [	CODE
LOW	src/local_deep_research/database/sqlcipher_utils.py	216	def set_sqlcipher_key_from_hex(cursor_or_conn: Any, hex_key: str) -> None:	CODE
LOW	src/local_deep_research/database/models/__init__.py	102	__all__ = [	CODE
LOW	src/local_deep_research/database/models/base.py	14	__all__ = ["Base"]	CODE
LOW	src/local_deep_research/database/backup/__init__.py	12	__all__ = [	CODE
LOW	…local_deep_research/advanced_search_system/__init__.py	7	__all__ = []	CODE
LOW	…research/advanced_search_system/candidates/__init__.py	5	__all__ = ["Candidate"]	CODE
LOW	…ep_research/advanced_search_system/filters/__init__.py	8	__all__ = ["CrossEngineFilter"]	CODE
LOW	…esearch/advanced_search_system/tools/fetch/__init__.py	414	__all__ = ["FETCH_MODES", "build_fetch_tool"]	CODE
LOW	…p_research/advanced_search_system/evidence/__init__.py	6	__all__ = [	CODE
LOW	…esearch/advanced_search_system/constraints/__init__.py	6	__all__ = ["Constraint", "ConstraintAnalyzer", "ConstraintType"]	CODE
LOW	…earch/advanced_search_system/summarization/__init__.py	11	__all__ = [	CODE
LOW	…research/advanced_search_system/strategies/__init__.py	7	__all__ = [	CODE
LOW	…advanced_search_system/strategies/followup/__init__.py	10	__all__ = ["EnhancedContextualFollowUpStrategy"]	CODE
LOW	…vanced_search_system/candidate_exploration/__init__.py	15	__all__ = [	CODE
LOW	…search/advanced_search_system/repositories/__init__.py	7	__all__ = ["FindingsRepository"]	CODE
LOW	…deep_research/advanced_search_system/findings/topic.py	41	def update_lead_source(self, new_lead: Dict[str, Any]) -> None:	CODE
LOW	…deep_research/advanced_search_system/findings/topic.py	100	def set_parent_child(self, parent_id: str, child_id: str) -> None:	CODE
LOW	…_research/advanced_search_system/questions/__init__.py	10	__all__ = [	CODE
LOW	…/advanced_search_system/questions/followup/__init__.py	11	__all__ = [	CODE
LOW	src/local_deep_research/llm/__init__.py	12	__all__ = [	CODE
LOW	src/local_deep_research/llm/providers/__init__.py	10	__all__ = [	CODE
LOW	src/local_deep_research/embeddings/__init__.py	29	__all__ = [	CODE
LOW	…c/local_deep_research/embeddings/providers/__init__.py	5	__all__ = ["BaseEmbeddingProvider"]	CODE
LOW	…earch/embeddings/providers/implementations/__init__.py	7	__all__ = [	CODE
LOW	…c/local_deep_research/embeddings/splitters/__init__.py	9	__all__ = ["get_text_splitter", "VALID_SPLITTER_TYPES"]	CODE
LOW	src/local_deep_research/chat/__init__.py	15	__all__ = [	CODE
LOW	src/local_deep_research/content_fetcher/__init__.py	19	__all__ = ["ContentFetcher", "URLClassifier", "URLType"]	CODE
LOW	src/local_deep_research/security/__init__.py	70	__all__ = [	CODE
LOW	src/local_deep_research/security/egress/audit_hook.py	73	def set_active_context(ctx) -> None:	CODE
LOW	src/local_deep_research/security/egress/__init__.py	39	__all__ = [	CODE
LOW	…ocal_deep_research/security/file_integrity/__init__.py	37	__all__ = [	CODE
LOW	…_research/security/file_integrity/integrity_manager.py	249	def update_checksum(self, file_path: Path) -> None:	CODE
LOW	…research/security/file_integrity/verifiers/__init__.py	5	__all__ = ["FAISSIndexVerifier"]	CODE
LOW	src/local_deep_research/research_library/__init__.py	20	__all__ = [	CODE
LOW	…al_deep_research/research_library/deletion/__init__.py	21	__all__ = [	CODE
LOW	…p_research/research_library/deletion/utils/__init__.py	5	__all__ = ["CascadeHelper"]	CODE
LOW	…_research/research_library/deletion/routes/__init__.py	5	__all__ = ["delete_bp"]	CODE
LOW	…esearch/research_library/deletion/services/__init__.py	7	__all__ = [	CODE
LOW	…deep_research/research_library/downloaders/__init__.py	19	__all__ = [	CODE
LOW	…ch/research_library/downloaders/extraction/__init__.py	21	__all__ = [	CODE
LOW	…ocal_deep_research/research_library/zotero/__init__.py	16	__all__ = [	CODE
LOW	…_deep_research/research_library/zotero/sync_service.py	345	def _set_progress(self, **fields) -> None:	CODE
LOW	…ocal_deep_research/research_library/search/__init__.py	12	__all__ = ["search_bp", "ResearchHistoryIndexer"]	CODE
LOW	…ep_research/research_library/search/routes/__init__.py	3	__all__ = ["search_bp"]	CODE
LOW	…_research/research_library/search/services/__init__.py	6	__all__ = ["ResearchHistoryIndexer", "auto_convert_research"]	CODE
LOW	src/local_deep_research/exporters/__init__.py	45	__all__ = [	CODE
LOW	src/local_deep_research/web/auth/__init__.py	9	__all__ = ["auth_bp", "current_user", "login_required"]	CODE
LOW	src/local_deep_research/web/queue/__init__.py	6	__all__ = ["QueueManager", "QueueProcessorV2"]	CODE
LOW	src/local_deep_research/web/themes/__init__.py	233	__all__ = [	CODE
LOW	src/local_deep_research/journal_quality/downloader.py	99	def _set_source_state(key: str, **updates) -> None:	CODE
LOW	…deep_research/journal_quality/data_sources/__init__.py	45	__all__ = ["DataSource", "ALL_SOURCES", "get_source"]	CODE
LOW	src/local_deep_research/scheduler/background.py	196	def set_app(self, app) -> None:	CODE
38 more matches not shown…

Cross-Language Confusion14 hits · 82 pts

Severity	File	Line	Snippet	Context
HIGH	.pre-commit-hooks/recommend-pr-description-update.py	64	The ``currentBranch`` key is a single object (or null) — not an array.	STRING
HIGH⚡	tests/config/test_thread_settings_high_value.py	128	# embeddings.openai.dimensions defaults to JSON null, then	COMMENT
HIGH⚡	…search_library/routes/test_rag_routes_gaps_coverage.py	929	# {"agent_enabled": null} → stored True (available), serialized True.	COMMENT
HIGH⚡	tests/web/warning_checks/test_hardware.py	319	config_file.write_text('{"port": null}', encoding="utf-8")	CODE
HIGH	tests/web/services/test_settings_manager_extended.py	692	ctx.push()	CODE
HIGH	tests/news/test_library_sweep.py	787	research orphan (research_id set, text not null, NO default-library link)	STRING
HIGH⚡	tests/news/test_topic_generator_coverage.py	113	result = self._run_with_llm_content('[123, "Valid", null, true]')	CODE
HIGH	…s/benchmarks/web_api/test_benchmark_export_metadata.py	140	"""A row with all new columns NULL must serialize as JSON null, not	STRING
HIGH	src/local_deep_research/config/thread_settings.py	25	# (e.g. embeddings.openai.dimensions, which defaults to JSON null) into the	COMMENT
HIGH	src/local_deep_research/security/url_validator.py	500	if (!url \|\| typeof url !== 'string') {	CODE
HIGH	src/local_deep_research/security/url_validator.py	531	if (trustedDomains.length > 0 && parsed.hostname) {	CODE
HIGH	src/local_deep_research/security/url_validator.py	552	if (!url) return null;	CODE
HIGH	src/local_deep_research/security/url_validator.py	556	return null;	CODE
HIGH	src/local_deep_research/security/url_validator.py	572	return null;	CODE

Fake / Example Data77 hits · 78 pts

Severity	File	Line	Snippet	Context
LOW	tests/test_search_engines_enhanced.py	167	Mock(name="John Doe"),	CODE
LOW⚡	tests/mock_fixtures.py	122	"authors": [{"name": "John Doe"}, {"name": "Jane Smith"}],	CODE
LOW⚡	tests/database/test_credential_store_behavior.py	340	special_user = "user@example.com"	CODE
LOW	tests/database/backup/test_backup_service.py	3274	"user@example.com", # Email format	CODE
LOW⚡	…/advanced_search_system/evidence/test_base_evidence.py	120	metadata = {"author": "John Doe", "publication": "Science Journal"}	CODE
LOW⚡	…/advanced_search_system/evidence/test_base_evidence.py	129	assert evidence.metadata["author"] == "John Doe"	CODE
LOW	…ystem/questions/followup/test_llm_followup_question.py	240	assert "placeholder" in docstring.lower() or "NOTE" in docstring	CODE
LOW⚡	tests/security/test_csrf_protection.py	87	"csrf_token": "invalid-fake-token-12345",	CODE
LOW	tests/js/utils/form-validation.test.js	271	expect(emailLike('user@example.com')).toBeNull();	CODE
LOW	…/research_library/downloaders/test_arxiv_downloader.py	254	assert "John Doe" in metadata	CODE
LOW	…esearch_library/downloaders/test_metadata_extractor.py	80	"author": {"name": "Jane Doe"},	CODE
LOW	…esearch_library/downloaders/test_metadata_extractor.py	90	assert "Jane Doe" in result	CODE
LOW⚡	…rary/downloaders/test_html_downloader_deep_coverage.py	425	<meta name="author" content="John Doe">	CODE
LOW⚡	…rary/downloaders/test_html_downloader_deep_coverage.py	434	assert meta["author"] == "John Doe"	STRING
LOW⚡	…ibrary/downloaders/test_metadata_extractor_expanded.py	157	item = {"headline": "Story", "author": "Jane Doe"}	CODE
LOW⚡	…ibrary/downloaders/test_metadata_extractor_expanded.py	160	assert "Jane Doe" in text	CODE
LOW	tests/search_engines/conftest.py	138	"authors": ["John Doe", "Jane Smith"],	CODE
LOW	…sts/search_engines/test_search_engine_stackexchange.py	345	"display_name": "John Doe",	CODE
LOW	…sts/search_engines/test_search_engine_stackexchange.py	375	assert previews[0]["author"] == "John Doe"	CODE
LOW⚡	tests/search_engines/test_search_engine_retriever.py	184	"author": "John Doe",	CODE
LOW⚡	tests/search_engines/test_search_engine_retriever.py	194	assert result["author"] == "John Doe"	CODE
LOW	tests/search_engines/test_search_engine_paperless.py	307	"correspondent_name": "Acme Corp",	CODE
LOW	tests/search_engines/test_search_engine_paperless.py	321	assert preview["author"] == "Acme Corp"	CODE
LOW	tests/search_engines/test_search_engine_arxiv.py	106	mock_result.authors = [Mock(name="John Doe"), Mock(name="Jane Smith")]	CODE
LOW⚡	tests/search_engines/test_search_engine_zenodo.py	132	{"name": "Jane Doe"},	CODE
LOW⚡	tests/search_engines/test_search_engine_zenodo.py	136	assert result == ["John Smith", "Jane Doe"]	CODE
LOW	tests/ui_tests/test_loading_feedback_ci.js	75	'[class*="placeholder"], ' +	CODE
LOW	tests/ui_tests/test_loading_feedback_ci.js	88	if (cssText.includes('skeleton') \|\| cssText.includes('placeholder') \|\|	CODE
LOW	tests/ui_tests/test_keyboard_accessibility_ci.js	593	const hasPlaceholder = input.hasAttribute('placeholder');	CODE
LOW	tests/ui_tests/playwright/tests/mobile-ui-audit.spec.js	87	text: (el.textContent \|\| el.getAttribute('placeholder') \|\| '').trim().slice(0, 30),	CODE
LOW	tests/ui_tests/playwright/tests/mobile-ui-audit.spec.js	101	text: (el.textContent \|\| el.getAttribute('placeholder') \|\| '').trim().slice(0, 30),	CODE
LOW	tests/ui_tests/playwright/tests/mobile-ui-audit.spec.js	191	const hasPlaceholder = input.getAttribute('placeholder');	CODE
LOW	tests/ui_tests/playwright/tests/mobile-ui-audit.spec.js	304	placeholder: textarea.getAttribute('placeholder'),	CODE
LOW⚡	tests/utilities/test_openalex_enrichment.py	305	results, email="researcher@example.org"	CODE
LOW⚡	tests/utilities/test_openalex_enrichment.py	308	assert call.kwargs["params"]["mailto"] == "researcher@example.org"	CODE
LOW⚡	tests/utilities/test_openalex_enrichment.py	309	assert "researcher@example.org" in call.kwargs["headers"]["User-Agent"]	CODE
LOW	tests/utilities/test_citation_normalizer.py	79	result = _parse_authors_list(["John Smith", "Jane Doe"])	CODE
LOW	tests/news/test_base_recommender.py	4114	user_id = "user@example.com"	CODE
LOW⚡	tests/news/test_preference_storage.py	868	"user_id": "user@example.com",	CODE
LOW⚡	tests/news/test_preference_storage.py	875	result = storage.get_user_preferences("user@example.com")	CODE
LOW⚡	tests/news/test_preference_storage.py	877	assert result["user_id"] == "user@example.com"	CODE
LOW⚡	tests/news/test_base_card_extended.py	879	"people": ["John Doe", "Jane Smith"],	CODE
LOW⚡	tests/news/test_base_card_extended.py	885	assert "John Doe" in card.entities["people"]	CODE
LOW⚡	tests/llm_providers/test_custom_openai_endpoint.py	163	assert call_kwargs["api_key"] == "dummy-key-for-models-list"	CODE
LOW	tests/llm_providers/test_custom_openai_endpoint.py	91	assert call_kwargs["api_key"] == "dummy-key-for-models-list"	CODE
LOW⚡	tests/llm_providers/test_openai_base_coverage.py	90	# dummy-key was passed	COMMENT
LOW	tests/llm_providers/test_openai_base_coverage.py	6	- create_llm() uses 'dummy-key' when api_key_setting is None (local providers)	STRING
LOW	tests/llm_providers/test_openai_base_coverage.py	9	- _create_llm_instance() uses dummy-key by default	STRING
LOW⚡	…lm_providers/implementations/test_lmstudio_provider.py	310	"""Falls back to parent's dummy-key path when no key is configured."""	STRING
LOW	…lm_providers/implementations/test_lmstudio_provider.py	327	assert call_kwargs["api_key"] == "dummy-key-for-models-list"	CODE
LOW⚡	tests/hooks/test_check_author_identity.py	76	assert not mod._is_noreply("user@example.com")	STRING
LOW	tests/document_loaders/test_upload_integration.py	218	assert "John Doe" in extracted or "name" in extracted	STRING
LOW⚡	…_engines/engines/test_search_engine_serper_coverage.py	100	"attributes": {"Author": "Jane Doe"},	CODE
LOW	…_engines/engines/test_search_engine_serper_coverage.py	111	assert p["attributes"] == {"Author": "Jane Doe"}	CODE
LOW	…_search_engines/engines/test_search_engine_openalex.py	164	{"author": {"display_name": "John Doe"}},	CODE
LOW	…_search_engines/engines/test_search_engine_openalex.py	189	assert "John Doe" in previews[0]["authors"]	CODE
LOW	…_search_engines/engines/test_search_engine_openalex.py	492	"authors": "John Doe",	CODE
LOW	…_search_engines/engines/test_search_engine_openalex.py	506	assert results[0]["metadata"]["authors"] == "John Doe"	CODE
LOW	…engines/engines/test_search_engine_semantic_scholar.py	504	"authors": [{"name": "John Doe"}],	CODE
LOW	…_search_engines/engines/test_search_engine_guardian.py	259	"byline": "John Doe",	CODE
17 more matches not shown…

AI Structural Patterns60 hits · 52 pts

Severity	File	Line	Context
LOW	tests/web/routes/test_research_routes_deep_coverage.py	48	CODE
LOW	tests/web/routes/_settings_route_helpers.py	27	CODE
LOW	tests/web/routes/test_settings_routes_deep_coverage2.py	56	CODE
LOW	tests/web/routes/test_context_overflow_coverage.py	168	CODE
LOW	tests/web/routes/test_research_routes_extra_coverage.py	50	CODE
LOW	tests/web/routes/test_context_overflow_logic.py	267	CODE
LOW	tests/web/services/test_settings_manager_extended.py	24	CODE
LOW	tests/web/services/test_settings_manager.py	21	CODE
LOW	tests/news/test_folder_manager_behavior.py	18	CODE
LOW	tests/web_search_engines/engines/test_arxiv_coverage.py	36	CODE
LOW	…s/web_search_engines/engines/test_guardian_coverage.py	50	CODE
LOW	…mples/benchmarks/browsecomp/run_browsecomp_fixed_v2.py	81	CODE
LOW	src/local_deep_research/search_system.py	58	CODE
LOW	…search_system/strategies/focused_iteration_strategy.py	54	CODE
LOW	…earch_system/strategies/topic_organization_strategy.py	25	CODE
LOW	…nced_search_system/strategies/source_based_strategy.py	60	CODE
LOW	…earch/research_library/services/library_rag_service.py	106	CODE
LOW	…_research/research_library/services/library_service.py	265	CODE
LOW	src/local_deep_research/news/api.py	1038	CODE
LOW	…/local_deep_research/benchmarks/benchmark_functions.py	25	CODE
LOW	…/local_deep_research/benchmarks/benchmark_functions.py	112	CODE
LOW	…/local_deep_research/benchmarks/benchmark_functions.py	199	CODE
LOW	src/local_deep_research/benchmarks/runners.py	41	CODE
LOW	src/local_deep_research/benchmarks/optimization/api.py	15	CODE
LOW	…p_research/benchmarks/optimization/optuna_optimizer.py	1068	CODE
LOW	…p_research/benchmarks/optimization/optuna_optimizer.py	98	CODE
LOW	src/local_deep_research/api/benchmark_functions.py	21	CODE
LOW	src/local_deep_research/api/benchmark_functions.py	75	CODE
LOW	src/local_deep_research/api/benchmark_functions.py	129	CODE
LOW	src/local_deep_research/api/research_functions.py	33	CODE
LOW	src/local_deep_research/api/research_functions.py	166	CODE
LOW	src/local_deep_research/api/research_functions.py	344	CODE
LOW	…p_research/web_search_engines/search_engine_factory.py	624	CODE
LOW	…deep_research/web_search_engines/search_engine_base.py	277	CODE
LOW	…web_search_engines/engines/search_engine_google_pse.py	24	CODE
LOW	…/web_search_engines/engines/search_engine_scaleserp.py	22	CODE
LOW	…search/web_search_engines/engines/search_engine_ddg.py	21	CODE
LOW	…rch/web_search_engines/engines/search_engine_mojeek.py	38	CODE
LOW	…ch/web_search_engines/engines/search_engine_serpapi.py	21	CODE
LOW	…rch/web_search_engines/engines/search_engine_tavily.py	22	CODE
LOW	…search/web_search_engines/engines/search_engine_exa.py	22	CODE
LOW	…rch/web_search_engines/engines/search_engine_pubmed.py	30	CODE
LOW	…_search_engines/engines/search_engine_stackexchange.py	57	CODE
LOW	…rch/web_search_engines/engines/search_engine_zenodo.py	34	CODE
LOW	…rch/web_search_engines/engines/search_engine_serper.py	28	CODE
LOW	…ch/web_search_engines/engines/search_engine_searxng.py	96	CODE
LOW	…h/web_search_engines/engines/search_engine_guardian.py	21	CODE
LOW	…arch/web_search_engines/engines/search_engine_brave.py	24	CODE
LOW	…arch/web_search_engines/engines/search_engine_arxiv.py	26	CODE
LOW	…h/web_search_engines/engines/search_engine_tinyfish.py	28	CODE
LOW	…eep_research/web_search_engines/engines/full_search.py	26	CODE
LOW	…h/web_search_engines/engines/search_engine_openalex.py	26	CODE
LOW	…rch/web_search_engines/engines/search_engine_github.py	32	CODE
LOW	…h/web_search_engines/engines/search_engine_nasa_ads.py	26	CODE
LOW	…arch/web_search_engines/engines/search_engine_sofya.py	48	CODE
LOW	…/web_search_engines/engines/search_engine_gutenberg.py	32	CODE
LOW	…arch_engines/engines/search_engine_semantic_scholar.py	31	CODE
LOW	…h/web_search_engines/engines/search_engine_wikinews.py	58	CODE
LOW	…_search_engines/engines/search_engine_elasticsearch.py	76	CODE
LOW	…/web_search_engines/engines/search_engine_paperless.py	46	CODE

Dead Code11 hits · 19 pts

Severity	File	Line	Context
MEDIUM	…ch_library/routes/test_rag_routes_indexing_coverage.py	228	CODE
MEDIUM	…search_library/routes/test_rag_routes_deep_coverage.py	1182	CODE
MEDIUM	…search_library/routes/test_rag_routes_deep_coverage.py	1209	CODE
MEDIUM	…search_library/routes/test_rag_routes_deep_coverage.py	1234	CODE
MEDIUM	tests/web/queue/test_queue_manager.py	35	CODE
MEDIUM	tests/web/routes/test_context_overflow_coverage.py	649	CODE
MEDIUM	tests/web/routes/test_context_overflow_coverage.py	873	CODE
MEDIUM	tests/web/routes/test_context_overflow_api_http.py	328	CODE
MEDIUM	tests/web/routes/test_context_overflow_api_http.py	476	CODE
MEDIUM	…rch_engines/engines/test_embedding_manager_coverage.py	481	CODE
MEDIUM	…rch_engines/engines/test_embedding_manager_coverage.py	626	CODE

Synthetic Comment Markers2 hits · 15 pts

Severity	File	Line	Snippet	Context
HIGH	tests/test_programmatic_custom_llm_retriever.py	76	# Using gemma3n:e4b as requested	COMMENT
HIGH	.github/workflows/release.yml	698	# 1. AI-generated narrative (model = vars.AI_MODEL). Fed the	COMMENT

Cross-Language Confusion (JS/TS)2 hits · 12 pts

Severity	File	Line	Snippet	Context
HIGH	tests/ui_tests/test_lib/test_results.js	203	print() {	CODE
HIGH	…cal_deep_research/web/static/js/components/settings.js	2698	* @return True if the content is valid.	COMMENT

Slop Phrases6 hits · 12 pts

Severity	File	Line	Snippet	Context
MEDIUM⚡	…tation_handlers/test_forced_answer_citation_handler.py	90	content = "I cannot provide a specific answer based on the sources."	CODE
MEDIUM	examples/optimization/example_quick_optimization.py	35	This is just for demonstration purposes.	STRING
MEDIUM	examples/optimization/example_quick_optimization.py	274	"\nNote: This is a simulation for demonstration purposes only. Real optimization"	CODE
MEDIUM	examples/optimization/multi_benchmark_simulation.py	176	"""Simulates Optuna optimizer for demonstration purposes."""	STRING
MEDIUM	examples/optimization/multi_benchmark_simulation.py	406	print("\nNote: This is a simulation for demonstration purposes only.")	CODE
MEDIUM	.github/workflows/codeql.yml	61	# If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how	COMMENT

Example Usage Blocks4 hits · 7 pts

Severity	File	Line	Snippet	Context
LOW⚡	docker-compose.gpu.override.yml	11	# Usage:	COMMENT
LOW	scripts/dev/restart_server.sh	4	# Usage:	COMMENT
LOW	.github/scripts/combine-ai-reviews.sh	13	# Usage:	COMMENT
LOW	src/local_deep_research/web/routes/route_registry.py	354	# Example usage	COMMENT

Overly Generic Function Names4 hits · 5 pts

Severity	File	Line	Snippet	Context
LOW	tests/security/test_env_vars_hook.py	120	def process_data(data):	CODE
LOW⚡	tests/utilities/test_thread_context.py	221	def my_function():	CODE
LOW	tests/utilities/test_db_utils.py	242	def my_function():	CODE
LOW⚡	tests/hooks/test_check_weak_tests.py	150	"def helper():\n assert True\n",	CODE