test: add 348 tests to improve non-UI coverage#3
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…y_storage - test_vocabulary_manager.py (60 tests): CRUD, import/export JSON/CSV, statistics, singleton, settings load/save, specialty/category filtering - test_recipient_manager.py (58 tests): CRUD, search FTS+fallback, CSV import, row mapping, address formatting, singleton isolation - test_key_storage.py (59 tests): Fernet encrypt/decrypt, salt lifecycle, legacy salt migration, machine ID, thread safety, provider listing All 177 tests pass; suite: 4277 passing, same 38 pre-existing Tkinter failures. Co-Authored-By: Paperclip <noreply@paperclip.ing>
…ding autosave Covers three critical untested paths identified in GOM-3 audit: - test_soap_generation_extended.py (35 tests): _prepare_soap_generation(), _postprocess_soap_result(), _validate_soap_output() ICD warning branches, create_soap_note_streaming(), create_soap_note_with_openai() - test_migration_manager_extended.py (36 tests): MigrationManager.migrate(), rollback(), get_applied_migrations(), get_pending_migrations(), _apply_migration(), _apply_migration_12(), run_migrations() - test_recording_autosave_manager.py (44 tests): full lifecycle (start/stop), recovery detection, get_recovery_info(), cleanup, _extract_audio_for_save(), thread safety All tests use mocked dependencies (no real AI calls, DB, or audio hardware). Co-Authored-By: Paperclip <noreply@paperclip.ing>
- test_exceptions.py (58 tests): full exception hierarchy and AIResult wrapper — success/failure factories, unwrap, bool, str, context, usage - test_timeout_config.py (38 tests): TimeoutConfig singleton, get_timeout, get_timeout_tuple, update_timeout, update_connect_timeout, reset_to_defaults, get_all_timeouts, settings integration, module-level convenience functions - test_audit_logger.py (49 tests): AuditEventType enum, singleton behaviour, _generate_session_hash, _redact_phi (PHI fields, nested dicts, length), log method (JSON output, timestamps, resource hashing, error truncation), log_api_key_operation, log_data_export, log_recording_access, log_security_event, audit_log convenience function, thread-safety Co-Authored-By: Paperclip <noreply@paperclip.ing>
…r_manager - test_sentry_config.py (43 tests): _scrub_data (PHI fields, nested dicts, long string truncation, list handling), _before_send (exception frame vars, breadcrumbs, extra/tags/user scrubbing), _before_send_transaction, init_sentry (no DSN, whitespace DSN, import error, init exception, env flags, PHI protection), _get_release_version (git SHA, fallback scenarios) - test_single_instance.py (28 tests): _get_lock_file_path (per-platform paths), _read_lock_file (valid, missing, invalid, whitespace), _write_lock_file (success, permission error), _remove_lock_file (exists, missing, OSError), _is_process_running (current PID, OSError), ensure_single_instance (first run, duplicate detection, stale lock cleanup, own PID, write failure) - test_data_folder_manager.py (21 tests): path properties (env_file, settings, vocabulary, database, config, logs, data), _ensure_folders_exist, migrate_existing_files (env file, no-overwrite, config folder), _migrate_from_bundle (macOS bundle migration, no-overwrite), singleton checks Co-Authored-By: Paperclip <noreply@paperclip.ing>
…rity_decorators, log_manager, analysis_storage, and text_processor - test_autosave_manager.py (87): register/unregister providers, start/stop lifecycle, perform_save hash detection + callbacks + disk I/O, _rotate_backups, load_latest fallback, clear_saves, get_save_info, settings provider filtering - test_base_provider_manager.py (55): concrete ProviderManager subclass tests, lazy provider init + caching, cache invalidation on settings change, get_provider_safe/test_connection_safe OperationResult wrapping, create_thread_safe_singleton thread-safety - test_security_decorators.py (42): rate_limited (allowed/blocked/identifier_arg), sanitize_inputs (string filtering, type passthrough, warning on change), require_api_key (missing/empty/invalid key), log_api_call (success/error logging), secure_api_call combined decorator - test_log_manager.py (26): _get_logging_settings defaults + merge + parse errors, LogManager init log level resolution + env override, setup_logging handler creation + module overrides, get_log_file_path/get_log_directory accessors - test_analysis_storage.py (63): save_medication/differential/compliance_analysis db delegation + error handling, get_analyses_for_recording, get/has per type, get_recent_* with limit, singleton reset - test_text_processor.py (25): initial state, clean_command_text (lowercase/strip/ punctuation), handle_text_command (all 12 known commands + unknown), capitalize_next flag, append_text_to_widget, delete_last_word Co-Authored-By: Paperclip <noreply@paperclip.ing>
Co-Authored-By: Paperclip <noreply@paperclip.ing>
… mocking) Co-Authored-By: Paperclip <noreply@paperclip.ing>
… RecordingSchema, QueueSchema, BatchSchema) Co-Authored-By: Paperclip <noreply@paperclip.ing>
…rocessingMixin pure logic Co-Authored-By: Paperclip <noreply@paperclip.ing>
…ts, QueueDatabaseSchema helpers) Co-Authored-By: Paperclip <noreply@paperclip.ing>
…s, completion) Co-Authored-By: Paperclip <noreply@paperclip.ing>
…singleton) Co-Authored-By: Paperclip <noreply@paperclip.ing>
…e, cancellation, status) Co-Authored-By: Paperclip <noreply@paperclip.ing>
…xception isolation Co-Authored-By: Paperclip <noreply@paperclip.ing>
…grity Co-Authored-By: Paperclip <noreply@paperclip.ing>
…URL getters, choice generators) Co-Authored-By: Paperclip <noreply@paperclip.ing>
…e index lookup) Co-Authored-By: Paperclip <noreply@paperclip.ing>
…tion, value validation) Co-Authored-By: Paperclip <noreply@paperclip.ing>
…singleton) Co-Authored-By: Paperclip <noreply@paperclip.ing>
…timed, RequestLogger) Co-Authored-By: Paperclip <noreply@paperclip.ing>
…aseTool validation) Co-Authored-By: Paperclip <noreply@paperclip.ing>
…on, query length, singleton) Co-Authored-By: Paperclip <noreply@paperclip.ing>
…s, enrich) and search_config Co-Authored-By: Paperclip <noreply@paperclip.ing>
…tribution, singletons) Co-Authored-By: Paperclip <noreply@paperclip.ing>
…en, StreamingSearchState) Co-Authored-By: Paperclip <noreply@paperclip.ing>
Covers SearchSyntaxParser (type/date/entity/score/exclude/phrase extraction, clean_query, full parse integration, singleton, convenience function) and all Pydantic models in rag/models.py (DocumentType, UploadStatus enums, DocumentMetadata, DocumentChunk, RAGDocument, EmbeddingRequest, VectorSearchQuery, HybridSearchResult, QueryExpansion.get_all_search_terms, RAGQueryRequest, TemporalInfo, RAGSettings, DocumentUploadRequest, DocumentUploadProgress). Co-Authored-By: Paperclip <noreply@paperclip.ing>
guidelines_models.py: covers all 8 enums (GuidelineSpecialty, GuidelineSource, GuidelineType, RecommendationClass, EvidenceLevel, ComplianceStatus, SectionType, GuidelineUploadStatus), 5 dataclasses (GuidelineReference, ComplianceItem, ComplianceResult, ConditionFinding, ConditionCompliance, ComplianceAnalysisResult), and Pydantic models (GuidelineMetadata, GuidelineChunk, GuidelineDocument, GuidelineSearchQuery, GuidelinesSettings, ComplianceCheckRequest, ComplianceCheckResponse). followup_detector.py: covers QueryIntent enum, FollowupResult.to_dict(), SemanticFollowupDetector class constants and all private methods (_compute_similarity, _detect_coreference, _check_topic_overlap, _check_followup_patterns, _calculate_confidence, _determine_intent), detect() integration, singleton, and convenience function. Co-Authored-By: Paperclip <noreply@paperclip.ing>
Covers RAGError (attributes, __str__ format with/without details, recoverable flag), all subclasses (EmbeddingError, VectorSearchError, GraphQueryError including long-query truncation, DocumentProcessingError, RAGConnectionError with credential-stripping, RAGConfigurationError with recoverable=False default, RateLimitError, CircuitBreakerOpenError), RAGErrorCodes constants, and helper functions (wrap_exception with __cause__ chaining, is_retriable_error for RAGError/OS/Timeout/message patterns, get_retry_delay with exponential backoff + cap at 60s + retry_after). Co-Authored-By: Paperclip <noreply@paperclip.ing>
Covers ExtractionResult defaults, _extract_recommendation_class (Class I/IIa/IIb/III, COR, standalone descriptors, case-insensitive), _extract_evidence_level (all LOE variants, parenthetical, colon format), _extract_section_type (warning/contraindication/monitoring/evidence/ rationale/default), extract() confidence calculation, and extract_batch(). Co-Authored-By: Paperclip <noreply@paperclip.ing>
Covers _cosine_similarity (identical, orthogonal, opposite, 45°, zero vector, mismatched lengths), _jaccard_similarity (identical, disjoint, half-overlap, subsets), _tokenize, rerank with MMR disabled/enabled, text-based fallback (Jaccard diversity), embedding-based MMR selection, calculate_diversity_score (single/empty/identical/disjoint/partial), and singleton helpers (get_mmr_reranker, reset, rerank_with_mmr). Co-Authored-By: Paperclip <noreply@paperclip.ing>
…try, and text processing Co-Authored-By: Paperclip <noreply@paperclip.ing>
…exporter, and STT failover Co-Authored-By: Paperclip <noreply@paperclip.ing>
… builder 2 tests marked xfail exposing Composition.subject List[Reference] bug in source. Co-Authored-By: Paperclip <noreply@paperclip.ing>
…nAgent pure-logic methods Co-Authored-By: Paperclip <noreply@paperclip.ing>
… factory Co-Authored-By: Paperclip <noreply@paperclip.ing>
Co-Authored-By: Paperclip <noreply@paperclip.ing>
Co-Authored-By: Paperclip <noreply@paperclip.ing>
…istry Co-Authored-By: Paperclip <noreply@paperclip.ing>
Co-Authored-By: Paperclip <noreply@paperclip.ing>
…Manager Co-Authored-By: Paperclip <noreply@paperclip.ing>
…thods Co-Authored-By: Paperclip <noreply@paperclip.ing>
…ic methods Co-Authored-By: Paperclip <noreply@paperclip.ing>
Co-Authored-By: Paperclip <noreply@paperclip.ing>
Co-Authored-By: Paperclip <noreply@paperclip.ing>
…ic methods Co-Authored-By: Paperclip <noreply@paperclip.ing>
…thods - test_error_handling.py (164 tests): sanitize_error_for_user, get_sanitized_error, OperationResult (success/failure/to_dict/unwrap/map), format_error_for_user, ErrorContext (capture/user_message/to_log_string/to_dict), handle_errors decorator (all 4 return types + CRITICAL re-raise), safe_execute - test_audit_logger.py (63 tests): AuditEventType enum values, _generate_session_hash (SHA-256 truncated to 12 chars, determinism, None path), _redact_phi (all 16 PHI field names, case-insensitive keys, nested dict recursion, non-string values) Co-Authored-By: Paperclip <noreply@paperclip.ing>
…ic methods - test_graph_data_provider.py (178 tests): EntityType.from_string (direct+fuzzy matching), GraphNode display_name/matches_search, GraphEdge display_type/ reliability_score/to_dict, RelationshipConfidenceCalculator.calculate_confidence/ merge_confidence/should_merge_relationships/merge_edges, GraphData node_count/ edge_count/get_node/get_edges_for_node/get_connected_nodes/filter_by_type/search - test_mcp_tool_wrapper_pure.py (81 tests): MCPToolWrapper.validate_args (required fields, type checking for string/number/boolean/array/object), _get_cache_key (MD5 determinism, sort_keys, non-serializable values) Co-Authored-By: Paperclip <noreply@paperclip.ing>
…_build_context - test_fallback_cache_provider.py (83 tests): FallbackCacheProvider init (healthy/ unhealthy primary), _get_provider with retry logic, get/set/get_batch/set_batch/ delete/clear/cleanup failover behavior, health_check, get_stats, close, concurrency - test_streaming_retriever_pure.py (44 tests): StreamingHybridRetriever._build_context with empty results, source numbering, chunk text, related entities truncation at 5, blank-line separators, exact output structure, multiple results ordering Co-Authored-By: Paperclip <noreply@paperclip.ing>
…ts mixin - tests/unit/test_analysis_panel_formatter.py: 180 tests for pure detection methods (_is_section_header, _detect_severity, _detect_confidence_level, _is_warning_line, _detect_warning_type, _is_red_flag, _is_recommendation) plus SeverityConfig dataclass and SEVERITY_COLORS/WARNING_COLORS constants - tests/unit/test_medication_prompts.py: 134 tests for all 7 prompt-building methods in MedicationPromptMixin, covering context injection, patient factor formatting, renal/hepatic sections, and de-prescribing triggers Co-Authored-By: Paperclip <noreply@paperclip.ing>
- tests/unit/test_security_validators.py: 59 tests for APIKeyValidator._validate_key_format (prefix, length, character-set rules for all 7 providers) and update_format, plus InputSanitizer._sanitize_generic (control-char removal, length limit, strip) - tests/unit/test_lru_cache.py: 88 tests for LRUCache in model_provider — get/set/remove/ clear, TTL expiry with mocked time.time, LRU eviction order verification, cleanup_expired count, stats dict, and concurrent thread-safety Co-Authored-By: Paperclip <noreply@paperclip.ing>
- tests/unit/test_tool_registry.py: 81 tests for ToolRegistry — default tool initialization (10 tools), get/register/remove/list operations, get_tools_for_agent filtering, agent-type case-insensitivity, default parameter structures - tests/unit/test_diagnostic_formatter.py: 76 tests for FormatterMixin._is_in_section — section boundary detection, whitespace stripping semantics, all 5 known section headers, real-world multi-section document scenarios, and edge cases Co-Authored-By: Paperclip <noreply@paperclip.ing>
…ator provider - tests/unit/test_medication_agent_pure.py: 76 tests for MedicationAgent._determine_task_type (all routing keywords, case-insensitive, first-match-wins), _parse_medication_list (dash/numbered prefixes, colon property parsing, key normalization, edge cases), TDM_DRUGS dict (16 drugs, required fields, spot-checks), BEERS_HIGH_RISK list - tests/unit/test_deep_translator_provider.py: 44 tests for DeepTranslatorProvider COMMON_LANGUAGES constant (100 entries, format), get_supported_languages (google/ microsoft returns COMMON_LANGUAGES, deepl returns shorter list without zh-CN), _map_to_deepl_code (all 7 mapped codes + passthrough for unmapped codes) Co-Authored-By: Paperclip <noreply@paperclip.ing>
…xamples - tests/unit/test_synopsis_agent_pure.py: 77 tests for SynopsisAgent._build_prompt (3-vs-4-part join structure, context guard), _clean_synopsis (markdown removal, prefix stripping, sequential double-strip), _truncate_to_word_limit (sentence boundary via max(period,question,exclamation), ellipsis fallback, limit=0 edge case) - tests/unit/test_entity_type_examples.py: 96 tests for ENTITY_TYPE_EXAMPLES data in generate_prototypes.py — 6 categories, 20 entries each, structure validation, specific term membership across all 6 categories, cross-category uniqueness Co-Authored-By: Paperclip <noreply@paperclip.ing>
Stubbing utils.security_decorators and utils.resilience in sys.modules was polluting test state and causing test_security_decorators.py to fail when run in the same session. Only external packages (deep_translator, deep_translator.exceptions) need stubbing. Co-Authored-By: Paperclip <noreply@paperclip.ing>
…, and managers Extends 11 existing test files and creates 1 new file (test_api_key_manager.py) to close coverage gaps in pure-logic and mockable service layers: - validation.py: 58% → 89% (audio, model, temperature, path, filename, whitelist) - health_checker.py: 66% → 99% (all 5 health check functions + startup diagnostics) - adaptive_threshold.py → 98%, entity_deduplicator.py → 97%, mmr_reranker.py → 98% - query_expander.py → 100%, temporal_reasoner.py → 91% - agent_manager.py → 86% (retry math, sub-agent concurrency, condition eval security) - feedback_manager.py → 78%, api_key_manager.py: 0% → 34% (non-GUI) Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
…ctured_logging - test_sentry_config: Use autouse fixture to properly manage sentry_sdk in sys.modules, preventing cross-test pollution when sentry_sdk is/isn't installed on CI runners - test_structured_logging_extended: Save/restore root logger handlers in setUp/tearDown so logging.basicConfig takes effect (it's a no-op when handlers already exist), and use format() call instead of private _fmt attribute for formatter validation Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
…ithout package The previous sys.modules approach failed on CI ubuntu where sentry_sdk is installed — Python's import cached the real module reference. Now intercepts at builtins.__import__ level which works regardless of whether sentry_sdk is installed. Also uses clear_env=True for environment tests to prevent MEDICAL_ASSISTANT_ENV leaking from CI env. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
The builtins.__import__ approach still failed on CI because pytest's
import machinery doesn't reliably intercept local function imports.
New approach: patch("sentry_sdk.init") directly on the real module —
the import resolves normally, we just mock the .init() call. Tests
skip gracefully if sentry_sdk is not installed.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
patch("sentry_sdk.init") failed on CI because Python's import resolution
under coverage.py doesn't reliably intercept the mock. Now pre-imports
sentry_sdk at module level and uses patch.object(_sentry_sdk, "init")
which directly replaces the attribute on the already-loaded module —
no import resolution involved.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Root cause found: sentry_config.py used logging.getLogger() (standard)
but called logger.info("...", environment=env) with a keyword arg that
only StructuredLogger supports. On CI, sentry_sdk.init() succeeded but
the logger.info() call threw "Logger._log() got an unexpected keyword
argument 'environment'", caught by the except Exception block, returning
False. Switched to get_logger() from structured_logging.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Summary
Test plan
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