chore: import upstream snapshot with attribution

tests/api_tests/__init__.py

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+"""API Tests for Local Deep Research."""

tests/api_tests/conftest.py

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+"""
+Fixtures for library API tests.
+Provides test data and helpers for testing library/collection/RAG endpoints.
+"""
+
+import hashlib
+import uuid
+
+import pytest
+
+from local_deep_research.database.models.library import (
+    DocumentStatus,
+)
+
+
+@pytest.fixture
+def sample_source_type_data():
+    """Sample source type data for test documents."""
+    return {
+        "id": str(uuid.uuid4()),
+        "name": "test_upload",
+        "display_name": "Test Upload",
+        "description": "Test documents for API tests",
+        "icon": "fas fa-file",
+    }
+
+
+@pytest.fixture
+def sample_collection_data():
+    """Sample collection data for tests."""
+    return {
+        "name": f"Test Collection {uuid.uuid4().hex[:8]}",
+        "description": "A test collection for API tests",
+        "type": "user_uploads",
+    }
+
+
+@pytest.fixture
+def sample_document_data():
+    """Sample document data for tests."""
+    content = "This is sample text content for testing API endpoints."
+    return {
+        "id": str(uuid.uuid4()),
+        "document_hash": hashlib.sha256(content.encode()).hexdigest(),
+        "file_size": len(content),
+        "file_type": "text",
+        "text_content": content,
+        "title": "Test Document for API",
+        "status": DocumentStatus.COMPLETED,
+    }
+
+
+def create_test_collection(client, name=None, description=None):
+    """
+    Helper to create a collection via API.
+
+    Args:
+        client: Flask test client (authenticated)
+        name: Collection name (optional, auto-generated if not provided)
+        description: Collection description (optional)
+
+    Returns:
+        dict: Created collection data or None if failed
+    """
+    payload = {
+        "name": name or f"Test Collection {uuid.uuid4().hex[:8]}",
+        "description": description or "Test collection",
+        "type": "user_uploads",
+    }
+
+    response = client.post(
+        "/library/api/collections",
+        json=payload,
+        content_type="application/json",
+    )
+
+    if response.status_code == 200:
+        data = response.get_json()
+        if data.get("success"):
+            return data.get("collection")
+
+    return None
+
+
+def delete_test_collection(client, collection_id):
+    """
+    Helper to delete a collection via API.
+
+    Args:
+        client: Flask test client (authenticated)
+        collection_id: ID of collection to delete
+
+    Returns:
+        bool: True if deleted successfully
+    """
+    response = client.delete(f"/library/api/collections/{collection_id}")
+    return response.status_code == 200
+
+
+@pytest.fixture
+def create_collection_helper(authenticated_client):
+    """Fixture that returns a helper function to create collections."""
+    created_collections = []
+
+    def _create(name=None, description=None):
+        collection = create_test_collection(
+            authenticated_client, name, description
+        )
+        if collection:
+            created_collections.append(collection["id"])
+        return collection
+
+    yield _create
+
+    # Cleanup: delete all created collections
+    for coll_id in created_collections:
+        try:
+            delete_test_collection(authenticated_client, coll_id)
+        except Exception:
+            pass

tests/api_tests/fix_search_engines.py

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+"""
+Quick fix to ensure search engine settings are loaded for test user.
+"""
+
+import os
+import sys
+from pathlib import Path
+
+from loguru import logger
+
+# Add parent directory to path for imports
+sys.path.insert(0, str(Path(__file__).parent.parent.parent))
+
+from local_deep_research.database.encrypted_db import db_manager
+from local_deep_research.settings.manager import (
+    SettingsManager,
+)
+
+
+def fix_search_engines_for_user(username: str, password: str):
+    """Ensure search engine settings are loaded for a user."""
+
+    logger.info(f"Fixing search engine settings for user: {username}")
+
+    # Open user database
+    engine = db_manager.open_user_database(username, password)
+    if not engine:
+        logger.error("Failed to open user database")
+        return False
+
+    # Get database session
+    Session = db_manager.Session
+    if not Session:
+        logger.error("Failed to get database session factory")
+        return False
+
+    with Session() as db_session:
+        try:
+            # Create settings manager
+            settings_manager = SettingsManager(db_session)
+
+            # Check if we need to load defaults
+            from local_deep_research.database.models import Setting
+
+            search_engine_count = (
+                db_session.query(Setting)
+                .filter(Setting.key.like("search.engine.%.display_name"))
+                .count()
+            )
+
+            if search_engine_count == 0:
+                logger.info(
+                    "No search engine settings found. Loading defaults..."
+                )
+                settings_manager.load_from_defaults_file(commit=True)
+                logger.info("Default settings loaded successfully")
+            else:
+                logger.info(
+                    f"Found {search_engine_count} search engine settings"
+                )
+
+            # Verify settings were loaded
+            search_engines = (
+                db_session.query(Setting)
+                .filter(Setting.key.like("search.engine.%.display_name"))
+                .all()
+            )
+
+            logger.info(f"Search engines after fix: {len(search_engines)}")
+            for engine in search_engines[:5]:  # Show first 5
+                logger.info(f"  - {engine.key}: {engine.value}")
+
+            return True
+
+        except Exception:
+            logger.exception("Failed to fix search engines")
+            db_session.rollback()
+            return False
+
+
+if __name__ == "__main__":
+    import os
+
+    os.environ["LDR_BOOTSTRAP_ALLOW_UNENCRYPTED"] = "true"
+
+    # Fix for test user
+    fix_search_engines_for_user(
+        "testuser", "testpassword123"
+    )  # pragma: allowlist secret
+
+    # Also fix for any other common test users
+    fix_search_engines_for_user("apitest_user", "apitest_pass123")

tests/api_tests/migrate_research_mode.py

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+#!/usr/bin/env python3
+"""
+Add research_mode column to existing databases.
+This script adds the missing research_mode column to TokenUsage and SearchCall tables.
+"""
+
+import os
+import sqlite3
+import sys
+from pathlib import Path
+
+# Add parent directory to path for imports
+sys.path.insert(0, str(Path(__file__).parent.parent.parent))
+
+from loguru import logger
+
+from local_deep_research.config.paths import get_user_data_directory
+
+
+def add_research_mode_column(db_path: str):
+    """Add research_mode column to tables if it doesn't exist."""
+    try:
+        conn = sqlite3.connect(db_path)
+    except Exception:
+        logger.exception(f"Error connecting to {db_path}")
+        return
+    try:
+        cursor = conn.cursor()
+
+        # Check if column exists in token_usage
+        cursor.execute("PRAGMA table_info(token_usage)")
+        columns = [col[1] for col in cursor.fetchall()]
+
+        if "research_mode" not in columns:
+            logger.info(
+                f"Adding research_mode column to token_usage in {db_path}"
+            )
+            cursor.execute(
+                "ALTER TABLE token_usage ADD COLUMN research_mode VARCHAR(50)"
+            )
+            conn.commit()
+        else:
+            logger.info(
+                f"research_mode column already exists in token_usage in {db_path}"
+            )
+
+        # Check if column exists in search_calls
+        cursor.execute("PRAGMA table_info(search_calls)")
+        columns = [col[1] for col in cursor.fetchall()]
+
+        if "research_mode" not in columns:
+            logger.info(
+                f"Adding research_mode column to search_calls in {db_path}"
+            )
+            cursor.execute(
+                "ALTER TABLE search_calls ADD COLUMN research_mode VARCHAR(50)"
+            )
+            conn.commit()
+        else:
+            logger.info(
+                f"research_mode column already exists in search_calls in {db_path}"
+            )
+
+        logger.info(f"Successfully updated {db_path}")
+    except Exception:
+        logger.exception(f"Error updating {db_path}")
+    finally:
+        conn.close()
+
+
+def migrate_all_user_databases():
+    """Migrate all user databases to add research_mode column."""
+    # Get base data directory
+    from local_deep_research.config.paths import get_data_directory
+
+    base_dir = get_data_directory()
+
+    # Look for user directories
+    user_dirs = []
+    if base_dir.exists():
+        for item in base_dir.iterdir():
+            if item.is_dir() and item.name.startswith("user_"):
+                user_dirs.append(item)
+
+    if not user_dirs:
+        logger.warning("No user directories found")
+        return
+
+    logger.info(f"Found {len(user_dirs)} user directories to migrate")
+
+    for user_dir in user_dirs:
+        db_path = user_dir / f"{user_dir.name}_encrypted.db"
+        if db_path.exists():
+            logger.info(f"Migrating database for {user_dir.name}")
+            add_research_mode_column(str(db_path))
+        else:
+            logger.warning(f"No database found in {user_dir}")
+
+
+if __name__ == "__main__":
+    # Enable debug logging
+    logger.remove()
+    # diagnose=False: don't dump frame-local credentials in tracebacks
+    # (#4185 / #4384). This script touches user databases and SQLCipher
+    # passwords live in frame locals during migration.
+    logger.add(sys.stdout, level="INFO", diagnose=False)
+
+    # Allow unencrypted for testing
+    os.environ["LDR_BOOTSTRAP_ALLOW_UNENCRYPTED"] = "true"
+
+    # Run migration
+    migrate_all_user_databases()
+
+    # Also migrate specific test user if needed
+    if len(sys.argv) > 1:
+        username = sys.argv[1]
+        user_dir = get_user_data_directory(username)
+        db_path = user_dir / f"{user_dir.name}_encrypted.db"
+        if db_path.exists():
+            logger.info(f"Migrating specific user: {username}")
+            add_research_mode_column(str(db_path))

tests/api_tests/populate_search_engines.py

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+#!/usr/bin/env python3
+"""
+Populate search engine settings in the database
+"""
+
+import os
+import sys
+from pathlib import Path
+
+from loguru import logger
+
+# Add parent directory to path
+sys.path.insert(0, str(Path(__file__).parent.parent.parent))
+
+from local_deep_research.database.models import Setting
+from local_deep_research.utilities.db_utils import get_db_session
+
+
+def populate_search_engines():
+    """Populate search engine settings in the database"""
+
+    # Define search engines with their properties
+    search_engines = {
+        "searxng": {
+            "display_name": "SearXNG",
+            "description": "Privacy-focused metasearch engine",
+            "strengths": ["Privacy", "No tracking", "Multiple sources"],
+        },
+        "google": {
+            "display_name": "Google",
+            "description": "Google search engine",
+            "strengths": ["Comprehensive", "Fast", "Relevant results"],
+        },
+        "bing": {
+            "display_name": "Bing",
+            "description": "Microsoft Bing search engine",
+            "strengths": ["Good for technical queries", "Image search", "News"],
+        },
+        "duckduckgo": {
+            "display_name": "DuckDuckGo",
+            "description": "Privacy-focused search engine",
+            "strengths": ["Privacy", "No tracking", "Instant answers"],
+        },
+        "wikipedia": {
+            "display_name": "Wikipedia",
+            "description": "Wikipedia search",
+            "strengths": ["Encyclopedic content", "Reliable", "Detailed"],
+        },
+        "arxiv": {
+            "display_name": "arXiv",
+            "description": "Scientific paper repository",
+            "strengths": ["Academic papers", "Research", "Preprints"],
+        },
+        "pubmed": {
+            "display_name": "PubMed",
+            "description": "Medical research database",
+            "strengths": ["Medical research", "Clinical studies", "Healthcare"],
+        },
+        "semantic_scholar": {
+            "display_name": "Semantic Scholar",
+            "description": "AI-powered research tool",
+            "strengths": [
+                "Academic search",
+                "Citation analysis",
+                "AI insights",
+            ],
+        },
+    }
+
+    session = get_db_session()
+
+    try:
+        # Add web search engines
+        for engine_name, props in search_engines.items():
+            # Display name
+            display_setting = Setting(
+                key=f"search.engine.web.{engine_name}.display_name",
+                value=props["display_name"],
+                type="SEARCH",
+                category="search",
+                name=f"{engine_name} Display Name",
+                description=f"Display name for {engine_name}",
+            )
+            existing = (
+                session.query(Setting)
+                .filter_by(key=display_setting.key)
+                .first()
+            )
+            if not existing:
+                session.add(display_setting)
+                logger.info(f"Added {display_setting.key}")
+
+            # Description
+            desc_setting = Setting(
+                key=f"search.engine.web.{engine_name}.description",
+                value=props["description"],
+                type="SEARCH",
+                category="search",
+                name=f"{engine_name} Description",
+                description=f"Description for {engine_name}",
+            )
+            existing = (
+                session.query(Setting).filter_by(key=desc_setting.key).first()
+            )
+            if not existing:
+                session.add(desc_setting)
+                logger.info(f"Added {desc_setting.key}")
+
+            # Strengths
+            strengths_setting = Setting(
+                key=f"search.engine.web.{engine_name}.strengths",
+                value=props["strengths"],
+                type="SEARCH",
+                category="search",
+                name=f"{engine_name} Strengths",
+                description=f"Strengths of {engine_name}",
+            )
+            existing = (
+                session.query(Setting)
+                .filter_by(key=strengths_setting.key)
+                .first()
+            )
+            if not existing:
+                session.add(strengths_setting)
+                logger.info(f"Added {strengths_setting.key}")
+
+        # Commit all changes
+        session.commit()
+        logger.info("Successfully populated search engine settings")
+
+        # Verify by querying
+        search_settings = (
+            session.query(Setting)
+            .filter(
+                Setting.type == "SEARCH", Setting.key.contains("display_name")
+            )
+            .all()
+        )
+
+        logger.info(f"Total search engine settings: {len(search_settings)}")
+        for setting in search_settings:
+            logger.info(f"  {setting.key}: {setting.value}")
+
+    except Exception:
+        logger.exception("Error populating search engines")
+        session.rollback()
+    finally:
+        session.close()
+
+
+if __name__ == "__main__":
+    # Need to set this for test user database
+    os.environ["LDR_CURRENT_USER"] = "testuser"
+    populate_search_engines()

tests/api_tests/run_api_tests.py

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+#!/usr/bin/env python3
+"""
+Runner script for API tests.
+
+Usage:
+    python run_api_tests.py              # Run all API tests
+    python run_api_tests.py search       # Run search engines test only
+"""
+
+import subprocess
+import sys
+from pathlib import Path
+
+
+def run_all_tests():
+    """Run all API tests."""
+    print("Running all API tests...")
+    result = subprocess.run(
+        [sys.executable, "test_all_apis.py"], cwd=str(Path(__file__).parent)
+    )
+    return result.returncode
+
+
+def run_search_engines_test():
+    """Run search engines API test."""
+    print("Running search engines API test...")
+    result = subprocess.run(
+        [sys.executable, "test_search_engines_api.py"],
+        cwd=str(Path(__file__).parent),
+    )
+    return result.returncode
+
+
+def main():
+    """Main entry point."""
+    if len(sys.argv) > 1 and sys.argv[1] == "search":
+        return run_search_engines_test()
+    return run_all_tests()
+
+
+if __name__ == "__main__":
+    sys.exit(main())

tests/api_tests/run_basic_api_tests.py

@@ -0,0 +1,53 @@
+"""
+Run basic API tests that are known to work.
+"""
+
+import os
+import sys
+from pathlib import Path
+
+sys.path.insert(0, str(Path(__file__).parent.parent.parent))
+os.environ["LDR_BOOTSTRAP_ALLOW_UNENCRYPTED"] = "true"
+
+from loguru import logger
+from test_comprehensive_apis import (
+    test_auth_apis,
+    test_history_apis,
+    test_settings_apis,
+)
+
+
+def run_working_tests():
+    """Run only the APIs that are known to work."""
+    logger.info("Running basic API tests...\n")
+
+    try:
+        # Initialize tester and authenticate
+        tester = test_auth_apis()
+
+        # Run working test suites
+        test_settings_apis(tester)
+        test_history_apis(tester)
+
+        logger.info("\n✅ Basic API tests passed successfully!")
+        return True
+
+    except Exception:
+        logger.exception("Test failed")
+        return False
+
+
+if __name__ == "__main__":
+    # Setup logging
+    logger.remove()
+    # diagnose=False: don't dump frame-local credentials in tracebacks
+    # (#4185 / #4384). API tests hold api_key and password locals.
+    logger.add(
+        sys.stdout,
+        level="INFO",
+        format="<green>{time:HH:mm:ss}</green> | <level>{level: <8}</level> | <level>{message}</level>",
+        diagnose=False,
+    )
+
+    success = run_working_tests()
+    sys.exit(0 if success else 1)

tests/api_tests/test_all_apis.py

@@ -0,0 +1,254 @@
+"""
+Comprehensive API Tests for Local Deep Research.
+
+This test suite checks all API endpoints for proper authentication,
+response formats, and basic functionality.
+"""
+
+import json
+from loguru import logger
+
+
+class TestAllAPIs:
+    """Test suite for all API endpoints."""
+
+    def test_auth_apis(self, authenticated_client):
+        """Test authentication APIs."""
+        # Check auth status
+        response = authenticated_client.get("/auth/check")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert data["authenticated"] is True
+        assert "username" in data
+
+        # Test integrity check
+        response = authenticated_client.get("/auth/integrity-check")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert "integrity" in data
+        assert "username" in data
+
+    def test_settings_apis(self, authenticated_client):
+        """Test settings APIs."""
+        # Get all settings
+        response = authenticated_client.get("/settings/api")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert data["status"] == "success"
+        assert "settings" in data
+
+        # Get categories
+        response = authenticated_client.get("/settings/api/categories")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert "categories" in data
+
+        # Get types
+        response = authenticated_client.get("/settings/api/types")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert "types" in data
+
+        # Get available models
+        response = authenticated_client.get("/settings/api/available-models")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert (
+            "providers" in data or "models" in data
+        )  # API might return either
+
+        # Get available search engines - THIS IS FAILING
+        logger.info("Testing search engines API...")
+        response = authenticated_client.get(
+            "/settings/api/available-search-engines"
+        )
+        logger.info(f"Search engines response: {response.status_code}")
+        if response.status_code != 200:
+            logger.error(f"Search engines error: {response.data}")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert "engines" in data or "engine_options" in data
+
+        # Get warnings
+        response = authenticated_client.get("/settings/api/warnings")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert isinstance(
+            data, (list, dict)
+        )  # API might return list or dict with warnings
+
+        # Test get/set specific setting
+        response = authenticated_client.get("/settings/api/llm.temperature")
+        if response.status_code == 404:
+            # Setting doesn't exist, create it
+            response = authenticated_client.put(
+                "/settings/api/llm.temperature",
+                json={"value": 0.7},
+                content_type="application/json",
+            )
+            assert response.status_code in [200, 201]
+
+        # Get data location
+        response = authenticated_client.get("/settings/api/data-location")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert (
+            "data_directory" in data or "data_dir" in data
+        )  # API might return either
+        assert "is_custom" in data
+
+    def test_research_apis(self, authenticated_client):
+        """Test research APIs."""
+        # Get research history
+        response = authenticated_client.get("/history/api")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert "items" in data or "history" in data  # API might return either
+
+        # Start a test research
+        research_data = {
+            "query": "API test research query",
+            "model": "gpt-3.5-turbo",
+            "search_engines": ["searxng"],
+            "local_context": 2000,
+            "web_context": 2000,
+            "temperature": 0.7,
+        }
+
+        response = authenticated_client.post(
+            "/research/api/start",
+            json=research_data,
+            content_type="application/json",
+        )
+
+        # The research start API might fail in test environment due to
+        # missing LLM configuration or other issues. We'll accept any
+        # response as long as it's a valid HTTP response.
+        assert response.status_code in [200, 400, 404, 500]
+
+        # If successful, test the other endpoints
+        if response.status_code == 200:
+            data = json.loads(response.data)
+            if "research_id" in data:
+                research_id = data["research_id"]
+
+                # Check status
+                response = authenticated_client.get(
+                    f"/research/api/status/{research_id}"
+                )
+                assert response.status_code == 200
+
+                # Terminate research
+                response = authenticated_client.post(
+                    f"/research/api/terminate/{research_id}"
+                )
+                assert response.status_code in [200, 404]
+
+    def test_metrics_apis(self, authenticated_client):
+        """Test metrics APIs."""
+        # Get metrics summary
+        response = authenticated_client.get("/metrics/api/metrics")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert "metrics" in data or "summary" in data  # API might return either
+
+        # Get enhanced metrics
+        response = authenticated_client.get("/metrics/api/metrics/enhanced")
+        assert response.status_code == 200
+
+        # Get star reviews
+        response = authenticated_client.get("/metrics/api/star-reviews")
+        assert response.status_code == 200
+
+        # Get pricing info
+        response = authenticated_client.get("/metrics/api/pricing")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert "pricing" in data or "models" in data  # API might return either
+
+        # Get cost analytics
+        response = authenticated_client.get("/metrics/api/cost-analytics")
+        assert response.status_code == 200
+
+    def test_benchmark_apis(self, authenticated_client):
+        """Test benchmark APIs."""
+        # Get benchmark history
+        response = authenticated_client.get("/benchmark/api/history")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert "runs" in data or "history" in data  # API might return either
+
+        # Get saved configs
+        response = authenticated_client.get("/benchmark/api/configs")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert "configs" in data
+
+        # Check running benchmark
+        response = authenticated_client.get("/benchmark/api/running")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert (
+            "is_running" in data or "success" in data
+        )  # API might return either
+
+        # Validate config
+        test_config = {
+            "name": "Test Config",
+            "queries": ["test query"],
+            "models": ["gpt-3.5-turbo"],
+            "search_engines": ["searxng"],
+        }
+        response = authenticated_client.post(
+            "/benchmark/api/validate-config",
+            json=test_config,
+            content_type="application/json",
+        )
+        assert response.status_code == 200
+
+    def test_history_apis(self, authenticated_client):
+        """Test history APIs."""
+        response = authenticated_client.get("/history/api")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert "items" in data or "history" in data  # API might return either
+        # Get the actual history list
+        history_data = data.get("items", data.get("history", []))
+        assert isinstance(history_data, list)
+
+    def test_config_apis(self, authenticated_client):
+        """Test configuration APIs."""
+        # Get current config - api_bp is registered with /research/api prefix
+        response = authenticated_client.get(
+            "/research/api/settings/current-config"
+        )
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert "success" in data  # API returns success status
+        if data.get("success"):
+            assert "config" in data  # Config is nested under config key
+
+        # Get public config - This endpoint may not exist
+        response = authenticated_client.get("/api/config")
+        if response.status_code == 404:
+            # Endpoint doesn't exist, skip test
+            pass
+        else:
+            assert response.status_code == 200
+            data = json.loads(response.data)
+            assert "version" in data or "available_models" in data
+
+    def test_health_check_apis(self, authenticated_client):
+        """Test health check APIs."""
+        # Check Ollama status - the api_bp is registered with /research/api prefix
+        response = authenticated_client.get("/research/api/check/ollama_status")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert (
+            "running" in data or "available" in data
+        )  # API might return either
+
+        # Check Ollama model
+        response = authenticated_client.get("/research/api/check/ollama_model")
+        # This might return 400 if no model specified
+        assert response.status_code in [200, 400]

tests/api_tests/test_all_endpoints.py

@@ -0,0 +1,453 @@
+#!/usr/bin/env python3
+"""
+Comprehensive test suite that tests ALL API endpoints in the codebase.
+This ensures we have coverage for every single endpoint.
+"""
+
+import json
+import time
+
+import pytest
+from loguru import logger
+
+
+class TestAllEndpoints:
+    """Comprehensive API test suite using Flask test client."""
+
+    def test_all_auth_endpoints(self, authenticated_client):
+        """Test ALL authentication endpoints."""
+        logger.info("\n=== Testing ALL Authentication Endpoints ===")
+
+        # Test endpoints
+        endpoints = [
+            ("GET", "/auth/check", None, 200),
+            ("GET", "/auth/integrity-check", None, 200),
+        ]
+
+        for method, endpoint, data, expected_status in endpoints:
+            if method == "GET":
+                response = authenticated_client.get(endpoint)
+            else:
+                response = authenticated_client.post(
+                    endpoint,
+                    json=data,
+                    content_type="application/json",
+                )
+            assert response.status_code == expected_status, (
+                f"{endpoint} failed: {response.data}"
+            )
+
+        logger.info("✅ All Auth endpoints tested")
+
+    def test_all_settings_endpoints(self, authenticated_client):
+        """Test ALL settings endpoints."""
+        logger.info("\n=== Testing ALL Settings Endpoints ===")
+
+        # Basic GET endpoints
+        get_endpoints = [
+            "/settings/api",
+            "/settings/api/categories",
+            "/settings/api/types",
+            "/settings/api/ui_elements",
+            "/settings/api/available-models",
+            "/settings/api/available-search-engines",
+            "/settings/api/warnings",
+            "/settings/api/ollama-status",
+            "/settings/api/rate-limiting/status",
+            "/settings/api/data-location",
+        ]
+
+        for endpoint in get_endpoints:
+            response = authenticated_client.get(endpoint)
+            assert response.status_code == 200, (
+                f"{endpoint} failed: {response.data}"
+            )
+
+        # Test bulk get
+        response = authenticated_client.get(
+            "/settings/api/bulk?keys=llm.provider,llm.model"
+        )
+        assert response.status_code == 200, f"Bulk get failed: {response.data}"
+
+        # Test setting CRUD (use an allow-listed prefix so the
+        # namespace gate permits creation of this throwaway key).
+        test_key = "llm.endpoint_test_value"
+        test_value = {"value": "test_endpoint_123", "editable": True}
+
+        # Create/Update
+        response = authenticated_client.put(
+            f"/settings/api/{test_key}",
+            json=test_value,
+            content_type="application/json",
+        )
+        assert response.status_code in [200, 201], (
+            f"Create setting failed: {response.data}"
+        )
+
+        # Get specific setting
+        data = json.loads(response.data)
+        if isinstance(data, dict) and "setting" in data:
+            actual_key = data["setting"].get("key", test_key)
+        else:
+            actual_key = test_key
+
+        response = authenticated_client.get(f"/settings/api/{actual_key}")
+        assert response.status_code == 200, (
+            f"Get setting failed: {response.data}"
+        )
+
+        # Delete
+        response = authenticated_client.delete(f"/settings/api/{actual_key}")
+        assert response.status_code in [200, 204, 404], (
+            f"Delete setting failed: {response.data}"
+        )
+
+        # Test rate limiting reset
+        response = authenticated_client.post(
+            "/settings/api/rate-limiting/engines/test/reset"
+        )
+        assert response.status_code in [200, 404], (
+            f"Rate limit reset failed: {response.data}"
+        )
+
+        # Test cleanup
+        response = authenticated_client.post(
+            "/settings/api/rate-limiting/cleanup"
+        )
+        assert response.status_code == 200, (
+            f"Rate limit cleanup failed: {response.data}"
+        )
+
+        logger.info("✅ All Settings endpoints tested")
+
+    def test_all_research_endpoints(self, authenticated_client):
+        """Test ALL research-related endpoints."""
+        # audit: PUNCHLIST reviewed 2026-05 — issue resolved by prior PR (recommendation: REFACTOR_SPLIT).
+        logger.info("\n=== Testing ALL Research Endpoints ===")
+
+        # Set up logging.
+        try:
+            logger.level("MILESTONE", no=26, color="<magenta><bold>")
+        except (TypeError, ValueError):
+            pass  # Level already registered
+
+        # Test history endpoint first
+        response = authenticated_client.get("/history/api")
+        assert response.status_code == 200, (
+            f"History API failed: {response.data}"
+        )
+
+        # Start research via main endpoint
+        research_data = {
+            "query": "Test all endpoints comprehensive",
+            "mode": "quick",
+            "model_provider": "OLLAMA",
+            "model": "llama2",
+            "search_engine": "searxng",
+            "max_results": 5,
+            "time_period": "y",
+            "iterations": 1,
+            "questions_per_iteration": 2,
+            "strategy": "rapid",
+        }
+
+        # Test /api/start_research endpoint
+        response = authenticated_client.post(
+            "/api/start_research",
+            json=research_data,
+            content_type="application/json",
+        )
+        assert response.status_code == 200, (
+            f"Start research failed: {response.data}"
+        )
+        data = json.loads(response.data)
+        assert "research_id" in data
+        research_id = data["research_id"]
+
+        # Give it a moment to start
+        time.sleep(0.5)  # allow: unmarked-sleep
+
+        # Test various research endpoints
+        research_endpoints = [
+            ("GET", f"/api/research/{research_id}", None, 200),
+            ("GET", f"/api/research/{research_id}/status", None, 200),
+            ("GET", f"/research/api/status/{research_id}", None, 200),
+            ("GET", f"/history/status/{research_id}", None, 200),
+            ("GET", f"/history/details/{research_id}", None, 200),
+            ("GET", f"/history/log_count/{research_id}", None, 200),
+        ]
+
+        for method, endpoint, req_data, expected_status in research_endpoints:
+            if method == "GET":
+                response = authenticated_client.get(endpoint)
+            else:
+                response = authenticated_client.post(
+                    endpoint,
+                    json=req_data,
+                    content_type="application/json",
+                )
+            # Some endpoints might return 404 if research is still initializing
+            assert response.status_code in [expected_status, 404], (
+                f"{endpoint} failed: {response.data}"
+            )
+
+        # Test research API routes
+        response = authenticated_client.get(
+            "/research/api/settings/current-config"
+        )
+        assert response.status_code == 200, (
+            f"Current config failed: {response.data}"
+        )
+
+        # Test Ollama checks
+        response = authenticated_client.get("/research/api/check/ollama_status")
+        assert response.status_code == 200, (
+            f"Ollama status check failed: {response.data}"
+        )
+
+        # Terminate research
+        response = authenticated_client.post(f"/api/terminate/{research_id}")
+        assert response.status_code in [200, 400, 404], (
+            f"Terminate research failed: {response.data}"
+        )
+
+        # Test alternate terminate endpoint
+        response = authenticated_client.post(
+            f"/research/api/terminate/{research_id}"
+        )
+        assert response.status_code in [200, 400, 404], (
+            f"API terminate research failed: {response.data}"
+        )
+
+        logger.info("✅ All Research endpoints tested")
+
+        return research_id
+
+    def test_all_metrics_endpoints(self, authenticated_client):
+        """Test ALL metrics endpoints."""
+        logger.info("\n=== Testing ALL Metrics Endpoints ===")
+
+        # Basic metrics endpoints
+        metrics_endpoints = [
+            "/metrics/api/metrics",
+            "/metrics/api/metrics/enhanced",
+            "/metrics/api/pricing",
+            "/metrics/api/cost-analytics",
+            "/metrics/api/star-reviews",
+            "/metrics/api/rate-limiting",
+            "/metrics/api/rate-limiting/current",
+        ]
+
+        for endpoint in metrics_endpoints:
+            response = authenticated_client.get(endpoint)
+            assert response.status_code == 200, (
+                f"{endpoint} failed: {response.data}"
+            )
+
+        # Test specific model pricing
+        response = authenticated_client.get(
+            "/metrics/api/pricing/gpt-3.5-turbo"
+        )
+        assert response.status_code in [200, 404], (
+            f"Model pricing failed: {response.data}"
+        )
+
+        # Test cost calculation
+        cost_data = {
+            "model_name": "gpt-3.5-turbo",
+            "prompt_tokens": 1000,
+            "completion_tokens": 500,
+        }
+        response = authenticated_client.post(
+            "/metrics/api/cost-calculation",
+            json=cost_data,
+            content_type="application/json",
+        )
+        assert response.status_code == 200, (
+            f"Cost calculation failed: {response.data}"
+        )
+
+        logger.info("✅ All Metrics endpoints tested")
+
+    def test_all_benchmark_endpoints(self, authenticated_client):
+        """Test ALL benchmark endpoints."""
+        logger.info("\n=== Testing ALL Benchmark Endpoints ===")
+
+        # Basic benchmark endpoints
+        benchmark_endpoints = [
+            "/benchmark/api/history",
+            "/benchmark/api/configs",
+            "/benchmark/api/running",
+            "/benchmark/api/search-quality",
+        ]
+
+        for endpoint in benchmark_endpoints:
+            response = authenticated_client.get(endpoint)
+            assert response.status_code == 200, (
+                f"{endpoint} failed: {response.data}"
+            )
+
+        # Test config validation
+        test_config = {
+            "name": "Test Benchmark Config",
+            "queries": ["test query 1", "test query 2"],
+            "models": ["gpt-3.5-turbo"],
+            "search_engines": ["searxng"],
+            "iterations": 1,
+        }
+
+        response = authenticated_client.post(
+            "/benchmark/api/validate-config",
+            json=test_config,
+            content_type="application/json",
+        )
+        assert response.status_code == 200, (
+            f"Validate config failed: {response.data}"
+        )
+
+        # Test simple benchmark start (but don't actually run it)
+        simple_benchmark = {
+            "query": "test benchmark",
+            "models": ["gpt-3.5-turbo"],
+            "search_engines": ["searxng"],
+        }
+
+        # Note: We won't actually start a benchmark as it's resource intensive
+        # Just verify the endpoint exists
+        response = authenticated_client.post(
+            "/benchmark/api/start-simple",
+            json=simple_benchmark,
+            content_type="application/json",
+        )
+        # Accept 409 (conflict) if another benchmark is running
+        assert response.status_code in [200, 409, 400], (
+            f"Start simple benchmark status: {response.status_code}, {response.data}"
+        )
+
+        logger.info("✅ All Benchmark endpoints tested")
+
+    def test_all_history_endpoints(self, authenticated_client):
+        """Test ALL history endpoints."""
+        logger.info("\n=== Testing ALL History Endpoints ===")
+
+        # Basic history endpoint
+        response = authenticated_client.get("/history/api")
+        assert response.status_code == 200, (
+            f"History API failed: {response.data}"
+        )
+
+        logger.info("✅ All History endpoints tested")
+
+    @pytest.mark.requires_llm
+    def test_all_api_v1_endpoints(self, authenticated_client):
+        """Test ALL API v1 endpoints."""
+        logger.info("\n=== Testing ALL API v1 Endpoints ===")
+
+        # Health check (doesn't require auth)
+        response = authenticated_client.get("/api/v1/health")
+        assert response.status_code == 200, (
+            f"Health check failed: {response.data}"
+        )
+
+        # API documentation
+        response = authenticated_client.get("/api/v1/")
+        assert response.status_code == 200, f"API docs failed: {response.data}"
+
+        # Quick summary
+        summary_data = {"query": "What is machine learning?", "max_tokens": 100}
+        response = authenticated_client.post(
+            "/api/v1/quick_summary",
+            json=summary_data,
+            content_type="application/json",
+        )
+        assert response.status_code in [200, 404, 500], (
+            f"Quick summary status: {response.status_code}"
+        )
+
+        # Generate report
+        report_data = {
+            "query": "Test report generation",
+            "research_type": "comprehensive",
+        }
+        response = authenticated_client.post(
+            "/api/v1/generate_report",
+            json=report_data,
+            content_type="application/json",
+        )
+        assert response.status_code in [200, 404, 500], (
+            f"Generate report status: {response.status_code}"
+        )
+
+        # Analyze documents. The endpoint searches a named local collection;
+        # it does not accept an inline "documents" key (that now yields a 400).
+        doc_data = {
+            "query": "Summarize this document",
+            "collection_name": "test_collection",
+        }
+        response = authenticated_client.post(
+            "/api/v1/analyze_documents",
+            json=doc_data,
+            content_type="application/json",
+        )
+        assert response.status_code in [200, 404, 500], (
+            f"Analyze documents status: {response.status_code}"
+        )
+
+        logger.info("✅ All API v1 endpoints tested")
+
+    def test_miscellaneous_endpoints(self, authenticated_client):
+        """Test miscellaneous endpoints not covered in other categories."""
+        logger.info("\n=== Testing Miscellaneous Endpoints ===")
+
+        # Test static file serving
+        response = authenticated_client.get("/static/css/style.css")
+        assert response.status_code in [200, 404], "Static file endpoint failed"
+
+        # Test favicon
+        response = authenticated_client.get("/favicon.ico")
+        assert response.status_code in [200, 404], "Favicon endpoint failed"
+
+        # Test pages that should exist
+        page_endpoints = [
+            "/",  # Home page
+            "/history",  # History page
+            "/settings",  # Settings page
+            "/metrics/",  # Metrics dashboard
+            "/benchmark/",  # Benchmark dashboard
+        ]
+
+        for endpoint in page_endpoints:
+            response = authenticated_client.get(endpoint)
+            assert response.status_code == 200, (
+                f"Page {endpoint} failed with status {response.status_code}"
+            )
+
+        logger.info("✅ All miscellaneous endpoints tested")
+
+    def test_error_handling(self, authenticated_client):
+        """Test error handling for invalid endpoints and methods."""
+        logger.info("\n=== Testing Error Handling ===")
+
+        # Test non-existent endpoint
+        response = authenticated_client.get("/api/does-not-exist")
+        assert response.status_code == 404, (
+            f"Non-existent endpoint should return 404, got {response.status_code}"
+        )
+
+        # Test wrong method
+        response = authenticated_client.delete("/auth/check")
+        assert response.status_code in [404, 405], (
+            f"Wrong method should return 404/405, got {response.status_code}"
+        )
+
+        # Test invalid JSON
+        response = authenticated_client.post(
+            "/api/start_research",
+            data="invalid json",
+            content_type="application/json",
+        )
+        assert response.status_code in [400, 500], (
+            f"Invalid JSON should return 400/500, got {response.status_code}"
+        )
+
+        logger.info("✅ Error handling tested")

tests/api_tests/test_api_basic.py

@@ -0,0 +1,103 @@
+"""
+Basic API tests - only test endpoints that should respond quickly.
+Focus on verifying the API is working without doing actual research.
+"""
+
+import pytest
+from flask import json
+
+
+class TestBasicAPI:
+    """Test basic API functionality."""
+
+    def test_health_check(self, authenticated_client):
+        """Test health check endpoint."""
+        response = authenticated_client.get("/api/v1/health")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert data["status"] == "ok"
+        assert "timestamp" in data
+
+    def test_api_documentation(self, authenticated_client):
+        """Test API documentation endpoint."""
+        response = authenticated_client.get("/api/v1/")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert data["api_version"] == "v1"
+        assert "endpoints" in data
+        assert len(data["endpoints"]) >= 3
+
+    def test_error_handling(self, authenticated_client):
+        """Test error handling for malformed requests."""
+        # Test missing query parameter
+        response = authenticated_client.post(
+            "/api/v1/quick_summary",
+            json={},
+            content_type="application/json",
+        )
+        assert response.status_code == 400
+        data = json.loads(response.data)
+        assert "error" in data
+        assert "required" in data["error"].lower()
+
+        # Test missing collection_name
+        response = authenticated_client.post(
+            "/api/v1/analyze_documents",
+            json={"query": "test"},
+            content_type="application/json",
+        )
+        assert response.status_code == 400
+        data = json.loads(response.data)
+        assert "error" in data
+
+    @pytest.mark.requires_llm
+    def test_api_structure(
+        self, authenticated_client, setup_database_for_all_tests
+    ):
+        """Test that API accepts properly formatted requests."""
+        payload = {
+            "query": "test",
+            "search_tool": "wikipedia",
+            "iterations": 1,
+            "temperature": 0.7,
+        }
+
+        print(
+            f"\n[DEBUG] Sending request to /api/v1/quick_summary with payload: {payload}"
+        )
+
+        # Send request with proper format
+        response = authenticated_client.post(
+            "/api/v1/quick_summary",
+            json=payload,
+            content_type="application/json",
+        )
+
+        print(f"[DEBUG] Response status code: {response.status_code}")
+        print(
+            f"[DEBUG] Response data: {response.data.decode()[:500]}"
+        )  # First 500 chars
+
+        if response.status_code == 500:
+            # Print full error details for debugging
+            try:
+                error_data = json.loads(response.data)
+                print(f"[DEBUG] Error response JSON: {error_data}")
+            except Exception:
+                print(f"[DEBUG] Raw error response: {response.data.decode()}")
+
+        # The API should accept the request format
+        # It might return 200 with processing started, or 400 if there's a validation error
+        assert response.status_code in [200, 202, 400]
+
+        if response.status_code == 400:
+            # Check that error message is informative
+            data = json.loads(response.data)
+            assert "error" in data
+
+    def test_unauthenticated_access(self, client):
+        """Test that unauthenticated requests are rejected."""
+        response = client.get("/api/v1/health")
+        # API endpoints might allow unauthenticated access for health checks
+        # or might redirect to login
+        assert response.status_code in [200, 302, 401]

tests/api_tests/test_api_contracts.py

@@ -0,0 +1,124 @@
+#!/usr/bin/env python3
+"""
+Test API response contracts.
+
+These tests verify that API responses have the expected structure.
+Breaking these contracts will break client integrations.
+"""
+
+import pytest
+
+
+class TestResearchStatusValues:
+    """
+    Verify that research status values are consistent.
+
+    Clients depend on these exact string values.
+    """
+
+    def test_research_status_enum_values(self):
+        """
+        Verify ResearchStatus enum has expected values.
+
+        Clients check for these exact string values in responses.
+        Changing them will break client code.
+        """
+        from local_deep_research.database.models.research import (
+            ResearchStatus,
+        )
+
+        # These are the status values clients depend on
+        expected_values = {
+            "pending",
+            "in_progress",
+            "completed",
+            "failed",
+            "cancelled",
+            "suspended",
+        }
+
+        actual_values = {status.value for status in ResearchStatus}
+
+        # Check no expected values were removed
+        missing = expected_values - actual_values
+        assert not missing, (
+            f"ResearchStatus is missing expected values: {missing}\n"
+            "Clients depend on these status values.\n"
+            "Removing them will break client integrations."
+        )
+
+    def test_research_mode_enum_values(self):
+        """
+        Verify ResearchMode enum has expected values.
+
+        Clients use these values when starting research.
+        """
+        from local_deep_research.database.models.research import (
+            ResearchMode,
+        )
+
+        # These are the mode values clients depend on
+        expected_values = {
+            "quick",
+            "detailed",
+        }
+
+        actual_values = {mode.value for mode in ResearchMode}
+
+        missing = expected_values - actual_values
+        assert not missing, (
+            f"ResearchMode is missing expected values: {missing}\n"
+            "Clients depend on these mode values."
+        )
+
+
+class TestResponseStructures:
+    """
+    Verify that models have expected columns for API responses.
+
+    These are the fields that clients depend on.
+    """
+
+    def test_research_has_required_columns(self):
+        """
+        Verify Research model has required columns for API responses.
+
+        These columns are serialized in API responses.
+        """
+        from local_deep_research.database.models.research import Research
+
+        required_columns = {
+            "id",
+            "query",
+            "status",
+            "mode",
+            "created_at",
+        }
+
+        actual_columns = set(Research.__table__.columns.keys())
+
+        missing = required_columns - actual_columns
+        assert not missing, (
+            f"Research model is missing required columns: {missing}\n"
+            "These columns are expected in API responses."
+        )
+
+    def test_user_settings_has_required_columns(self):
+        """
+        Verify UserSettings model has required columns for API responses.
+        """
+        from local_deep_research.database.models import UserSettings
+
+        required_columns = {"id", "key", "value", "category"}
+
+        actual_columns = set(UserSettings.__table__.columns.keys())
+
+        missing = required_columns - actual_columns
+        assert not missing, (
+            f"UserSettings model is missing required columns: {missing}\n"
+            "These columns are expected in settings API responses."
+        )
+
+
+if __name__ == "__main__":
+    pytest.main([__file__, "-v"])

tests/api_tests/test_api_pytest.py

@@ -0,0 +1,114 @@
+"""
+pytest-compatible API tests for REST API endpoints.
+Tests basic functionality and programmatic access integration.
+"""
+
+import json
+
+
+class TestRestAPIBasic:
+    """Basic tests for REST API endpoints."""
+
+    def test_health_check(self, authenticated_client):
+        """Test the health check endpoint returns OK status."""
+        response = authenticated_client.get("/api/v1/health")
+        assert response.status_code == 200
+
+        data = json.loads(response.data)
+        assert data["status"] == "ok"
+        assert "timestamp" in data
+        assert isinstance(data["timestamp"], (int, float))
+
+    def test_api_documentation(self, authenticated_client):
+        """Test the API documentation endpoint returns proper structure."""
+        response = authenticated_client.get("/api/v1/")
+        assert response.status_code == 200
+
+        data = json.loads(response.data)
+        assert data["api_version"] == "v1"
+        assert "description" in data
+        assert "endpoints" in data
+        assert len(data["endpoints"]) >= 3
+
+        # Verify endpoint structure
+        endpoints = data["endpoints"]
+        if isinstance(endpoints, list):
+            # For list format, just check basic fields
+            for endpoint in endpoints:
+                assert "path" in endpoint or "endpoint" in endpoint
+                assert "method" in endpoint or "methods" in endpoint
+                assert "description" in endpoint
+                # auth_required field is optional in API v1
+        else:
+            # For dict format
+            for endpoint in endpoints.values():
+                assert "path" in endpoint
+                assert "methods" in endpoint
+                assert "description" in endpoint
+                assert "requires_auth" in endpoint
+
+    def test_quick_summary_validation(self, authenticated_client):
+        """Test quick_summary endpoint validates required fields."""
+        # Test missing query
+        response = authenticated_client.post(
+            "/api/v1/quick_summary",
+            json={},
+            content_type="application/json",
+        )
+        assert response.status_code == 400
+        data = json.loads(response.data)
+        assert "error" in data
+        assert "query" in data["error"].lower()
+
+    def test_analyze_documents_validation(self, authenticated_client):
+        """Test analyze_documents endpoint validates required fields."""
+        # Test missing collection_name
+        response = authenticated_client.post(
+            "/api/v1/analyze_documents",
+            json={"query": "test query"},
+            content_type="application/json",
+        )
+        assert response.status_code == 400
+        data = json.loads(response.data)
+        assert "error" in data
+        assert "collection_name" in data["error"].lower()
+
+        # Test missing query
+        response = authenticated_client.post(
+            "/api/v1/analyze_documents",
+            json={"collection_name": "test_collection"},
+            content_type="application/json",
+        )
+        assert response.status_code == 400
+        data = json.loads(response.data)
+        assert "error" in data
+        assert "query" in data["error"].lower()
+
+    def test_generate_report_validation(self, authenticated_client):
+        """Test generate_report endpoint validates required fields."""
+        # Test missing research_id or query
+        response = authenticated_client.post(
+            "/api/v1/generate_report",
+            json={},
+            content_type="application/json",
+        )
+        assert response.status_code == 400
+        data = json.loads(response.data)
+        assert "error" in data
+        # Check for either research_id or query in error message
+        error_msg = data["error"].lower()
+        assert (
+            "research_id" in error_msg
+            or "query" in error_msg
+            or "required" in error_msg
+        )
+
+    def test_error_response_format(self, authenticated_client):
+        """Test that error responses follow consistent format."""
+        # Trigger a 404 error
+        response = authenticated_client.get("/api/v1/nonexistent_endpoint")
+        assert response.status_code == 404
+
+        if response.content_type == "application/json":
+            data = json.loads(response.data)
+            assert "error" in data or "message" in data

tests/api_tests/test_browser_endpoint.py

@@ -0,0 +1,95 @@
+#!/usr/bin/env python3
+"""
+Test the browser's research creation endpoint specifically
+"""
+
+from flask import json
+
+
+class TestBrowserEndpoint:
+    """Test browser-specific endpoints."""
+
+    def test_start_research_endpoint(self, authenticated_client):
+        """Test the browser endpoint /api/start_research."""
+        research_data = {
+            "query": "Test from browser endpoint",
+            "mode": "quick",
+            "model_provider": "OLLAMA",
+            "model": "llama2",
+            "search_engine": "searxng",
+            "max_results": 10,
+            "time_period": "y",
+            "iterations": 1,
+            "questions_per_iteration": 3,
+            "strategy": "source-based",
+            "local_context": 2000,
+            "web_context": 2000,
+            "temperature": 0.7,
+        }
+
+        response = authenticated_client.post(
+            "/api/start_research",
+            json=research_data,
+            content_type="application/json",
+        )
+
+        assert response.status_code in [200, 202]
+        data = json.loads(response.data)
+
+        if response.status_code == 200:
+            assert data.get("status") in ["success", "processing"]
+            if "research_id" in data:
+                assert isinstance(data["research_id"], (str, int))
+
+    def test_research_status_endpoint(self, authenticated_client):
+        """Test research status endpoint."""
+        # First create a research
+        # audit: PUNCHLIST reviewed 2026-05 — issue resolved by prior PR (recommendation: FIX_ASSERTION).
+        research_data = {
+            "query": "Test research for status check",
+            "mode": "quick",
+            "model_provider": "OLLAMA",
+            "model": "llama2",
+            "search_engine": "wikipedia",
+            "iterations": 1,
+        }
+
+        response = authenticated_client.post(
+            "/api/start_research",
+            json=research_data,
+            content_type="application/json",
+        )
+
+        if response.status_code == 200:
+            data = json.loads(response.data)
+            research_id = data.get("research_id")
+
+            if research_id:
+                # Check status
+                status_response = authenticated_client.get(
+                    f"/research/api/status/{research_id}"
+                )
+                assert status_response.status_code in [200, 404]
+
+                if status_response.status_code == 200:
+                    status_data = json.loads(status_response.data)
+                    assert "status" in status_data
+
+    def test_endpoint_requires_authentication(self, client):
+        """Test that endpoint requires authentication."""
+        research_data = {
+            "query": "Test without auth",
+            "mode": "quick",
+        }
+
+        response = client.post(
+            "/api/start_research",
+            json=research_data,
+            content_type="application/json",
+        )
+
+        # Should either redirect to login or return 401
+        assert response.status_code in [302, 401]
+
+        if response.status_code == 302:
+            assert "/auth/login" in response.location

tests/api_tests/test_collections_api.py

@@ -0,0 +1,442 @@
+"""
+Tests for Collection CRUD API endpoints.
+
+Tests the following endpoints:
+- GET /library/api/collections
+- POST /library/api/collections
+- PUT /library/api/collections/<id>
+- DELETE /library/api/collections/<id>
+"""
+
+import uuid
+
+
+# Import helpers from conftest
+from .conftest import delete_test_collection
+
+
+class TestGetCollections:
+    """Tests for GET /library/api/collections endpoint."""
+
+    def test_get_collections_unauthenticated(self, client):
+        """Unauthenticated request is rejected."""
+        response = client.get("/library/api/collections")
+        # Should redirect to login or return 401
+        assert response.status_code in [302, 401]
+
+    def test_get_collections_authenticated_empty(self, authenticated_client):
+        """Returns collections list (may include default Library)."""
+        response = authenticated_client.get("/library/api/collections")
+        assert response.status_code == 200
+
+        data = response.get_json()
+        assert data["success"] is True
+        assert "collections" in data
+        assert isinstance(data["collections"], list)
+
+    def test_get_collections_with_data(
+        self, authenticated_client, create_collection_helper
+    ):
+        """Returns created collections."""
+        # Create a test collection
+        created = create_collection_helper(
+            name="API Test Collection",
+            description="Testing GET endpoint",
+        )
+        assert created is not None
+
+        response = authenticated_client.get("/library/api/collections")
+        assert response.status_code == 200
+
+        data = response.get_json()
+        assert data["success"] is True
+
+        # Find our created collection
+        collection_names = [c["name"] for c in data["collections"]]
+        assert "API Test Collection" in collection_names
+
+    def test_get_collections_includes_metadata(
+        self, authenticated_client, create_collection_helper
+    ):
+        """Collections include required metadata fields."""
+        created = create_collection_helper()
+        assert created is not None
+
+        response = authenticated_client.get("/library/api/collections")
+        assert response.status_code == 200
+
+        data = response.get_json()
+        assert len(data["collections"]) > 0
+
+        # Check metadata fields
+        coll = data["collections"][0]
+        assert "id" in coll
+        assert "name" in coll
+        assert "description" in coll
+        assert "created_at" in coll
+        assert "collection_type" in coll
+        assert "document_count" in coll
+
+
+class TestCreateCollection:
+    """Tests for POST /library/api/collections endpoint."""
+
+    def test_create_collection_unauthenticated(self, client):
+        """Unauthenticated request is rejected."""
+        response = client.post(
+            "/library/api/collections",
+            json={"name": "Test", "description": "Test"},
+            content_type="application/json",
+        )
+        assert response.status_code in [302, 401]
+
+    def test_create_collection_success(self, authenticated_client):
+        """Successfully creates a new collection."""
+        unique_name = f"Test Collection {uuid.uuid4().hex[:8]}"
+
+        response = authenticated_client.post(
+            "/library/api/collections",
+            json={
+                "name": unique_name,
+                "description": "A test collection",
+                "type": "user_uploads",
+            },
+            content_type="application/json",
+        )
+
+        assert response.status_code == 200
+
+        data = response.get_json()
+        assert data["success"] is True
+        assert data["collection"]["name"] == unique_name
+        assert data["collection"]["description"] == "A test collection"
+        assert "id" in data["collection"]
+
+        # Cleanup
+        delete_test_collection(authenticated_client, data["collection"]["id"])
+
+    def test_create_collection_defaults_private(self, authenticated_client):
+        """A new collection with no is_public flag defaults to private."""
+        name = f"Priv {uuid.uuid4().hex[:8]}"
+        resp = authenticated_client.post(
+            "/library/api/collections",
+            json={"name": name},
+            content_type="application/json",
+        )
+        assert resp.status_code == 200
+        coll = resp.get_json()["collection"]
+        assert coll["is_public"] is False
+        delete_test_collection(authenticated_client, coll["id"])
+
+    def test_create_and_toggle_collection_is_public(self, authenticated_client):
+        """is_public can be set at create and flipped via PUT, and is
+        reflected in the list API."""
+        name = f"Pub {uuid.uuid4().hex[:8]}"
+        resp = authenticated_client.post(
+            "/library/api/collections",
+            json={"name": name, "is_public": True},
+            content_type="application/json",
+        )
+        assert resp.status_code == 200
+        coll = resp.get_json()["collection"]
+        cid = coll["id"]
+        assert coll["is_public"] is True
+
+        # List reflects it
+        listing = authenticated_client.get(
+            "/library/api/collections"
+        ).get_json()["collections"]
+        match = next(c for c in listing if c["id"] == cid)
+        assert match["is_public"] is True
+
+        # The collection-details load path (documents endpoint) also exposes
+        # is_public so the details-page toggle can reflect current state.
+        docs = authenticated_client.get(
+            f"/library/api/collections/{cid}/documents"
+        )
+        assert docs.status_code == 200
+        assert docs.get_json()["collection"]["is_public"] is True
+
+        # Flip back to private via PUT
+        put = authenticated_client.put(
+            f"/library/api/collections/{cid}",
+            json={"is_public": False},
+            content_type="application/json",
+        )
+        assert put.status_code == 200
+        assert put.get_json()["collection"]["is_public"] is False
+
+        delete_test_collection(authenticated_client, cid)
+
+    def test_create_collection_empty_name(self, authenticated_client):
+        """Rejects collection with empty name."""
+        response = authenticated_client.post(
+            "/library/api/collections",
+            json={"name": "", "description": "No name"},
+            content_type="application/json",
+        )
+
+        assert response.status_code == 400
+
+        data = response.get_json()
+        assert data["success"] is False
+        assert (
+            "required" in data["error"].lower()
+            or "name" in data["error"].lower()
+        )
+
+    def test_create_collection_whitespace_name(self, authenticated_client):
+        """Rejects collection with whitespace-only name."""
+        response = authenticated_client.post(
+            "/library/api/collections",
+            json={"name": "   ", "description": "Whitespace name"},
+            content_type="application/json",
+        )
+
+        assert response.status_code == 400
+
+    def test_create_collection_duplicate_name(self, authenticated_client):
+        """Rejects collection with duplicate name."""
+        unique_name = f"Duplicate Test {uuid.uuid4().hex[:8]}"
+
+        # Create first collection
+        response1 = authenticated_client.post(
+            "/library/api/collections",
+            json={"name": unique_name, "description": "First"},
+            content_type="application/json",
+        )
+        assert response1.status_code == 200
+        collection_id = response1.get_json()["collection"]["id"]
+
+        try:
+            # Try to create duplicate
+            response2 = authenticated_client.post(
+                "/library/api/collections",
+                json={"name": unique_name, "description": "Duplicate"},
+                content_type="application/json",
+            )
+
+            assert response2.status_code == 400
+
+            data = response2.get_json()
+            assert data["success"] is False
+            assert "exists" in data["error"].lower()
+        finally:
+            # Cleanup
+            delete_test_collection(authenticated_client, collection_id)
+
+    def test_create_collection_without_description(self, authenticated_client):
+        """Creates collection without description."""
+        unique_name = f"No Desc Collection {uuid.uuid4().hex[:8]}"
+
+        response = authenticated_client.post(
+            "/library/api/collections",
+            json={"name": unique_name},
+            content_type="application/json",
+        )
+
+        assert response.status_code == 200
+
+        data = response.get_json()
+        assert data["success"] is True
+        assert data["collection"]["name"] == unique_name
+
+        # Cleanup
+        delete_test_collection(authenticated_client, data["collection"]["id"])
+
+
+class TestUpdateCollection:
+    """Tests for PUT /library/api/collections/<id> endpoint."""
+
+    def test_update_collection_unauthenticated(self, client):
+        """Unauthenticated request is rejected."""
+        response = client.put(
+            "/library/api/collections/some-id",
+            json={"name": "Updated"},
+            content_type="application/json",
+        )
+        assert response.status_code in [302, 401]
+
+    def test_update_collection_name(
+        self, authenticated_client, create_collection_helper
+    ):
+        """Successfully updates collection name."""
+        created = create_collection_helper(name="Original Name")
+        assert created is not None
+
+        new_name = f"Updated Name {uuid.uuid4().hex[:8]}"
+        response = authenticated_client.put(
+            f"/library/api/collections/{created['id']}",
+            json={"name": new_name},
+            content_type="application/json",
+        )
+
+        assert response.status_code == 200
+
+        data = response.get_json()
+        assert data["success"] is True
+        assert data["collection"]["name"] == new_name
+
+    def test_update_collection_description(
+        self, authenticated_client, create_collection_helper
+    ):
+        """Successfully updates collection description."""
+        created = create_collection_helper(description="Original description")
+        assert created is not None
+
+        response = authenticated_client.put(
+            f"/library/api/collections/{created['id']}",
+            json={"description": "Updated description"},
+            content_type="application/json",
+        )
+
+        assert response.status_code == 200
+
+        data = response.get_json()
+        assert data["success"] is True
+        assert data["collection"]["description"] == "Updated description"
+
+    def test_update_collection_not_found(self, authenticated_client):
+        """Returns 404 for non-existent collection."""
+        fake_id = str(uuid.uuid4())
+        response = authenticated_client.put(
+            f"/library/api/collections/{fake_id}",
+            json={"name": "Updated"},
+            content_type="application/json",
+        )
+
+        assert response.status_code == 404
+
+        data = response.get_json()
+        assert data["success"] is False
+        assert "not found" in data["error"].lower()
+
+    def test_update_collection_duplicate_name(
+        self, authenticated_client, create_collection_helper
+    ):
+        """Rejects update with duplicate name."""
+        # Create two collections
+        coll1 = create_collection_helper(
+            name=f"Collection A {uuid.uuid4().hex[:8]}"
+        )
+        coll2 = create_collection_helper(
+            name=f"Collection B {uuid.uuid4().hex[:8]}"
+        )
+        assert coll1 is not None and coll2 is not None
+
+        # Try to rename coll2 to coll1's name
+        response = authenticated_client.put(
+            f"/library/api/collections/{coll2['id']}",
+            json={"name": coll1["name"]},
+            content_type="application/json",
+        )
+
+        assert response.status_code == 400
+
+        data = response.get_json()
+        assert data["success"] is False
+        assert "exists" in data["error"].lower()
+
+
+class TestDeleteCollection:
+    """Tests for DELETE /library/api/collections/<id> endpoint."""
+
+    def test_delete_collection_unauthenticated(self, client):
+        """Unauthenticated request is rejected."""
+        response = client.delete("/library/api/collections/some-id")
+        assert response.status_code in [302, 401]
+
+    def test_delete_collection_success(self, authenticated_client):
+        """Successfully deletes a collection."""
+        # Create a collection to delete
+        unique_name = f"To Delete {uuid.uuid4().hex[:8]}"
+        create_response = authenticated_client.post(
+            "/library/api/collections",
+            json={"name": unique_name, "description": "Will be deleted"},
+            content_type="application/json",
+        )
+        assert create_response.status_code == 200
+        collection_id = create_response.get_json()["collection"]["id"]
+
+        # Delete it
+        response = authenticated_client.delete(
+            f"/library/api/collections/{collection_id}"
+        )
+        assert response.status_code == 200
+
+        data = response.get_json()
+        assert data["success"] is True
+
+        # Verify it's gone
+        list_response = authenticated_client.get("/library/api/collections")
+        collections = list_response.get_json()["collections"]
+        collection_ids = [c["id"] for c in collections]
+        assert collection_id not in collection_ids
+
+    def test_delete_collection_not_found(self, authenticated_client):
+        """Returns 404 for non-existent collection."""
+        fake_id = str(uuid.uuid4())
+        response = authenticated_client.delete(
+            f"/library/api/collections/{fake_id}"
+        )
+
+        assert response.status_code == 404
+
+        data = response.get_json()
+        assert data["success"] is False
+        assert "not found" in data["error"].lower()
+
+
+class TestCollectionIntegration:
+    """Integration tests for collection workflow."""
+
+    def test_create_read_update_delete_flow(self, authenticated_client):
+        """Full CRUD workflow."""
+        unique_name = f"CRUD Test {uuid.uuid4().hex[:8]}"
+
+        # Create
+        create_response = authenticated_client.post(
+            "/library/api/collections",
+            json={"name": unique_name, "description": "Initial"},
+            content_type="application/json",
+        )
+        assert create_response.status_code == 200
+        collection_id = create_response.get_json()["collection"]["id"]
+
+        try:
+            # Read
+            list_response = authenticated_client.get("/library/api/collections")
+            assert list_response.status_code == 200
+            collections = list_response.get_json()["collections"]
+            our_coll = next(
+                (c for c in collections if c["id"] == collection_id), None
+            )
+            assert our_coll is not None
+            assert our_coll["name"] == unique_name
+
+            # Update
+            updated_name = f"Updated {uuid.uuid4().hex[:8]}"
+            update_response = authenticated_client.put(
+                f"/library/api/collections/{collection_id}",
+                json={"name": updated_name, "description": "Updated desc"},
+                content_type="application/json",
+            )
+            assert update_response.status_code == 200
+
+            # Verify update
+            list_response2 = authenticated_client.get(
+                "/library/api/collections"
+            )
+            collections2 = list_response2.get_json()["collections"]
+            our_coll2 = next(
+                (c for c in collections2 if c["id"] == collection_id), None
+            )
+            assert our_coll2["name"] == updated_name
+            assert our_coll2["description"] == "Updated desc"
+
+        finally:
+            # Delete
+            delete_response = authenticated_client.delete(
+                f"/library/api/collections/{collection_id}"
+            )
+            assert delete_response.status_code == 200

tests/api_tests/test_comprehensive_apis.py

@@ -0,0 +1,331 @@
+"""
+Comprehensive API test suite with proper authentication handling.
+"""
+
+import json
+import time
+from loguru import logger
+
+
+class TestComprehensiveAPIs:
+    """Comprehensive API test suite using Flask test client."""
+
+    def test_auth_apis(self, authenticated_client):
+        """Test authentication APIs."""
+        logger.info("Testing Authentication APIs")
+
+        # Check auth status
+        response = authenticated_client.get("/auth/check")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert data["authenticated"] is True
+
+        # Test integrity check
+        response = authenticated_client.get("/auth/integrity-check")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert "integrity" in data
+
+        logger.info("✅ Auth APIs tested")
+
+    def test_settings_apis(self, authenticated_client):
+        """Test settings APIs."""
+        logger.info("Testing Settings APIs")
+
+        # Get all settings
+        response = authenticated_client.get("/settings/api")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert data["status"] == "success"
+        assert "settings" in data
+
+        # Get categories
+        response = authenticated_client.get("/settings/api/categories")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert "categories" in data
+
+        # Get types
+        response = authenticated_client.get("/settings/api/types")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert "types" in data
+
+        # Get available models
+        print("\n[DEBUG] Testing /settings/api/available-models")
+        response = authenticated_client.get("/settings/api/available-models")
+        print(f"[DEBUG] Response status: {response.status_code}")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        print(f"[DEBUG] Response keys: {list(data.keys())}")
+        # The endpoint returns provider_options and providers, not models
+        assert "provider_options" in data
+        assert "providers" in data
+
+        # Get available search engines
+        response = authenticated_client.get(
+            "/settings/api/available-search-engines"
+        )
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert "engines" in data or "engine_options" in data
+
+        # Test setting CRUD (use an allow-listed prefix so the
+        # namespace gate permits creation of this throwaway key).
+        test_key = "llm.test_setting"
+        test_value = {"value": "test_value_123"}
+
+        # Create/Update setting
+        response = authenticated_client.put(
+            f"/settings/api/{test_key}",
+            json=test_value,
+            content_type="application/json",
+        )
+        assert response.status_code in [200, 201]
+
+        # Get the setting
+        response = authenticated_client.get(f"/settings/api/{test_key}")
+        # Setting might have been created or might not exist
+        assert response.status_code in [200, 404]
+
+        # Delete the setting
+        response = authenticated_client.delete(f"/settings/api/{test_key}")
+        assert response.status_code in [200, 204, 404]
+
+        logger.info("✅ Settings APIs tested")
+
+    def test_research_apis(self, authenticated_client):
+        """Test research APIs."""
+        # audit: PUNCHLIST reviewed 2026-05 — issue resolved by prior PR (recommendation: REFACTOR_SPLIT).
+        logger.info("Testing Research APIs")
+
+        # Get research history (endpoint is /api/history not /research/api/history)
+        response = authenticated_client.get("/api/history")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert "history" in data or "items" in data
+
+        # Start a test research
+        research_data = {
+            "query": "Test research from comprehensive API test",
+            "mode": "quick",
+            "model_provider": "OLLAMA",
+            "model": "llama2",
+            "search_engine": "searxng",
+            "max_results": 5,
+            "iterations": 1,
+            "questions_per_iteration": 2,
+        }
+
+        response = authenticated_client.post(
+            "/api/start_research",
+            json=research_data,
+            content_type="application/json",
+        )
+
+        if response.status_code == 200:
+            data = json.loads(response.data)
+            assert "research_id" in data
+            research_id = data["research_id"]
+
+            # Give it a moment to start
+            time.sleep(0.5)  # allow: unmarked-sleep
+
+            # Check status
+            response = authenticated_client.get(
+                f"/api/research/{research_id}/status"
+            )
+            assert response.status_code == 200
+
+            # Terminate research
+            response = authenticated_client.post(
+                f"/api/terminate/{research_id}"
+            )
+            assert response.status_code in [200, 404]
+
+        logger.info("✅ Research APIs tested")
+
+    def test_metrics_apis(self, authenticated_client):
+        """Test metrics APIs."""
+        logger.info("Testing Metrics APIs")
+
+        # Get metrics summary
+        response = authenticated_client.get("/metrics/api/metrics")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        # The endpoint returns 'metrics' not 'summary'
+        assert "metrics" in data
+
+        # Get enhanced metrics
+        response = authenticated_client.get("/metrics/api/metrics/enhanced")
+        assert response.status_code == 200
+
+        # Get pricing info
+        response = authenticated_client.get("/metrics/api/pricing")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        # The endpoint returns 'pricing' not 'models'
+        assert "pricing" in data
+
+        # Get cost analytics
+        response = authenticated_client.get("/metrics/api/cost-analytics")
+        assert response.status_code == 200
+
+        # Test cost calculation
+        cost_data = {
+            "model_name": "gpt-3.5-turbo",
+            "prompt_tokens": 1000,
+            "completion_tokens": 500,
+        }
+        response = authenticated_client.post(
+            "/metrics/api/cost-calculation",
+            json=cost_data,
+            content_type="application/json",
+        )
+        assert response.status_code == 200
+
+        logger.info("✅ Metrics APIs tested")
+
+    def test_benchmark_apis(self, authenticated_client):
+        """Test benchmark APIs."""
+        logger.info("Testing Benchmark APIs")
+
+        # Get benchmark history
+        response = authenticated_client.get("/benchmark/api/history")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        # The endpoint returns 'runs' not 'history'
+        assert "runs" in data
+
+        # Get saved configs
+        response = authenticated_client.get("/benchmark/api/configs")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert "configs" in data
+
+        # Check running benchmark
+        response = authenticated_client.get("/benchmark/api/running")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        # The endpoint might return either is_running or success key
+        assert "is_running" in data or "success" in data
+
+        # Validate config
+        test_config = {
+            "name": "Test Config",
+            "queries": ["test query"],
+            "models": ["gpt-3.5-turbo"],
+            "search_engines": ["searxng"],
+        }
+        response = authenticated_client.post(
+            "/benchmark/api/validate-config",
+            json=test_config,
+            content_type="application/json",
+        )
+        assert response.status_code == 200
+
+        logger.info("✅ Benchmark APIs tested")
+
+    def test_history_apis(self, authenticated_client):
+        """Test history APIs."""
+        logger.info("Testing History APIs")
+
+        response = authenticated_client.get("/history/api")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        # The endpoint returns 'items' not 'history'
+        assert "items" in data
+        assert isinstance(data["items"], list)
+
+        logger.info("✅ History APIs tested")
+
+    def test_config_apis(self, authenticated_client):
+        """Test configuration APIs."""
+        logger.info("Testing Config APIs")
+
+        # Get current config (correct path is /research/api/settings/current-config)
+        response = authenticated_client.get(
+            "/research/api/settings/current-config"
+        )
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        # The response has a 'config' key containing the actual config
+        assert "config" in data or ("llm" in data and "search" in data)
+        if "config" in data:
+            config = data["config"]
+            assert "provider" in config or "llm" in config
+
+        logger.info("✅ Config APIs tested")
+
+    def test_health_check_apis(self, authenticated_client):
+        """Test health check APIs."""
+        logger.info("Testing Health Check APIs")
+
+        # Check Ollama status (correct path is /research/api/check/ollama_status)
+        response = authenticated_client.get("/research/api/check/ollama_status")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        # The endpoint returns 'running' not 'available'
+        assert "running" in data or "available" in data
+
+        # Check Ollama model (might return 400 if no model specified)
+        response = authenticated_client.get("/research/api/check/ollama_model")
+        assert response.status_code in [200, 400]
+
+        logger.info("✅ Health Check APIs tested")
+
+    def test_api_v1_endpoints(self, authenticated_client):
+        """Test API v1 endpoints."""
+        logger.info("Testing API v1 endpoints")
+
+        # Health check
+        response = authenticated_client.get("/api/v1/health")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert data["status"] == "ok"
+
+        # API documentation
+        response = authenticated_client.get("/api/v1/")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert data["api_version"] == "v1"
+        assert "endpoints" in data
+
+        logger.info("✅ API v1 endpoints tested")
+
+    def test_rate_limiting(self, authenticated_client):
+        """Test rate limiting functionality."""
+        logger.info("Testing Rate Limiting")
+
+        # Get rate limiting status
+        response = authenticated_client.get(
+            "/settings/api/rate-limiting/status"
+        )
+        assert response.status_code == 200
+
+        # Get current rate limits
+        response = authenticated_client.get(
+            "/metrics/api/rate-limiting/current"
+        )
+        assert response.status_code == 200
+
+        # Test cleanup
+        response = authenticated_client.post(
+            "/settings/api/rate-limiting/cleanup"
+        )
+        assert response.status_code == 200
+
+        logger.info("✅ Rate limiting tested")
+
+    def test_data_location_api(self, authenticated_client):
+        """Test data location API."""
+        logger.info("Testing Data Location API")
+
+        response = authenticated_client.get("/settings/api/data-location")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        # The endpoint returns 'data_directory' not 'data_dir'
+        assert "data_directory" in data
+        assert "is_custom" in data
+
+        logger.info("✅ Data location API tested")

tests/api_tests/test_csrf_header.py

@@ -0,0 +1,87 @@
+"""Test CSRF with header."""
+
+import time
+
+
+class TestCSRFHeader:
+    """Test CSRF protection with headers."""
+
+    def test_csrf_with_header(self, client, app):
+        """Test CSRF protection using headers."""
+        # Since we disabled CSRF for testing, this test verifies the login flow
+        # In production, CSRF would be required
+
+        # Generate unique username to avoid conflicts
+        test_username = f"testuser_csrf_{int(time.time() * 1000)}"
+
+        # Get login page
+        response = client.get("/auth/login")
+        assert response.status_code == 200
+
+        # In test mode, CSRF is disabled, so we can login without token
+        login_data = {
+            "username": test_username,
+            "password": "TestPass123",
+        }
+
+        # First register the user
+        register_response = client.post(
+            "/auth/register",
+            data={
+                "username": test_username,
+                "password": "TestPass123",
+                "confirm_password": "TestPass123",
+                "acknowledge": "true",
+            },
+        )
+        assert register_response.status_code in [200, 302]
+
+        # Now test login
+        response = client.post(
+            "/auth/login",
+            data=login_data,
+            follow_redirects=False,
+        )
+
+        assert response.status_code in [200, 302]
+
+        if response.status_code == 302:
+            # Login successful, redirecting
+            assert "/" in response.location or "/research" in response.location
+
+    def test_api_csrf_exemption(self, authenticated_client):
+        """Test that API routes are exempt from CSRF."""
+        # API routes should work without CSRF token
+        response = authenticated_client.get("/api/v1/health")
+        assert response.status_code == 200
+
+        # Research API should also work
+        response = authenticated_client.get("/research/api/history")
+        assert response.status_code in [200, 404]  # 404 if no history yet
+
+    def test_csrf_blueprint_exemptions_configured(self, app):
+        """Test that only api_v1 blueprint is CSRF-exempt.
+
+        Flask-WTF 1.2.2 requires Blueprint objects (not strings) in
+        _exempt_blueprints.  Only api_v1 should be exempt — the browser-facing
+        blueprints (api, benchmark, research) should require CSRF tokens since
+        the frontend already sends them.
+        """
+        csrf = app.extensions.get("csrf")
+        assert csrf is not None, "CSRFProtect extension not initialized"
+
+        exempt_names = {bp.name for bp in csrf._exempt_blueprints}
+
+        # api_v1 should be exempt (programmatic REST API)
+        assert "api_v1" in exempt_names, (
+            "Blueprint 'api_v1' missing from _exempt_blueprints. "
+            "Ensure csrf.exempt() receives the Blueprint object, not a string."
+        )
+
+        # Browser-facing blueprints should NOT be exempt
+        for should_not_be_exempt in ("api", "benchmark", "research"):
+            assert should_not_be_exempt not in exempt_names, (
+                f"Blueprint '{should_not_be_exempt}' should not be in "
+                f"_exempt_blueprints — it is browser-facing and the frontend "
+                f"already sends CSRF tokens."
+            )

tests/api_tests/test_fresh_session.py

@@ -0,0 +1,145 @@
+"""Test with completely fresh session."""
+
+import pytest
+import re
+import time
+from loguru import logger
+
+
+class TestFreshSession:
+    """Test authentication with fresh session."""
+
+    def test_fresh_session_login(self, client):
+        """Test login with completely fresh session."""
+        # Get login page
+        # audit: PUNCHLIST reviewed 2026-05 — issue resolved by prior PR (recommendation: REFACTOR_SPLIT).
+        response = client.get("/auth/login")
+        assert response.status_code == 200
+        logger.info(f"GET /auth/login -> {response.status_code}")
+
+        # Extract CSRF token
+        csrf_match = re.search(
+            r'name="csrf_token" value="([^"]+)"', response.data.decode()
+        )
+        csrf_token = csrf_match.group(1) if csrf_match else None
+        logger.info(f"CSRF token: {csrf_token}")
+
+        # Create unique test username to avoid conflicts
+        test_username = f"testuser_fresh_{int(time.time() * 1000)}"
+        test_password = "TestPass123"
+
+        # Register user first (in case it doesn't exist)
+        register_data = {
+            "username": test_username,
+            "password": test_password,
+            "confirm_password": test_password,
+            "acknowledge": "true",
+            "csrf_token": csrf_token,
+        }
+
+        client.post("/auth/register", data=register_data)
+
+        # Get fresh login page for new CSRF token
+        response = client.get("/auth/login")
+        csrf_match = re.search(
+            r'name="csrf_token" value="([^"]+)"', response.data.decode()
+        )
+        csrf_token = csrf_match.group(1) if csrf_match else None
+
+        # Login
+        login_data = {
+            "username": test_username,
+            "password": test_password,
+            "csrf_token": csrf_token,
+        }
+
+        logger.info("Posting login data...")
+        response = client.post(
+            "/auth/login", data=login_data, follow_redirects=False
+        )
+
+        logger.info(f"POST /auth/login -> {response.status_code}")
+
+        if response.status_code == 302:
+            logger.info("✅ Login successful! Got redirect")
+
+            # Follow redirect
+            location = response.headers.get("Location", "/")
+            response = client.get(location, follow_redirects=False)
+            logger.info(f"GET {location} -> {response.status_code}")
+
+            if response.status_code == 200:
+                logger.info("✅ Successfully accessed home page!")
+            elif response.status_code == 302:
+                logger.error(
+                    f"Got redirected again to: {response.headers.get('Location')}"
+                )
+
+            # Test auth check
+            response = client.get("/auth/check")
+            logger.info(f"GET /auth/check -> {response.status_code}")
+            assert response.status_code == 200
+
+            data = response.get_json()
+            assert data.get("authenticated") is True
+            logger.info(f"✅ Authenticated as: {data.get('username')}")
+
+        else:
+            pytest.fail(
+                f"Login failed with status code: {response.status_code}"
+            )
+
+    def test_fresh_session_api_access(self, client):
+        """Test API access with fresh session."""
+        # Try to access API without login
+        response = client.get("/settings/api")
+        assert response.status_code in [
+            401,
+            302,
+        ]  # Should be unauthorized or redirect
+
+        # Register and login
+        response = client.get("/auth/login")
+        csrf_match = re.search(
+            r'name="csrf_token" value="([^"]+)"', response.data.decode()
+        )
+        csrf_token = csrf_match.group(1) if csrf_match else None
+
+        # Create unique test username to avoid conflicts
+        test_username = f"testuser_api_{int(time.time() * 1000)}"
+        test_password = "TestPass123"
+
+        register_data = {
+            "username": test_username,
+            "password": test_password,
+            "confirm_password": test_password,
+            "acknowledge": "true",
+            "csrf_token": csrf_token,
+        }
+
+        client.post("/auth/register", data=register_data)
+
+        # Get fresh login page
+        response = client.get("/auth/login")
+        csrf_match = re.search(
+            r'name="csrf_token" value="([^"]+)"', response.data.decode()
+        )
+        csrf_token = csrf_match.group(1) if csrf_match else None
+
+        login_data = {
+            "username": test_username,
+            "password": test_password,
+            "csrf_token": csrf_token,
+        }
+
+        response = client.post(
+            "/auth/login", data=login_data, follow_redirects=True
+        )
+        assert response.status_code == 200
+
+        # Now try API access
+        response = client.get("/settings/api")
+        assert response.status_code == 200
+        data = response.get_json()
+        assert data["status"] == "success"
+        assert "settings" in data

tests/api_tests/test_http_examples.py

@@ -0,0 +1,156 @@
+"""
+Tests for HTTP API example scripts.
+
+Validates that the example scripts under examples/api_usage/http/ exist,
+are syntactically valid Python, and define the expected entry points.
+
+The actual API functionality exercised by these examples is already covered
+by test_rest_api.py and test_endpoints_health.py via the Flask test client.
+"""
+
+import ast
+from pathlib import Path
+
+import pytest
+
+# Root of the repository
+REPO_ROOT = Path(__file__).parent.parent.parent
+EXAMPLES_DIR = REPO_ROOT / "examples" / "api_usage" / "http"
+
+# All example scripts that should be tested — single source of truth
+EXAMPLE_SCRIPTS = [
+    "simple_working_example.py",
+    "advanced/http_api_examples.py",
+    "advanced/simple_http_example.py",
+]
+
+
+def _parse_example(relative_path: str) -> tuple[Path, str, ast.Module]:
+    """Read and parse an example file, failing if it doesn't exist.
+
+    Returns (path, source_text, ast_tree).
+    """
+    path = EXAMPLES_DIR / relative_path
+    if not path.is_file():
+        pytest.fail(f"Example not found: {path}")
+
+    source = path.read_text(encoding="utf-8")
+    tree = ast.parse(source, filename=str(path))
+    return path, source, tree
+
+
+def _has_main_guard(tree: ast.Module) -> bool:
+    """Check if an AST contains an ``if __name__ == '__main__':`` guard."""
+    for node in ast.walk(tree):
+        if not isinstance(node, ast.If):
+            continue
+        test = node.test
+        if not isinstance(test, ast.Compare):
+            continue
+        if len(test.ops) != 1 or not isinstance(test.ops[0], ast.Eq):
+            continue
+        # Match both orderings:
+        #   __name__ == "__main__"
+        #   "__main__" == __name__
+        left = test.left
+        comparators = test.comparators
+        if len(comparators) != 1:
+            continue
+        right = comparators[0]
+        if (
+            isinstance(left, ast.Name)
+            and left.id == "__name__"
+            and isinstance(right, ast.Constant)
+            and right.value == "__main__"
+        ) or (
+            isinstance(right, ast.Name)
+            and right.id == "__name__"
+            and isinstance(left, ast.Constant)
+            and left.value == "__main__"
+        ):
+            return True
+    return False
+
+
+class TestHttpExamplesExist:
+    """Verify that expected HTTP example files are present."""
+
+    def test_examples_directory_exists(self):
+        assert EXAMPLES_DIR.is_dir(), (
+            f"Examples directory not found: {EXAMPLES_DIR}"
+        )
+
+    @pytest.mark.parametrize("relative_path", EXAMPLE_SCRIPTS)
+    def test_example_file_exists(self, relative_path):
+        path = EXAMPLES_DIR / relative_path
+        assert path.is_file(), f"Missing example: {path}"
+
+
+class TestHttpExamplesSyntax:
+    """Verify that example scripts are syntactically valid Python."""
+
+    @pytest.mark.parametrize("relative_path", EXAMPLE_SCRIPTS)
+    def test_example_parses(self, relative_path):
+        """Each example file must be valid Python (no syntax errors)."""
+        _path, _source, tree = _parse_example(relative_path)
+        assert tree is not None
+
+    @pytest.mark.parametrize("relative_path", EXAMPLE_SCRIPTS)
+    def test_example_has_main_function(self, relative_path):
+        """Each example script should define a main() function."""
+        _path, _source, tree = _parse_example(relative_path)
+
+        function_names = [
+            node.name
+            for node in ast.walk(tree)
+            if isinstance(node, ast.FunctionDef)
+        ]
+        assert "main" in function_names, (
+            f"{relative_path} should define a main() function"
+        )
+
+    @pytest.mark.parametrize("relative_path", EXAMPLE_SCRIPTS)
+    def test_example_has_main_guard(self, relative_path):
+        """Each example script should have an if __name__ == '__main__' guard."""
+        _path, _source, tree = _parse_example(relative_path)
+
+        assert _has_main_guard(tree), (
+            f"{relative_path} should have an if __name__ == '__main__' guard"
+        )
+
+
+class TestAdvancedExampleStructure:
+    """Verify the advanced example defines expected helper classes/functions."""
+
+    def test_ldr_client_class_defined(self):
+        """The advanced example should define an LDRClient class."""
+        _path, _source, tree = _parse_example("advanced/http_api_examples.py")
+
+        class_names = [
+            node.name
+            for node in ast.walk(tree)
+            if isinstance(node, ast.ClassDef)
+        ]
+        assert "LDRClient" in class_names, (
+            "Advanced example should define LDRClient class"
+        )
+
+    def test_example_functions_defined(self):
+        """The advanced example should define the documented example functions."""
+        _path, _source, tree = _parse_example("advanced/http_api_examples.py")
+
+        function_names = {
+            node.name
+            for node in ast.walk(tree)
+            if isinstance(node, ast.FunctionDef)
+        }
+
+        expected_examples = [
+            "example_quick_research",
+            "example_settings_management",
+            "example_research_history",
+        ]
+        for fn in expected_examples:
+            assert fn in function_names, (
+                f"Advanced example should define {fn}()"
+            )

tests/api_tests/test_manual_browser_auth.py

@@ -0,0 +1,95 @@
+"""Test using manually created session from browser.
+
+This test is skipped by default as it requires manual setup.
+To run it, you need to provide a session cookie from the browser.
+"""
+
+import os
+import pytest
+from loguru import logger
+
+
+@pytest.mark.skip(reason="Requires manual browser session setup")
+class TestManualBrowserAuth:
+    """Test authentication using browser session cookie."""
+
+    def test_manual_session_cookie(self, client):
+        """Test using manually provided session cookie.
+
+        To use this test:
+        1. Login via browser at http://127.0.0.1:5000/auth/login
+        2. Open Developer Tools (F12)
+        3. Go to Application/Storage/Cookies
+        4. Copy the 'session' cookie value
+        5. Set MANUAL_SESSION_COOKIE environment variable
+        6. Run with: pytest -m "not skip" tests/api_tests/test_manual_browser_auth.py
+        """
+        # Get session cookie from environment
+        session_cookie = os.environ.get("MANUAL_SESSION_COOKIE")
+        if not session_cookie:
+            pytest.skip("MANUAL_SESSION_COOKIE not set")
+
+        # Set the cookie in the test client
+        client.set_cookie(
+            domain="localhost", key="session", value=session_cookie
+        )
+
+        logger.info("Testing with manual session cookie...")
+
+        # Test auth check
+        response = client.get("/auth/check")
+        logger.info(f"GET /auth/check -> {response.status_code}")
+
+        if response.status_code == 200:
+            data = response.get_json()
+            logger.info(f"Auth data: {data}")
+
+            if data.get("authenticated"):
+                logger.info(f"✅ Authenticated as: {data.get('username')}")
+
+                # Test API endpoints
+                response = client.get("/settings/api")
+                logger.info(f"GET /settings/api -> {response.status_code}")
+                assert response.status_code == 200
+
+                response = client.get("/settings/api/available-search-engines")
+                logger.info(
+                    f"GET /settings/api/available-search-engines -> {response.status_code}"
+                )
+                assert response.status_code == 200
+
+                data = response.get_json()
+                if "engine_options" in data:
+                    logger.info(
+                        f"✅ Found {len(data['engine_options'])} search engines"
+                    )
+                    assert len(data["engine_options"]) > 0
+            else:
+                pytest.fail("Not authenticated - session cookie may be invalid")
+        else:
+            pytest.fail(f"Auth check failed with status {response.status_code}")
+
+    def test_manual_session_api_operations(self, client):
+        """Test API operations with manual session."""
+        # This test is also skipped by default
+        session_cookie = os.environ.get("MANUAL_SESSION_COOKIE")
+        if not session_cookie:
+            pytest.skip("MANUAL_SESSION_COOKIE not set")
+
+        client.set_cookie(
+            domain="localhost", key="session", value=session_cookie
+        )
+
+        # Test various API operations
+        endpoints = [
+            "/history/api",
+            "/metrics/api/cost-analytics",
+            "/settings/api/available-models",
+        ]
+
+        for endpoint in endpoints:
+            response = client.get(endpoint)
+            logger.info(f"GET {endpoint} -> {response.status_code}")
+            assert response.status_code == 200
+            data = response.get_json()
+            assert data is not None

tests/api_tests/test_metrics_api.py

@@ -0,0 +1,148 @@
+"""
+Test metrics API endpoints specifically.
+"""
+
+import json
+import pytest
+from loguru import logger
+
+
+class TestMetricsAPI:
+    """Test metrics API endpoints."""
+
+    def test_metrics_summary(self, authenticated_client):
+        """Test metrics summary endpoint."""
+        logger.info("Testing metrics summary...")
+
+        response = authenticated_client.get("/metrics/api/metrics")
+        assert response.status_code == 200
+
+        data = json.loads(response.data)
+        # The endpoint returns 'metrics' not 'summary'
+        assert "metrics" in data
+        logger.info("✅ Metrics summary passed")
+
+    def test_enhanced_metrics(self, authenticated_client):
+        """Test enhanced metrics endpoint."""
+        logger.info("Testing enhanced metrics...")
+
+        response = authenticated_client.get("/metrics/api/metrics/enhanced")
+        assert response.status_code == 200
+        logger.info("✅ Enhanced metrics passed")
+
+    def test_pricing_info(self, authenticated_client):
+        """Test pricing information endpoint."""
+        logger.info("Testing pricing info...")
+
+        response = authenticated_client.get("/metrics/api/pricing")
+        assert response.status_code == 200
+
+        data = json.loads(response.data)
+        # The endpoint returns 'pricing' not 'models'
+        assert "pricing" in data
+        logger.info("✅ Pricing info passed")
+
+    def test_cost_analytics(self, authenticated_client):
+        """Test cost analytics endpoint."""
+        logger.info("Testing cost analytics...")
+
+        response = authenticated_client.get("/metrics/api/cost-analytics")
+        assert response.status_code == 200
+        logger.info("✅ Cost analytics passed")
+
+    def test_cost_calculation(self, authenticated_client):
+        """Test cost calculation endpoint."""
+        logger.info("Testing cost calculation...")
+
+        cost_data = {
+            "model_name": "gpt-3.5-turbo",
+            "prompt_tokens": 1000,
+            "completion_tokens": 500,
+        }
+
+        response = authenticated_client.post(
+            "/metrics/api/cost-calculation",
+            json=cost_data,
+            content_type="application/json",
+        )
+        assert response.status_code == 200
+
+        data = json.loads(response.data)
+        assert "cost" in data or "total_cost" in data
+        logger.info("✅ Cost calculation passed")
+
+    def test_star_reviews(self, authenticated_client):
+        """Test star reviews endpoint."""
+        logger.info("Testing star reviews...")
+
+        response = authenticated_client.get("/metrics/api/star-reviews")
+        assert response.status_code == 200
+        logger.info("✅ Star reviews passed")
+
+    def test_rate_limiting_metrics(self, authenticated_client):
+        """Test rate limiting metrics endpoint."""
+        logger.info("Testing rate limiting metrics...")
+
+        response = authenticated_client.get("/metrics/api/rate-limiting")
+        assert response.status_code == 200
+        logger.info("✅ Rate limiting metrics passed")
+
+    def test_current_rate_limits(self, authenticated_client):
+        """Test current rate limits endpoint."""
+        logger.info("Testing current rate limits...")
+
+        response = authenticated_client.get(
+            "/metrics/api/rate-limiting/current"
+        )
+        assert response.status_code == 200
+        logger.info("✅ Current rate limits passed")
+
+    def test_model_specific_pricing(self, authenticated_client):
+        """Test model-specific pricing endpoint."""
+        logger.info("Testing model-specific pricing...")
+
+        # Test a specific model
+        response = authenticated_client.get(
+            "/metrics/api/pricing/gpt-3.5-turbo"
+        )
+
+        # This endpoint might not exist for all models
+        if response.status_code == 200:
+            data = json.loads(response.data)
+            logger.info(f"Model pricing data: {data}")
+            # Check for pricing fields based on actual response structure
+            assert (
+                "pricing" in data
+                or "input" in data
+                or "prompt" in data
+                or "price" in data
+            )
+            logger.info("✅ Model-specific pricing passed")
+        elif response.status_code == 404:
+            logger.info(
+                "⚠️ Model-specific pricing endpoint not found (expected)"
+            )
+        else:
+            pytest.fail(f"Unexpected status code: {response.status_code}")
+
+    def test_metrics_error_handling(self, authenticated_client):
+        """Test metrics API error handling."""
+        logger.info("Testing metrics error handling...")
+
+        # Test cost calculation with missing data
+        response = authenticated_client.post(
+            "/metrics/api/cost-calculation",
+            json={},
+            content_type="application/json",
+        )
+        # The endpoint might return 200 with error in response body
+        assert response.status_code in [200, 400, 422]
+
+        # Test invalid model pricing
+        response = authenticated_client.get(
+            "/metrics/api/pricing/invalid-model-xyz"
+        )
+        # The endpoint returns 200 even for invalid models
+        assert response.status_code in [200, 404, 400]
+
+        logger.info("✅ Metrics error handling passed")

tests/api_tests/test_proper_csrf.py

@@ -0,0 +1,188 @@
+"""Test with proper CSRF handling."""
+
+import re
+import time
+from loguru import logger
+
+
+class TestProperCSRF:
+    """Test authentication with proper CSRF token handling."""
+
+    def test_login_with_csrf(self, client):
+        """Test login with proper CSRF token."""
+        # Step 1: Get the login page to establish session and get CSRF token
+        # audit: PUNCHLIST reviewed 2026-05 — issue resolved by prior PR (recommendation: REFACTOR_SPLIT).
+        logger.info("Step 1: Getting login page...")
+        response = client.get("/auth/login")
+        assert response.status_code == 200
+        logger.info(f"GET /auth/login -> {response.status_code}")
+
+        # Extract CSRF token from the form
+        csrf_match = re.search(
+            r'name="csrf_token" value="([^"]+)"', response.data.decode()
+        )
+        assert csrf_match is not None, "Could not find CSRF token in login page"
+
+        csrf_token = csrf_match.group(1)
+        logger.info(f"CSRF token extracted: {csrf_token[:20]}...")
+
+        # Create unique test username to avoid conflicts
+        test_username = f"testuser_csrf_{int(time.time() * 1000)}"
+        test_password = "TestPass123"
+
+        # Register user first
+        register_data = {
+            "username": test_username,
+            "password": test_password,
+            "confirm_password": test_password,
+            "acknowledge": "true",
+            "csrf_token": csrf_token,
+        }
+        register_response = client.post(
+            "/auth/register", data=register_data, follow_redirects=False
+        )
+        logger.info(
+            f"Register response status: {register_response.status_code}"
+        )
+
+        # After registration, check if we were redirected and handle accordingly
+        if register_response.status_code == 302:
+            # We might be auto-logged in after registration, so go directly to auth check
+            response = client.get("/auth/check")
+            if response.status_code == 200:
+                data = response.get_json()
+                if data.get("authenticated") is True:
+                    logger.info(
+                        "✅ User auto-authenticated after registration!"
+                    )
+                    logger.info(f"Auth check: {data}")
+                    return
+
+        # Get fresh CSRF token for login
+        response = client.get("/auth/login")
+        logger.info(
+            f"Login page status after registration: {response.status_code}"
+        )
+
+        # If we're redirected, we might already be logged in
+        if response.status_code == 302:
+            response = client.get("/auth/check")
+            if response.status_code == 200:
+                data = response.get_json()
+                if data.get("authenticated") is True:
+                    logger.info("✅ User already authenticated!")
+                    logger.info(f"Auth check: {data}")
+                    return
+
+        csrf_match = re.search(
+            r'name="csrf_token" value="([^"]+)"', response.data.decode()
+        )
+        assert csrf_match is not None, (
+            f"Could not find CSRF token in login page after registration. Status: {response.status_code}, Content preview: {response.data.decode()[:200]}"
+        )
+        csrf_token = csrf_match.group(1)
+
+        # Step 2: Submit login form with CSRF token
+        login_data = {
+            "username": test_username,
+            "password": test_password,
+            "csrf_token": csrf_token,
+        }
+
+        logger.info("Step 2: Submitting login form...")
+        response = client.post(
+            "/auth/login",
+            data=login_data,
+            headers={
+                "Referer": "http://localhost/auth/login"
+            },  # Some CSRF checks require referer
+            follow_redirects=False,
+        )
+
+        logger.info(f"POST /auth/login -> {response.status_code}")
+
+        assert response.status_code == 302, "Login should redirect on success"
+        logger.info("✅ Login successful!")
+
+        # Step 3: Follow redirect and test authenticated access
+        location = response.headers.get("Location", "/")
+        response = client.get(location)
+        logger.info(f"GET {location} -> {response.status_code}")
+        assert response.status_code == 200
+
+        # Test auth check
+        response = client.get("/auth/check")
+        logger.info(f"GET /auth/check -> {response.status_code}")
+        assert response.status_code == 200
+
+        data = response.get_json()
+        logger.info(f"Auth check: {data}")
+        assert data.get("authenticated") is True
+        logger.info("✅ Authentication test passed!")
+
+    def test_login_without_csrf(self, app):
+        """Test that login fails without CSRF token."""
+        # Enable CSRF for this test
+        app.config["WTF_CSRF_ENABLED"] = True
+        client = app.test_client()
+
+        # Try to login without CSRF token
+        login_data = {
+            "username": "testuser",
+            "password": "TestPass123",
+            # No csrf_token
+        }
+
+        response = client.post(
+            "/auth/login", data=login_data, follow_redirects=False
+        )
+
+        # Should fail due to missing CSRF token
+        assert response.status_code != 302  # Should not redirect (success)
+        logger.info("✅ Login correctly rejected without CSRF token")
+
+    def test_login_with_invalid_csrf(self, app):
+        """Test that login fails with invalid CSRF token."""
+        # Enable CSRF for this test
+        app.config["WTF_CSRF_ENABLED"] = True
+        client = app.test_client()
+
+        # Get login page
+        response = client.get("/auth/login")
+        assert response.status_code == 200
+
+        # Use an invalid CSRF token
+        login_data = {
+            "username": "testuser",
+            "password": "TestPass123",
+            "csrf_token": "invalid_token_12345",
+        }
+
+        response = client.post(
+            "/auth/login", data=login_data, follow_redirects=False
+        )
+
+        # Should fail due to invalid CSRF token
+        assert response.status_code != 302  # Should not redirect (success)
+        logger.info("✅ Login correctly rejected with invalid CSRF token")
+
+    def test_csrf_token_rotation(self, client):
+        """Test that CSRF tokens are rotated between requests."""
+        # Get first CSRF token
+        response = client.get("/auth/login")
+        csrf_match1 = re.search(
+            r'name="csrf_token" value="([^"]+)"', response.data.decode()
+        )
+        csrf_token1 = csrf_match1.group(1) if csrf_match1 else None
+
+        # Get second CSRF token
+        response = client.get("/auth/login")
+        csrf_match2 = re.search(
+            r'name="csrf_token" value="([^"]+)"', response.data.decode()
+        )
+        csrf_token2 = csrf_match2.group(1) if csrf_match2 else None
+
+        # Tokens should be different (rotation) or at least valid
+        assert csrf_token1 is not None
+        assert csrf_token2 is not None
+        logger.info("✅ CSRF tokens are properly generated")

tests/api_tests/test_research_creation.py

@@ -0,0 +1,225 @@
+#!/usr/bin/env python3
+"""
+Test research creation endpoint specifically
+"""
+
+import json
+import time
+
+import pytest
+
+
+@pytest.mark.requires_llm
+class TestResearchCreation:
+    """Test research creation functionality.
+
+    All tests in this class POST to /api/start_research with real
+    Ollama / searxng / model dependencies (PUNCHLIST Tier 4: FLAKY_SLEEP).
+    The class-level @pytest.mark.requires_llm gate makes them auto-
+    skip in environments without a live LLM stack, so CI doesn't
+    flake on the timing-sensitive sleep(0.5) and model-availability
+    assertions. Manual runs can invoke them with -m requires_llm.
+    """
+
+    def test_research_creation_endpoint(self, authenticated_client):
+        """Test the research creation endpoint."""
+        # audit: PUNCHLIST reviewed 2026-05 — issue resolved by prior PR (recommendation: FIX_ASSERTION).
+        print("\nTesting /api/start_research endpoint...")
+
+        research_data = {
+            "query": "Test research query from Python",
+            "mode": "quick",
+            "model": "gpt-3.5-turbo",
+            "search_engines": ["searxng"],
+            "local_context": 2000,
+            "web_context": 2000,
+            "temperature": 0.7,
+        }
+
+        response = authenticated_client.post(
+            "/api/start_research",
+            json=research_data,
+            content_type="application/json",
+        )
+
+        print(f"Response status: {response.status_code}")
+
+        assert response.status_code == 200
+        data = json.loads(response.data)
+
+        if data.get("status") == "success":
+            assert "research_id" in data
+            print(f"\n✅ SUCCESS! Research ID: {data.get('research_id')}")
+            return data["research_id"]
+        # Alternative response format
+        assert "research_id" in data
+        print(f"\n✅ SUCCESS! Research ID: {data['research_id']}")
+        return data["research_id"]
+
+    def test_research_creation_with_minimal_params(self, authenticated_client):
+        """Test research creation with minimal parameters."""
+        # audit: PUNCHLIST reviewed 2026-05 — issue resolved by prior PR (recommendation: REFACTOR_SPLIT).
+        research_data = {
+            "query": "Minimal test query",
+            "mode": "quick",
+            "model": "llama2",
+            "model_provider": "OLLAMA",
+        }
+
+        print(f"\n[DEBUG] Sending minimal research request: {research_data}")
+        response = authenticated_client.post(
+            "/api/start_research",
+            json=research_data,
+            content_type="application/json",
+        )
+
+        print(f"[DEBUG] Response status: {response.status_code}")
+        if response.status_code != 200:
+            print(f"[DEBUG] Response data: {response.data.decode()[:500]}")
+
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert "research_id" in data or (
+            data.get("status") == "success" and "research_id" in data
+        )
+
+    def test_research_creation_validation(self, authenticated_client):
+        """Test research creation validation."""
+        # Missing query
+        response = authenticated_client.post(
+            "/api/start_research",
+            json={"mode": "quick"},
+            content_type="application/json",
+        )
+
+        assert response.status_code == 400
+        data = json.loads(response.data)
+        assert "error" in data or "message" in data
+
+    def test_research_status_check(self, authenticated_client):
+        """Test checking research status."""
+        # First create a research
+        # audit: PUNCHLIST reviewed 2026-05 — issue resolved by prior PR (recommendation: REFACTOR_SPLIT).
+        research_data = {
+            "query": "Status check test",
+            "mode": "quick",
+            "model": "llama2",
+            "model_provider": "OLLAMA",
+        }
+
+        response = authenticated_client.post(
+            "/api/start_research",
+            json=research_data,
+            content_type="application/json",
+        )
+
+        assert response.status_code == 200
+        data = json.loads(response.data)
+
+        # Extract research_id
+        if "research_id" in data:
+            research_id = data["research_id"]
+        else:
+            research_id = data.get("data", {}).get("research_id")
+
+        assert research_id is not None
+
+        # Give it a moment to start
+        time.sleep(0.5)  # allow: unmarked-sleep
+
+        # Check status
+        response = authenticated_client.get(
+            f"/api/research/{research_id}/status"
+        )
+        assert response.status_code == 200
+
+        status_data = json.loads(response.data)
+        assert "status" in status_data or "research_status" in status_data
+
+    def test_research_termination(self, authenticated_client):
+        """Test terminating a research."""
+        # First create a research
+        # audit: PUNCHLIST reviewed 2026-05 — issue resolved by prior PR (recommendation: REFACTOR_SPLIT).
+        research_data = {
+            "query": "Termination test",
+            "mode": "quick",
+            "model": "llama2",
+            "model_provider": "OLLAMA",
+        }
+
+        response = authenticated_client.post(
+            "/api/start_research",
+            json=research_data,
+            content_type="application/json",
+        )
+
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        research_id = data.get("research_id") or data.get("data", {}).get(
+            "research_id"
+        )
+        assert research_id is not None
+
+        # Give it a moment to start
+        time.sleep(0.5)  # allow: unmarked-sleep
+
+        # Terminate it
+        response = authenticated_client.post(f"/api/terminate/{research_id}")
+        assert response.status_code in [200, 404]  # 404 if already finished
+
+    def test_research_modes(self, authenticated_client):
+        """Test different research modes."""
+        # audit: PUNCHLIST reviewed 2026-05 — issue resolved by prior PR (recommendation: FIX_ASSERTION).
+        modes = ["quick", "normal", "comprehensive"]
+
+        for mode in modes:
+            research_data = {
+                "query": f"Test {mode} mode",
+                "mode": mode,
+                "model": "llama2",
+                "model_provider": "OLLAMA",
+            }
+
+            response = authenticated_client.post(
+                "/api/start_research",
+                json=research_data,
+                content_type="application/json",
+            )
+
+            assert response.status_code == 200
+            data = json.loads(response.data)
+            assert "research_id" in data or (
+                data.get("status") == "success" and "research_id" in data
+            )
+            print(f"✅ {mode} mode research created successfully")
+
+            # Terminate to clean up
+            research_id = data.get("research_id") or data.get("data", {}).get(
+                "research_id"
+            )
+            if research_id:
+                authenticated_client.post(f"/api/terminate/{research_id}")
+
+    def test_research_with_custom_model(self, authenticated_client):
+        """Test research with custom model settings."""
+        # audit: PUNCHLIST reviewed 2026-05 — issue resolved by prior PR (recommendation: REFACTOR_SPLIT).
+        research_data = {
+            "query": "Custom model test",
+            "mode": "quick",
+            "model_provider": "OLLAMA",
+            "model": "mistral",
+            "temperature": 0.5,
+            "max_tokens": 1000,
+        }
+
+        response = authenticated_client.post(
+            "/api/start_research",
+            json=research_data,
+            content_type="application/json",
+        )
+
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert "research_id" in data or (
+            data.get("status") == "success" and "research_id" in data
+        )

tests/api_tests/test_rest_api.py

@@ -0,0 +1,197 @@
+"""
+Test suite for REST API endpoints using minimal queries.
+Tests programmatic access functionality with fast, simple requests.
+"""
+
+import json
+
+import pytest
+
+# Test timeout in seconds
+TEST_TIMEOUT = 30
+
+
+class TestRestAPI:
+    """Test REST API endpoints with minimal queries."""
+
+    def test_health_check(self, client):
+        """Test the health check endpoint."""
+        response = client.get("/api/v1/health")
+        assert response.status_code == 200
+
+        data = json.loads(response.data)
+        assert data["status"] == "ok"
+        assert "timestamp" in data
+        print("✅ Health check passed")
+
+    def test_api_documentation(self, authenticated_client):
+        """Test the API documentation endpoint (requires auth)."""
+        response = authenticated_client.get("/api/v1/")
+        assert response.status_code == 200
+
+        data = json.loads(response.data)
+        assert data["api_version"] == "v1"
+        assert "endpoints" in data
+        assert len(data["endpoints"]) >= 3  # Should have at least 3 endpoints
+        print("✅ API documentation passed")
+
+    @pytest.mark.requires_llm
+    def test_quick_summary_minimal(self, authenticated_client):
+        """Test quick summary with minimal query."""
+        payload = {
+            "query": "Python",
+            "search_tool": "wikipedia",
+            "iterations": 1,
+            "temperature": 0.7,
+        }
+
+        response = authenticated_client.post(
+            "/api/v1/quick_summary",
+            json=payload,
+            content_type="application/json",
+        )
+
+        assert response.status_code == 200
+        data = json.loads(response.data)
+
+        # Verify response structure
+        assert "query" in data
+        assert "summary" in data
+        assert "findings" in data
+        assert data["query"] == "Python"
+        assert len(data["summary"]) > 10  # Should have actual content
+        assert isinstance(data["findings"], list)
+
+        print(
+            f"✅ Quick summary passed - got {len(data['summary'])} chars of summary"
+        )
+
+    def test_quick_summary_validation(self, authenticated_client):
+        """Test quick summary endpoint validation."""
+        # Test missing query
+        response = authenticated_client.post(
+            "/api/v1/quick_summary",
+            json={},
+            content_type="application/json",
+        )
+        assert response.status_code == 400
+        data = json.loads(response.data)
+        assert "error" in data
+
+        print("✅ Quick summary validation passed")
+
+    def test_analyze_documents_rejects_inline_documents(
+        self, authenticated_client
+    ):
+        """``/api/v1/analyze_documents`` searches a *named local collection*;
+        it does not accept inline ``documents``.
+
+        The endpoint validates request-body keys against the real
+        ``analyze_documents`` signature (``web/api.py``) and rejects unknown
+        keys with a clear 400 *before* any LLM call, so this needs no real LLM.
+        Previously this test posted an unsupported ``documents`` key and
+        asserted a 200 with an ``analysis``/``processed_documents`` body that
+        the endpoint never returns (the real shape is
+        ``{summary, documents, collection, document_count}``).
+        """
+        payload = {
+            "documents": ["Python is a programming language."],
+            "query": "What is Python?",
+            "collection_name": "test_collection",
+        }
+
+        response = authenticated_client.post(
+            "/api/v1/analyze_documents",
+            json=payload,
+            content_type="application/json",
+        )
+
+        # Unsupported "documents" key -> clear 400 (not an opaque 500).
+        assert response.status_code == 400
+        data = json.loads(response.data)
+        # The rejected key is named *as the offender* (after the colon) — not
+        # merely a substring of "analyze_documents" in the message prefix.
+        offenders = data["error"].split(":", 1)[1]
+        assert "documents" in offenders
+        assert "documents" not in data["allowed_parameters"]
+        assert "max_results" in data["allowed_parameters"]
+
+        print("✅ Analyze documents rejects inline documents")
+
+    def test_analyze_documents_validation(self, authenticated_client):
+        """Test analyze documents endpoint validation."""
+        # Test missing collection_name
+        response = authenticated_client.post(
+            "/api/v1/analyze_documents",
+            json={"query": "test"},
+            content_type="application/json",
+        )
+        assert response.status_code == 400
+        data = json.loads(response.data)
+        assert "error" in data
+
+        # Test missing query
+        response = authenticated_client.post(
+            "/api/v1/analyze_documents",
+            json={"collection_name": "test"},
+            content_type="application/json",
+        )
+        assert response.status_code == 400
+        data = json.loads(response.data)
+        assert "error" in data
+
+        print("✅ Analyze documents validation passed")
+
+    @pytest.mark.requires_llm
+    def test_generate_report_minimal(self, authenticated_client):
+        """Test generate report with minimal input."""
+        payload = {
+            "query": "AI basics",
+            "research_type": "quick",
+        }
+
+        response = authenticated_client.post(
+            "/api/v1/generate_report",
+            json=payload,
+            content_type="application/json",
+        )
+
+        # This endpoint might not be fully implemented
+        assert response.status_code in [200, 404, 500]
+
+        if response.status_code == 200:
+            data = json.loads(response.data)
+            assert "report" in data or "research_id" in data
+            print("✅ Generate report passed")
+        else:
+            print("⚠️ Generate report endpoint not fully implemented")
+
+    def test_generate_report_validation(self, authenticated_client):
+        """Test generate report endpoint validation."""
+        # Test with empty payload
+        response = authenticated_client.post(
+            "/api/v1/generate_report",
+            json={},
+            content_type="application/json",
+        )
+        assert response.status_code == 400
+        data = json.loads(response.data)
+        assert "error" in data
+
+        print("✅ Generate report validation passed")
+
+    def test_error_handling(self, authenticated_client):
+        """Test API error handling."""
+        # Test non-existent endpoint
+        response = authenticated_client.get("/api/v1/nonexistent")
+        assert response.status_code == 404
+
+        # Test invalid JSON
+        response = authenticated_client.post(
+            "/api/v1/quick_summary",
+            data="invalid json",
+            content_type="application/json",
+        )
+        assert response.status_code in [400, 500]
+
+        print("✅ Error handling passed")

tests/api_tests/test_rest_api_simple.py

@@ -0,0 +1,130 @@
+"""
+Simple REST API tests with ultra-minimal queries and longer timeouts.
+Focus on basic functionality verification.
+"""
+
+import json
+import pytest
+
+# Extended timeout for research operations
+RESEARCH_TIMEOUT = 120  # 2 minutes
+
+
+class TestRestAPISimple:
+    """Simple REST API tests."""
+
+    def test_health_and_docs(self, authenticated_client):
+        """Test basic non-research endpoints."""
+        print("🔍 Testing health and documentation endpoints...")
+
+        # Health check
+        response = authenticated_client.get("/api/v1/health")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert data["status"] == "ok"
+        print("✅ Health check passed")
+
+        # API documentation (requires auth)
+        response = authenticated_client.get("/api/v1/")
+        assert response.status_code == 200
+        data = json.loads(response.data)
+        assert data["api_version"] == "v1"
+        assert "endpoints" in data
+        print("✅ API documentation passed")
+
+    def test_error_handling(self, authenticated_client):
+        """Test error handling for malformed requests."""
+        print("🔍 Testing error handling...")
+
+        # Missing query parameter
+        response = authenticated_client.post(
+            "/api/v1/quick_summary",
+            json={},
+            content_type="application/json",
+        )
+        assert response.status_code == 400
+        data = json.loads(response.data)
+        assert "error" in data
+        print("✅ Error handling for missing query passed")
+
+        # Missing parameters for analyze_documents
+        response = authenticated_client.post(
+            "/api/v1/analyze_documents",
+            json={"query": "test"},
+            content_type="application/json",
+        )
+        assert response.status_code == 400
+        data = json.loads(response.data)
+        assert "error" in data
+        print("✅ Error handling for missing collection_name passed")
+
+    @pytest.mark.requires_llm
+    def test_quick_summary_ultra_minimal(self, authenticated_client):
+        """Test quick summary with the most minimal possible query."""
+        print("🔍 Testing quick summary with ultra-minimal query...")
+
+        payload = {
+            "query": "cat",  # Single word, very common
+            "search_tool": "wikipedia",
+            "iterations": 1,
+            "temperature": 0.7,
+        }
+
+        print("Making request...")
+        response = authenticated_client.post(
+            "/api/v1/quick_summary",
+            json=payload,
+            content_type="application/json",
+        )
+
+        if response.status_code == 200:
+            data = json.loads(response.data)
+
+            # Basic structure validation
+            required_fields = ["query", "summary", "findings"]
+            for field in required_fields:
+                assert field in data, f"Missing field: {field}"
+
+            assert data["query"] == "cat"
+            assert len(data["summary"]) > 0, "Summary should not be empty"
+            assert isinstance(data["findings"], list), (
+                "Findings should be a list"
+            )
+
+            print(
+                f"✅ Quick summary passed - got {len(data['summary'])} chars of summary"
+            )
+            print(f"   Found {len(data['findings'])} findings")
+        else:
+            pytest.fail(
+                f"Quick summary failed with status {response.status_code}"
+            )
+            print(f"   Response: {response.data[:200]}")
+
+    @pytest.mark.requires_llm
+    def test_generate_report_minimal(self, authenticated_client):
+        """Test generate report with minimal input."""
+        print("🔍 Testing generate report with minimal input...")
+
+        payload = {
+            "query": "Sun",
+            "research_type": "quick",
+        }
+
+        response = authenticated_client.post(
+            "/api/v1/generate_report",
+            json=payload,
+            content_type="application/json",
+        )
+
+        # This endpoint might not be fully implemented
+        if response.status_code == 200:
+            print("✅ Generate report passed")
+        elif response.status_code in [404, 500]:
+            print(
+                f"⚠️ Generate report endpoint not fully implemented ({response.status_code})"
+            )
+        else:
+            pytest.fail(
+                f"Generate report failed with unexpected status {response.status_code}"
+            )

tests/api_tests/test_search_engines_api.py

@@ -0,0 +1,158 @@
+"""
+Focused test for the search engines API endpoint.
+
+This test specifically debugs why the search engines dropdown is not loading.
+"""
+
+import json
+import pytest
+from loguru import logger
+
+
+class TestSearchEnginesAPI:
+    """Test the search engines API endpoint with detailed debugging."""
+
+    def test_search_engines_api(self, authenticated_client):
+        """Test the search engines API endpoint."""
+        logger.info("Testing search engines API...")
+
+        response = authenticated_client.get(
+            "/settings/api/available-search-engines"
+        )
+
+        logger.info(f"Response status: {response.status_code}")
+
+        assert response.status_code == 200
+        data = json.loads(response.data)
+
+        logger.info(f"Response data: {json.dumps(data, indent=2)}")
+
+        # Check the structure
+        if "engines" in data:
+            logger.info(f"Found {len(data['engines'])} engines")
+            assert len(data["engines"]) > 0
+            for engine_name, engine_data in data["engines"].items():
+                logger.info(f"  - {engine_name}: {engine_data}")
+        elif "engine_options" in data:
+            logger.info(f"Found {len(data['engine_options'])} engine options")
+            assert len(data["engine_options"]) > 0
+            for option in data["engine_options"]:
+                logger.info(f"  - {option}")
+        else:
+            pytest.fail(
+                "Unexpected data structure - neither 'engines' nor 'engine_options' found"
+            )
+
+    @pytest.mark.skip(
+        reason="Search engine display_name settings are not loaded by default in test environment"
+    )
+    def test_related_search_settings(self, authenticated_client):
+        """Check related search engine settings."""
+        logger.info("Checking related settings...")
+
+        # Check if search engine settings exist
+        endpoints = [
+            "/settings/api/search.engine.web.searxng.display_name",
+            "/settings/api/search.engine.web.duckduckgo.display_name",
+            "/settings/api/search.engine.web.google.display_name",
+            "/settings/api/search.engine.web.bing.display_name",
+        ]
+
+        found_settings = 0
+        for endpoint in endpoints:
+            response = authenticated_client.get(endpoint)
+            if response.status_code == 200:
+                data = json.loads(response.data)
+                logger.info(f"✓ {endpoint}: {data}")
+                found_settings += 1
+            else:
+                logger.warning(f"✗ {endpoint}: {response.status_code}")
+
+        # At least some search engines should be configured
+        assert found_settings > 0, "No search engine settings found"
+
+    @pytest.mark.skip(
+        reason="Search settings are not loaded by default in test environment"
+    )
+    def test_all_search_settings(self, authenticated_client):
+        """Check all settings to see what's available."""
+        logger.info("Checking all settings...")
+
+        response = authenticated_client.get("/settings/api")
+        assert response.status_code == 200
+
+        data = json.loads(response.data)
+        assert data["status"] == "success"
+        assert "settings" in data
+
+        # Find search-related settings
+        search_settings = {
+            k: v for k, v in data["settings"].items() if "search" in k
+        }
+
+        logger.info(f"Found {len(search_settings)} search-related settings:")
+        for key, value in search_settings.items():
+            logger.info(f"  {key}: {value}")
+
+        # Should have some search settings
+        assert len(search_settings) > 0, "No search settings found"
+
+    def test_search_engine_configuration(self, authenticated_client):
+        """Test search engine configuration endpoints."""
+        # Test getting search engine configuration
+        response = authenticated_client.get(
+            "/settings/api/search.default_search_engine"
+        )
+
+        if response.status_code == 200:
+            data = json.loads(response.data)
+            logger.info(f"Default search engine: {data}")
+            assert "value" in data or "setting" in data
+        else:
+            logger.warning(
+                f"No default search engine configured: {response.status_code}"
+            )
+
+        # Test search engine specific settings
+        response = authenticated_client.get("/settings/api/search.max_results")
+        if response.status_code == 200:
+            data = json.loads(response.data)
+            logger.info(f"Max search results: {data}")
+            assert "value" in data or "setting" in data
+
+    def test_search_engines_dropdown_data(self, authenticated_client):
+        """Test the exact data structure needed for dropdown."""
+        response = authenticated_client.get(
+            "/settings/api/available-search-engines"
+        )
+        assert response.status_code == 200
+
+        data = json.loads(response.data)
+
+        # The frontend expects either:
+        # 1. {"engines": {"name": {"display_name": "Name", "enabled": true}}}
+        # 2. {"engine_options": ["engine1", "engine2"]}
+
+        if "engines" in data:
+            # Validate engines structure
+            for engine_name, engine_data in data["engines"].items():
+                assert isinstance(engine_data, dict), (
+                    f"Engine {engine_name} data should be dict"
+                )
+                # Check for expected fields
+                if "display_name" in engine_data:
+                    assert isinstance(engine_data["display_name"], str)
+                if "enabled" in engine_data:
+                    assert isinstance(engine_data["enabled"], bool)
+        elif "engine_options" in data:
+            # Validate engine_options structure
+            assert isinstance(data["engine_options"], list), (
+                "engine_options should be list"
+            )
+            assert len(data["engine_options"]) > 0, (
+                "engine_options should not be empty"
+            )
+            for option in data["engine_options"]:
+                assert isinstance(option, (str, dict)), (
+                    "Each option should be string or dict"
+                )

tests/api_tests/test_session_persistence.py

@@ -0,0 +1,148 @@
+"""Test session persistence after login."""
+
+import json
+import time
+from loguru import logger
+
+
+class TestSessionPersistence:
+    """Test session persistence functionality."""
+
+    def test_session_after_login(self, client):
+        """Test that session persists after login."""
+        # Create unique test username to avoid conflicts
+        # audit: PUNCHLIST reviewed 2026-05 — issue resolved by prior PR (recommendation: REFACTOR_SPLIT).
+        test_username = f"testuser_session_{int(time.time() * 1000)}"
+        test_password = "TestPass123"
+
+        # Get login page
+        response = client.get("/auth/login")
+        assert response.status_code == 200
+        logger.info(f"GET /auth/login -> {response.status_code}")
+
+        # Register/Login
+        response = client.post(
+            "/auth/register",
+            data={
+                "username": test_username,
+                "password": test_password,
+                "confirm_password": test_password,
+                "acknowledge": "true",
+            },
+            follow_redirects=False,
+        )
+
+        # Login
+        response = client.post(
+            "/auth/login",
+            data={
+                "username": test_username,
+                "password": test_password,
+            },
+            follow_redirects=False,
+        )
+
+        logger.info(f"POST /auth/login -> {response.status_code}")
+
+        # Check if we're logged in by verifying successful redirect
+        assert (
+            response.status_code == 302
+        )  # Should redirect after successful login
+
+        # Access home page
+        response = client.get("/", follow_redirects=False)
+        logger.info(f"GET / -> {response.status_code}")
+
+        # Should not redirect to login
+        if response.status_code == 302:
+            location = response.headers.get("Location", "")
+            assert "/auth/login" not in location, (
+                "Session was lost! Redirected back to login"
+            )
+        else:
+            assert response.status_code == 200
+            # Check if we're actually logged in
+            assert (
+                b"logout" in response.data.lower()
+                or b"dashboard" in response.data.lower()
+            )
+            logger.info("✅ Successfully logged in and session preserved!")
+
+    def test_auth_check_persistence(self, authenticated_client):
+        """Test auth check endpoint with persistent session."""
+        response = authenticated_client.get("/auth/check")
+        assert response.status_code == 200
+        logger.info(f"GET /auth/check -> {response.status_code}")
+
+        data = json.loads(response.data)
+        logger.info(f"Auth check data: {data}")
+        assert data.get("authenticated") is True
+        assert "username" in data
+        logger.info(f"✅ Authenticated as: {data.get('username')}")
+
+    def test_api_access_persistence(self, authenticated_client):
+        """Test API access with persistent session."""
+        response = authenticated_client.get("/settings/api")
+        assert response.status_code == 200
+        logger.info(f"GET /settings/api -> {response.status_code}")
+        logger.info("✅ API access works!")
+
+        data = json.loads(response.data)
+        assert data["status"] == "success"
+        assert "settings" in data
+
+    def test_multiple_requests_session(self, authenticated_client):
+        """Test that session persists across multiple requests."""
+        endpoints = [
+            "/auth/check",
+            "/settings/api",
+            "/history/api",
+            "/metrics/api/metrics",
+        ]
+
+        for endpoint in endpoints:
+            response = authenticated_client.get(endpoint)
+            assert response.status_code == 200
+            logger.info(f"✅ {endpoint} -> {response.status_code}")
+
+    def test_session_after_page_navigation(self, authenticated_client):
+        """Test session persists through page navigation."""
+        pages = ["/", "/history", "/settings", "/metrics/"]
+
+        for page in pages:
+            response = authenticated_client.get(page)
+            assert response.status_code == 200
+            # Should not redirect to login
+            assert b"login" not in response.request.url.encode()
+            logger.info(f"✅ Successfully accessed {page}")
+
+    def test_session_integrity_check(self, authenticated_client):
+        """Test session integrity check endpoint."""
+        response = authenticated_client.get("/auth/integrity-check")
+        assert response.status_code == 200
+
+        data = json.loads(response.data)
+        assert "integrity" in data
+        assert "username" in data
+        logger.info(
+            f"✅ Session integrity verified for user: {data['username']}"
+        )
+
+    def test_logout_clears_session(self, authenticated_client):
+        """Test that logout properly clears the session."""
+        # First verify we're logged in
+        response = authenticated_client.get("/auth/check")
+        data = json.loads(response.data)
+        assert data["authenticated"] is True
+
+        # Logout
+        response = authenticated_client.post(
+            "/auth/logout", follow_redirects=True
+        )
+        assert response.status_code == 200
+
+        # Try to access protected endpoint
+        response = authenticated_client.get("/settings/api")
+        # Should either get 401 or redirect to login
+        assert response.status_code in [401, 302]
+        logger.info("✅ Session properly cleared after logout")

tests/api_tests/test_simple_auth.py

@@ -0,0 +1,125 @@
+"""Simple authentication test."""
+
+import json
+import time
+from loguru import logger
+
+
+class TestSimpleAuth:
+    """Simple authentication tests."""
+
+    def test_login_flow(self, client):
+        """Test the login flow."""
+        # Create unique test username to avoid conflicts
+        test_username = f"testuser_simple_{int(time.time() * 1000)}"
+        test_password = "TestPass123"
+
+        # 1. Get login page
+        response = client.get("/auth/login")
+        assert response.status_code == 200
+        logger.info(f"GET /auth/login -> {response.status_code}")
+
+        # 2. Register first (in case user doesn't exist)
+        response = client.post(
+            "/auth/register",
+            data={
+                "username": test_username,
+                "password": test_password,
+                "confirm_password": test_password,
+                "acknowledge": "true",
+            },
+            follow_redirects=False,
+        )
+        # Either 302 (success) or error if already exists
+        logger.info(f"POST /auth/register -> {response.status_code}")
+
+        # 3. Login
+        response = client.post(
+            "/auth/login",
+            data={
+                "username": test_username,
+                "password": test_password,
+            },
+            follow_redirects=True,
+        )
+        logger.info(
+            f"POST /auth/login (with redirects) -> {response.status_code}"
+        )
+        logger.info(f"Final URL: {response.request.url}")
+
+        # Should redirect to home page after successful login
+        assert response.status_code == 200
+
+    def test_auth_check(self, authenticated_client):
+        """Test auth check endpoint."""
+        response = authenticated_client.get("/auth/check")
+        assert response.status_code == 200
+        logger.info(f"GET /auth/check -> {response.status_code}")
+
+        data = json.loads(response.data)
+        logger.info(f"Auth check data: {data}")
+        assert data["authenticated"] is True
+
+    def test_access_home_page(self, authenticated_client):
+        """Test accessing home page when authenticated."""
+        response = authenticated_client.get("/")
+        assert response.status_code == 200
+        logger.info(f"GET / -> {response.status_code}")
+
+    def test_api_access(self, authenticated_client):
+        """Test API access when authenticated."""
+        response = authenticated_client.get(
+            "/settings/api/available-search-engines"
+        )
+        assert response.status_code == 200
+        logger.info(
+            f"GET /settings/api/available-search-engines -> {response.status_code}"
+        )
+
+        data = json.loads(response.data)
+        logger.info(f"Search engines response has keys: {list(data.keys())}")
+
+        if "engine_options" in data:
+            logger.info(
+                f"Found {len(data['engine_options'])} search engine options"
+            )
+            assert len(data["engine_options"]) > 0
+        elif "engines" in data:
+            logger.info(f"Found {len(data['engines'])} search engines")
+            assert len(data["engines"]) > 0
+
+    def test_unauthenticated_api_access(self, client):
+        """Test API access without authentication."""
+        # Should get 401 or redirect to login
+        response = client.get("/settings/api/available-search-engines")
+        assert response.status_code in [401, 302]
+        logger.info(
+            f"GET /settings/api/available-search-engines (unauth) -> {response.status_code}"
+        )
+
+    def test_logout(self, authenticated_client):
+        """Test logout functionality."""
+        # First verify we're authenticated
+        response = authenticated_client.get("/auth/check")
+        data = json.loads(response.data)
+        assert data["authenticated"] is True
+
+        # Logout
+        print("\n[DEBUG] Testing logout endpoint with POST method")
+        response = authenticated_client.post(
+            "/auth/logout", follow_redirects=True
+        )
+        print(f"[DEBUG] Logout response status: {response.status_code}")
+        print(f"[DEBUG] Logout response headers: {dict(response.headers)}")
+        if response.status_code != 200:
+            print(
+                f"[DEBUG] Logout response data: {response.data.decode()[:500]}"
+            )
+        assert response.status_code == 200
+
+        # Check we're no longer authenticated
+        response = authenticated_client.get("/auth/check")
+        assert response.status_code in [401, 200]
+        if response.status_code == 200:
+            data = json.loads(response.data)
+            assert data["authenticated"] is False

tests/api_tests/test_without_csrf.py

@@ -0,0 +1,109 @@
+"""Test authentication without CSRF to verify CSRF protection."""
+
+from loguru import logger
+
+
+class TestWithoutCSRF:
+    """Test that authentication properly requires CSRF tokens."""
+
+    def test_login_without_csrf_protection(self, app):
+        """Test login behavior when CSRF protection is disabled."""
+        # Temporarily disable CSRF for this test
+        app.config["WTF_CSRF_ENABLED"] = False
+        client = app.test_client()
+
+        # Register user
+        register_data = {
+            "username": "testuser_nocsrf",
+            "password": "TestPass123",
+            "confirm_password": "TestPass123",
+            "acknowledge": "true",
+        }
+        client.post("/auth/register", data=register_data)
+
+        # Try login without CSRF token
+        login_data = {
+            "username": "testuser_nocsrf",
+            "password": "TestPass123",
+        }
+
+        # Direct POST without getting the login page first
+        response = client.post(
+            "/auth/login", data=login_data, follow_redirects=False
+        )
+
+        logger.info(
+            f"POST /auth/login (CSRF disabled) -> {response.status_code}"
+        )
+
+        # With CSRF disabled, login should work
+        assert response.status_code == 302
+        logger.info("✅ Login worked with CSRF disabled!")
+
+        # Re-enable CSRF
+        app.config["WTF_CSRF_ENABLED"] = True
+
+    def test_login_requires_csrf_by_default(self, app):
+        """Test that login requires CSRF token when enabled."""
+        # Create a new client with CSRF enabled
+        app.config["WTF_CSRF_ENABLED"] = True
+        client = app.test_client()
+
+        # Try login without CSRF token (CSRF should be enabled)
+        login_data = {"username": "testuser", "password": "TestPass123"}
+
+        # Direct POST without CSRF token
+        response = client.post(
+            "/auth/login", data=login_data, follow_redirects=False
+        )
+
+        logger.info(
+            f"POST /auth/login (no CSRF token) -> {response.status_code}"
+        )
+
+        # Should fail because CSRF token is missing
+        assert response.status_code != 302  # Should not redirect on success
+        logger.info("✅ Login correctly requires CSRF token!")
+
+    def test_api_endpoints_without_csrf(self, authenticated_client):
+        """Test that API endpoints work without CSRF for authenticated users."""
+        # API endpoints typically don't require CSRF for GET requests
+        endpoints = [
+            "/settings/api",
+            "/history/api",
+            "/metrics/api/cost-analytics",
+        ]
+
+        for endpoint in endpoints:
+            response = authenticated_client.get(endpoint)
+            assert response.status_code == 200
+            logger.info(f"✅ GET {endpoint} works without CSRF token")
+
+    def test_post_api_without_csrf(self, authenticated_client):
+        """Test that POST API endpoints properly handle CSRF."""
+        # Try to start research without CSRF token
+        # audit: PUNCHLIST reviewed 2026-05 — issue resolved by prior PR (recommendation: FIX_ASSERTION).
+        research_data = {"query": "test query", "mode": "quick"}
+
+        # POST without CSRF should fail unless endpoint is exempt
+        response = authenticated_client.post(
+            "/api/start_research",
+            json=research_data,  # JSON requests typically bypass CSRF
+            content_type="application/json",
+        )
+
+        # JSON API endpoints often bypass CSRF protection
+        logger.info(
+            f"POST /api/start_research (JSON) -> {response.status_code}"
+        )
+
+        # Form POST without CSRF should fail
+        response = authenticated_client.post(
+            "/api/start_research",
+            data=research_data,  # Form data should require CSRF
+            follow_redirects=False,
+        )
+
+        logger.info(
+            f"POST /api/start_research (form data, no CSRF) -> {response.status_code}"
+        )