Avoid coercing missing SiteID, Decimal, and age boundaries to hardcoded defaults so payload intent is retained across test creation and reference range inserts. Align patient result age checks and OpenAPI examples with day-based age bounds, with feature coverage for create variants.
Use the base test row's RefType and ResultType to decide refnum/reftxt loading, and fetch discipline/department joins directly in getTestById to avoid redundant relation queries. Add feature coverage for show response behavior and include the related workspace cleanup changes so the branch state is consistent.
Rename legacy boolean helpers to is* naming across test definitions, patient models, and infrastructure data to match rest of backend.
Update controllers, models, migrations, seeders, tests, and OpenAPI docs/bundled spec so contracts and runtime align.
Normalize formatting/line endings across configs, controllers, models, tests, and OpenAPI specs.
Update rule expression/rule engine implementation and remove obsolete RuleAction controller/model.
Add unit tests for rule expression syntax and multi-action behavior, and include docs updates.
- Add /api/rules CRUD, nested actions, and expr validation
- Add rules migration, models, and RuleEngine/Expression services
- Run ORDER_CREATED rules after order create (non-blocking) and refresh tests
- Update OpenAPI tags/schemas/paths and bundled docs
- Add full CRUD operations for results (index, show, update, delete)
- Implement result validation with reference range checking (L/H flags)
- Add cumulative patient results retrieval across all orders
- Create ReportController for HTML lab report generation
- Add lab report view with patient info, order details, and test results
- Implement soft delete for results with transaction safety
- Update API routes with /api/results/* endpoints for CRUD
- Add /api/reports/{orderID} endpoint for report viewing
- Update OpenAPI docs with results and reports schemas/paths
- Add documentation for manual result entry and MVP plan
Major updates to order system:
- Add specimen and test data to order responses (index, show, create, update, status update)
- Implement getOrderSpecimens() and getOrderTests() private methods in OrderTestController
- Support 'include=details' query parameter for expanded order data
- Update OrderTestModel with enhanced query capabilities and transaction handling
API documentation:
- Update OpenAPI specs for orders, patient-visits, and tests
- Add new schemas for order specimens and tests
- Regenerate bundled API documentation
Database:
- Add Requestable field to TestDefSite migration
- Create OrderSeeder and ClearOrderDataSeeder for test data
- Update DBSeeder to include order seeding
Patient visits:
- Add filtering by PatientID, PatientName, and date ranges
- Include LastLocation in visit queries
Testing:
- Add OrderCreateTest with comprehensive test coverage
Documentation:
- Update AGENTS.md with improved controller structure examples
- Add TestMapDetailController for managing test mapping details
- Create TestMapDetailModel with CRUD operations
- Add migration for TestSiteID column in testmap table
- Update TestMapController and TestMapModel
- Update routes, seeder and PatVisitModel
- Regenerate API documentation bundle
- Add TestMapController for managing test-to-analyzer mappings
- Create TestMapModel with database operations for test mappings
- Update TestsController to support test mapping operations
- Add testmap API routes to Routes.php
- Create migration updates for test definitions table
- Add OpenAPI specification for test mapping endpoints
- Include unit tests for TestDef models
- Update bundled API documentation
Major Features:
- Add comprehensive audit logging system with AuditService
- Create AuditLogs database migration for tracking changes
- Implement TestValidationService for test data validation
- Add FRONTEND_TEST_MANAGEMENT_PROMPT.md documentation
Controllers:
- Update TestsController with improved test management
Models:
- Enhance PatientModel with additional functionality
- Update TestDefSiteModel for better site management
Database:
- Add CreateAuditLogs migration (2026-02-20-000011)
- Update TestSeeder with new test data
Services:
- Add AuditService for comprehensive audit trail logging
Documentation:
- Update AGENTS.md with improved guidelines
- Update audit-logging-plan.md with implementation details
- Add FRONTEND_TEST_MANAGEMENT_PROMPT.md for frontend guidance
API Documentation:
- Update api-docs.bundled.yaml
- Update tests.yaml schema definitions
- Update tests.yaml paths
Testing:
- Enhance TestsControllerTest with new test cases
- Update TestDefModelsTest for model coverage
- Add audit-logging-plan.md with comprehensive logging implementation guide
- Update AGENTS.md with project guidelines
- Refactor test models: remove RefTHoldModel, RefVSetModel, TestDefTechModel
- Update TestDefSiteModel and related migrations
- Update seeder and test data files
- Update API documentation (OpenAPI specs)
- Extract PatIdt, PatCom, PatAtt arrays before patient insert to prevent MySQL error 1241
- Fix Custodian handling when InternalPID is null
- Apply same fix to updatePatient method
This commit marks a significant architectural shift, transitioning the CLQMS backend to a fully headless REST API. All view-related components have been removed to focus solely on providing a robust, stateless API for clinical laboratory workflows.
### Architectural Changes
- **Headless API Transition:**
- Removed all view files (`app/Views/v2`), associated page controllers (`PagesController`), and routes (`Routes.php`). The application no longer serves a front-end UI.
- The root endpoint (`/`) now returns a simple "Backend Running" status message.
- **Developer Tooling & Guidance:**
- Replaced `CLAUDE.md` with `GEMINI.md` to provide updated context and instructional guidelines for Gemini agents.
- Updated `.serena/project.yml` with project configuration.
### Feature Enhancements
- **Advanced Order Management (`OrderTestModel`):**
- **Test Expansion:** The `createOrder` process now automatically expands `GROUP` (panel) tests into their individual components and recursively includes all parameter dependencies for `CALC` (calculated) tests.
- **Order Comments:** Added support for attaching comments to an order via the `ordercom` table.
- **Status Tracking:** Order status updates are now correctly recorded in the `orderstatus` table.
- **Schema Alignment:** Switched from `OrderID` to `InternalOID` as the primary key for internal operations.
- **Reference Range Refactor (`TestsController`):**
- Simplified reference range logic by consolidating `refthold` and `refvset` into the main `refnum` and `reftxt` tables.
- Standardized `RefType` handling to support `NMRC`, `TEXT`, `THOLD`, and `VSET` codes from the `reference_type` ValueSet.
### Other Changes
- **Documentation:**
- `PRD.md`, `README.md`, and `TODO.md` were updated to reflect the headless architecture, refined scope, and current project priorities.
- **Database:**
- Removed obsolete `RefTHoldID` and `RefVSetID` columns from the `patres` table migration.
- **Testing:**
- Added new feature tests for `ContactController`, `OrganizationController`, and `TestsController`.
- PatientModel: Convert Custodian from array to integer InternalPID when received as object
- PatientModel: Convert LinkTo from array of objects to comma-separated InternalPID string
- API docs: Add LinkedPatient, Custodian, and PatAttEntry schema definitions
- API docs: Extend Patient schema with DeathIndicator, TimeOfDeath, PatCom,
PatAtt, Province, City, Country, Race, MaritalStatus, Religion, Ethnic fields
- Add AGENTS.md to .gitignore
Complete overhaul of the valueset system to use human-readable names
instead of numeric IDs for improved maintainability and API consistency.
- PatientController: Renamed 'Gender' field to 'Sex' in validation rules
- ValuesetController: Changed API endpoints from ID-based (/:num) to name-based (/:any)
- TestsController: Refactored to use ValueSet library instead of direct valueset queries
- Added ValueSet library (app/Libraries/ValueSet.php) with static lookup methods:
- getOptions() - returns dropdown format [{value, label}]
- getLabel(, ) - returns label for a value
- transformLabels(, ) - batch transform records
- get() and getRaw() for Lookups compatibility
- Added ValueSetApiController for public valueset API endpoints
- Added ValueSet refresh endpoint (POST /api/valueset/refresh)
- Added DemoOrderController for testing order creation without auth
- 2026-01-12-000001: Convert valueset references from VID to VValue
- 2026-01-12-000002: Rename patient.Gender column to Sex
- OrderTestController: Now uses OrderTestModel with proper model pattern
- TestsController: Uses ValueSet library for all lookup operations
- ValueSetController: Simplified to use name-based lookups
- Updated all organization (account/site/workstation) dialogs and index views
- Updated specimen container dialogs and index views
- Updated tests_index.php with ValueSet integration
- Updated patient dialog form and index views
- Removed .factory/config.json and CLAUDE.md (replaced by AGENTS.md)
- Consolidated lookups in Lookups.php (removed inline valueset constants)
- Updated all test files to match new field names
- 32 modified files, 17 new files, 2 deleted files
- Net: +661 insertions, -1443 deletions (significant cleanup)
- Remove pagination from ValueSetController::index() and ValueSetModel::getValueSets()
- Delete duplicate AGENTS.md documentation (consolidated into CLAUDE.md)
- Update .gitignore to exclude .claude folder
- Add CLAUDE.md with comprehensive agent instructions for Valueset queries
- Document new Lookups static library in README.md
- Add Phone/Email fields to LocationAddressModel allowedFields
- Fix saveLocation() to throw exceptions instead of returning error arrays
- Update controller to properly handle model responses
- Include actual database error message in transaction failures
- Rename all controllers from X.php to XController.php format
- Add new RefTxtModel for text-based reference ranges
- Rename group_dialog.php to grp_dialog.php and remove title_dialog.php
- Add comprehensive test suite for v2/master/TestDef module
- Update Routes.php to reflect controller renames
- Remove obsolete data files (clqms_v2.sql, lab.dbml)
- Refactor Tests.php controller with updated logic and error handling
- Update Test migration with schema improvements
- Enhance TestDefCalModel, TestDefGrpModel, TestDefTechModel with CRUD operations
- Improve TestMapModel with better test mapping relationships
- Redesign test dialog views (calc, group, param) with improved UX
- Update tests_index view with better data presentation
- Add CSS styles for test management UI components
- Add TestDefSiteTest feature test for site-based test definitions
- Add TestDefModelsTest unit test for model validation
- Remove obsolete Test Management.docx documentation
- Add new dialog forms for test calc, group, param, and title management
- Refactor test_dialog.php to new location (master/tests/)
- Update TestDefCalModel, TestDefSiteModel, TestDefTechModel, TestMapModel
- Modify Tests controller and Routes for new dialog handlers
- Update migration schema for test definitions
- Add new styles for v2 test management interface
- Include Test Management documentation files
- Consolidate page controllers into unified PagesController
- Remove deprecated V2 pages, layouts, and controllers (AuthPage, DashboardPage, V2Page)
- Add Edge resource with migration and model (EdgeResModel)
- Implement new main_layout.php for consistent page structure
- Reorganize patient views into dedicated module with dialog form
- Update routing configuration in Routes.php
- Enhance AuthFilter for improved authentication handling
- Clean up unused V2 assets (CSS, JS) and legacy images
- Update README.md with latest project information
This refactoring improves code organization, removes technical debt, and
establishes a cleaner foundation for future development.
- Implemented dynamic VID retrieval from ValueSetModel for all test definitions
- Aligned ResultType, RefType, and SpcType with the valueset table
- Updated sample data for Hematology, Chemistry, and Urinalysis tests
- Ensured consistency between ValueSetSeeder and TestSeeder data
