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.
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)
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`.
- ValueSet::transformLabels() was outputting values incorrectly:
- Field contained label text (e.g., Race: 'Jawa')
- *Key contained original value (e.g., RaceKey: 'JAWA')
- Fixed to output correct format for all static JSON ValueSets:
- Field contains original value (e.g., Race: 'JAWA')
- *Label contains label text (e.g., RaceLabel: 'Jawa')
- Affected ValueSets: Race, Sex, Country, Religion, Ethnic,
DeathIndicator, MaritalStatus
- Patient show endpoint now returns: Race:'JAWA', RaceLabel:'Jawa',
Sex:'1', SexLabel:'Female' as expected
● refactor: update API responses to use {field}Label format
- Transform coded fields to lowercase with Label suffix for display text - Controllers: OrderTestController, DemoOrderController, SpecimenController,
SpecimenStatusController, SpecimenCollectionController, ContainerDefController,
ContactController, TestMapController
- Example: Priority: "R" → priority: "R", priorityLabel: "Routine"
- Update api-docs.yaml with new OpenAPI schema definitions
- Add API docs reminder to CLAUDE.md
- Consolidate ValueSet routes from multiple nested groups to flat structure
- Delete deprecated ValueSet\ namespaced controllers (ValueSetController, ValueSetDefController)
- Remove ValueSetSeeder and ValueSetCountrySeeder from DBSeeder
- Simplify seeders (LocationSeeder, OrganizationSeeder, PatientSeeder, TestSeeder)
to use literal string values instead of ValueSet lookups
- Add new ValueSetController and ValueSetDefController in root namespace
- Update test files for new controller structure
The key changes are:
1. Routes: Consolidated from nested ValueSet\ namespace routes to flat ValueSetController routes with /items sub-endpoints
2. Controllers: Deleted old app/Controllers/ValueSet/ directory, created new root-level controllers
3. Seeders: Removed ValueSet dependencies, using literal values like 'ROOM', '1', 'TEST' instead of [12]['ROOM'] etc.
4. Tests: Updated tests to match new controller structure
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
