Allow update endpoints to validate only provided fields, avoid overwriting unchanged data, and preserve existing PatDiag when omitted from PatVisit PATCH payloads.
Implement true PATCH behavior so omitted fields stay unchanged, while null can explicitly clear nullable nested data. Align patient update tests and OpenAPI schemas/responses with the new 200/400/404 contract.
Align CALC/GROUP request and response payloads to use the testdefgrp.members structure in controller handling, feature tests, and OpenAPI schemas/examples for a consistent API contract.
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
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 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)
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`.
● 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
- Deleted obsolete v2 master test files and support classes:
- tests/_support/v2/MasterTestCase.php
- tests/unit/v2/master/TestDef/TestDefSiteModelTest.php
- tests/unit/v2/master/TestDef/TestDefTechModelTest.php
- tests/unit/v2/master/TestDef/TestMapModelTest.php
- tests/feature/v2/master/TestDef/TestDefSiteTest.php
- Cleaned up formatting and logic in tests/unit/HealthTest.php.
- 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)
Added an alternative route alias 'container' that points to ContainerDefController,
providing backward compatibility and flexibility in API endpoint naming.
- Routes '/api/specimen/container' to ContainerDefController methods
- Supports GET, GET with ID, POST, and PATCH operations
- Existing '/api/specimen/containerdef' routes remain unchanged
File: app/Config/Routes.php (+7 lines)
---
refactor(seeds): update and standardize seed data across multiple seeders
Improved data consistency and coverage in database seeds:
AreaGeoSeeder.php:
- Updated geographic area data for better regional coverage
- Standardized data format and field values
DummySeeder.php:
- Refactored dummy data generation for test environments
- Improved data integrity and relationships
PatientSeeder.php:
- Enhanced patient test data with more realistic scenarios
- Updated patient demographic information
- Improved test result distributions
Total: 111 lines changed across seed files
---
docs: add CLQMS project documentation
- Added project documentation file: "prj_clinical laboratory quality management system_3a.docx"
- Comprehensive project specification and requirements document
---
test: remove deprecated TestDefSiteTest.php
- Removed obsolete test file that is no longer needed
- Test coverage consolidated into other test classes
File: tests/feature/TestDef/TestDefSiteTest.php (-374 lines)
---
Summary:
- +58 lines added (routes, seeds, docs)
- -434 lines removed (deprecated test file)
- 6 files affected
- 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
- 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
