- 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
- 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
- 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.
- Restructure valueset pages from single master page to separate views:
- Library Valuesets (read-only lookup browser)
- Result Valuesets (CRUD for valueset table)
- Valueset Definitions (CRUD for valuesetdef table)
- Add new ResultValueSetController for result-specific valueset operations
- Move views from master/valuesets to result/valueset and result/valuesetdef
- Convert valueset sidebar to collapsible nested menu
- Add search filtering to ValueSetController index
- Remove deprecated welcome_message.php and old nested CRUD view
- Update routes to organize under /result namespace
Summary of changes: This commit reorganizes the valueset management UI by splitting the monolithic master/valuesets page into three distinct sections, adds a new controller for result-related valueset operations, and restructures the sidebar navigation for better usability.
- 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
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
- Create AreaGeoSeeder to import area geo data from external zones table
- Add field mapping: zonecode→AreaCode, zoneclass→Class, zonename→AreaName, parentzoneid→Parent
- Support same-server external databases using direct SQL queries
- Register seeder in DBSeeder for inclusion in main seeding workflow
- 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)
- Remove deprecated docs folder with outdated documentation
- Add new plans directory with ref_range_multiple_support_plan.md
- Update test migrations, seeds, and views for improved functionality
- 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
- Implement JWT authentication with HTTP-only cookies
- Create /v2/* namespace to avoid conflicts with existing frontend
- Upgrade to DaisyUI 5 + Tailwind CSS 4
- Add light/dark theme toggle with smooth transitions
- Build login page, dashboard, and patient list UI
- Protect V2 routes with auth middleware
- Add comprehensive documentation
No breaking changes - all new features under /v2/* namespace
- 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
- Corrected ASCII row formatting in logs to ensure proper line breaks.
- Resolved issue causing empty result outbox during HL7 result simulation.
- Ensured messages are correctly processed and translation errors are handled.
