- 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)
- TestsController: Remove duplicate rangeTypeOptions assignment that was being
set inside the NUM condition block, causing it to be set unnecessarily
when it's also handled elsewhere
- ResponseTrait: Convert global helper function convert_empty_strings_to_null()
to private class method convertEmptyStringsToNull() for better encapsulation
and to avoid dependency on global functions
- Database schema: Update clqms_database.dbml with accurate table structure
derived from app/Models/ directory, reorganizing tables by functional
categories (Patient, Visit, Organization, Location, Test, Specimen,
Order, Contact management)
- Create App\Traits\ResponseTrait that wraps CodeIgniter\API\ResponseTrait
- Add json_helper with convert_empty_strings_to_null() and prepare_json_response() functions
- Replace all imports of CodeIgniter\API\ResponseTrait with App\Traits\ResponseTrait across all controllers
- Add 'json' helper to BaseController helpers array
- Ensure consistent API response formatting across the application
- Add PatVisitController with CRUD operations
- Add use case documentation (docx and md files)
- Update API documentation in api-docs.yaml
- Remove USER_STORIES.md (migrated to docs/)
- Update TODO.md with current tasks
- Update Routes.php for new endpoints
- Update DummySeeder with additional test data
- 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
- 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
