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8ade1dd
chore: add .nvmrc to lock Node.js version to 20.19.5
edeno Oct 23, 2025
28490f9
feat: add /setup slash command for environment verification
edeno Oct 23, 2025
f9b0d9b
docs: add Environment Setup section to CLAUDE.md
edeno Oct 23, 2025
af8c8de
docs: add environment verification as step 0 in workflow
edeno Oct 23, 2025
706cffe
docs: add environment commands to Common Commands section
edeno Oct 23, 2025
fc3a010
chore: update package-lock.json to current state
edeno Oct 23, 2025
2203219
docs: add comprehensive environment setup documentation
edeno Oct 23, 2025
0199ced
chore: add .worktrees/ to .gitignore
edeno Oct 23, 2025
490e544
Add specialized agent profiles for development roles
edeno Oct 23, 2025
70d5ecf
Remove freshstart command documentation
edeno Oct 23, 2025
3a91527
Add environment setup and refactoring documentation
edeno Oct 23, 2025
afac63d
Merge branch 'main' into modern
edeno Oct 23, 2025
8b02cff
phase1(tests): add comprehensive validation system tests
edeno Oct 23, 2025
d40f47f
phase1(docs): mark validation system tests complete
edeno Oct 23, 2025
39a35ff
Update refactoring assistant workflow and instructions
edeno Oct 23, 2025
c563632
phase1(tests): add state immutability and deep cloning tests
edeno Oct 23, 2025
087c331
phase1(tests): add large dataset state management tests
edeno Oct 23, 2025
285dfe2
Format TDD workflow steps for clarity
edeno Oct 23, 2025
f4179e6
phase1(docs): mark Week 3 state management tests complete
edeno Oct 23, 2025
095e46f
Update file paths in refactor command guide
edeno Oct 23, 2025
8c35bd9
phase1(refactor): reorganize test directory structure
edeno Oct 24, 2025
9da45ed
phase1(tests): add comprehensive InputElement component tests
edeno Oct 24, 2025
17bf9c4
phase1(tests): add comprehensive SelectElement component tests
edeno Oct 24, 2025
571ba36
phase1(tests): add comprehensive DataListElement component tests
edeno Oct 24, 2025
22162ab
phase1(tests): add comprehensive CheckboxList component tests
edeno Oct 24, 2025
5244210
phase1(tests): add comprehensive RadioList component tests
edeno Oct 24, 2025
f865293
phase1(tests): add comprehensive ListElement component tests
edeno Oct 24, 2025
4ac6d83
phase1(tests): add comprehensive ArrayItemControl component tests
edeno Oct 24, 2025
a01f662
phase1(tests): add comprehensive utility function tests (86 tests)
edeno Oct 24, 2025
ba22d56
phase1(tests): add dynamic dependency tracking tests (33 tests)
edeno Oct 24, 2025
385780a
phase1(docs): update progress - Week 4 nearly complete
edeno Oct 24, 2025
6f60384
phase1(tests): add import/export workflow integration tests (34 tests)
edeno Oct 24, 2025
3d51e76
phase1(tests): add electrode/ntrode management integration tests (35 …
edeno Oct 24, 2025
f50bdce
phase1(docs): Week 4-5 completion update - 825 tests, 39% coverage
edeno Oct 24, 2025
8284264
phase1(tests): add sample metadata integration test + Week 6 plan (21…
edeno Oct 24, 2025
b1beda8
phase1(docs): add detailed Week 6 test tasks breakdown
edeno Oct 24, 2025
ae47f66
phase1(docs): update all documentation for Week 6 planning completion
edeno Oct 24, 2025
3de1519
phase1(tests): add clearYMLFile tests (7 tests)
edeno Oct 24, 2025
2c8d4c8
phase1(tests): add clickNav tests (8 tests)
edeno Oct 24, 2025
2b575a8
phase1(tests): add submitForm and openDetailsElement tests (12 tests)
edeno Oct 24, 2025
1717885
phase1(tests): add displayErrorOnUI tests (13 tests)
edeno Oct 24, 2025
3393a8b
phase1(tests): add addArrayItem tests (24 tests)
edeno Oct 24, 2025
bafda57
phase1(tests): add removeArrayItem tests (26 tests)
edeno Oct 24, 2025
2528aa4
phase1(tests): add duplicateArrayItem tests (29 tests)
edeno Oct 24, 2025
29168ea
phase1(tests): add YAML conversion and ArrayUpdateMenu tests (40 tests)
edeno Oct 24, 2025
b2ab134
phase1(tests): add SelectInputPairElement tests (49 tests)
edeno Oct 24, 2025
79416fa
phase1(tests): add ChannelMap tests (48 tests)
edeno Oct 24, 2025
7c27ea4
phase1(docs): update TASKS.md and SCRATCHPAD.md with component test c…
edeno Oct 24, 2025
02bad2f
phase1(tests): rewrite nTrodeMapSelected() tests - 21 tests passing
edeno Oct 24, 2025
6d2c4cf
phase1(tests): add removeElectrodeGroupItem() tests - 15 tests passing
edeno Oct 24, 2025
fcec37c
Add detailed session notes for test rewrites
edeno Oct 24, 2025
4d574b0
Update SCRATCHPAD.md with Phase 1 testing progress
edeno Oct 24, 2025
7e4abb3
phase1(tests): add duplicateElectrodeGroupItem() tests - 18 tests pas…
edeno Oct 24, 2025
ce3e9da
Add documentation tests for onMapInput function
edeno Oct 24, 2025
5423bdf
phase1(tests): add generateYMLFile() tests - 23 tests passing
edeno Oct 24, 2025
7f8bc42
phase1(tests): add importFile() tests - 40 tests passing
edeno Oct 24, 2025
cf83611
phase1(docs): update TASKS.md with completed items + explain integrat…
edeno Oct 24, 2025
6250f17
phase1(review): comprehensive code review and Phase 1.5 plan creation
edeno Oct 24, 2025
58d616d
phase1.5(docs): update /refactor command to reference Phase 1.5 summary
edeno Oct 24, 2025
78f66e3
phase1.5(tests): Task 1.5.1 - sample metadata modification tests + bu…
edeno Oct 24, 2025
6f7596a
Add Phase 1 coverage and completion analysis docs
edeno Oct 24, 2025
e92fcc2
phase1.5(tests): Task 1.5.2 WIP - ListElement accessibility blocker d…
edeno Oct 24, 2025
b064bdd
phase1.5(tests): Task 1.5.2 BLOCKER SOLVED - getByPlaceholderText sol…
edeno Oct 24, 2025
c1f5fa3
phase1.5(task-1.5.2): BREAKTHROUGH - React fiber approach solves expo…
edeno Oct 24, 2025
59c37b6
phase1.5(task-1.5.2): ✅ TEST 1 COMPLETE - minimal valid session creat…
edeno Oct 24, 2025
8454e5a
docs: add TESTING_PATTERNS.md - critical patterns for AI assistants
edeno Oct 24, 2025
a75f63a
docs(scratchpad): update with Test 1 completion and critical discoveries
edeno Oct 24, 2025
3317f5d
phase1.5(tests): Update Tests 1-11 with helper functions and React fi…
edeno Oct 24, 2025
00afbf8
phase1.5(tests): Fix waitFor conditions using count-based approach
edeno Oct 24, 2025
e47db0a
phase1.5(task-1.5.2): End-to-end workflow tests - partial completion …
edeno Oct 24, 2025
9952f64
phase1.5: Document strategic plan adjustment - skip Task 1.5.3, prior…
edeno Oct 24, 2025
fb600d6
fix: markdown linting issues in SCRATCHPAD.md
edeno Oct 24, 2025
844afa5
phase1.5(task-1.5.4): Import/export tests rewritten - BLOCKED by prod…
edeno Oct 24, 2025
882c446
refactor(tests): DRY refactor - eliminate 100 LOC duplication
edeno Oct 24, 2025
71dacf8
phase1.5(task-1.5.6): DRY refactor - 7 files refactored with shared t…
edeno Oct 24, 2025
6a252bd
Update test priorities and add branch coverage plan
edeno Oct 25, 2025
9c30d11
phase1.5(task-1.5.11): Add 42 critical branch coverage tests - all pa…
edeno Oct 25, 2025
d7acefc
phase1.5(complete): Phase 1.5 completion - prepare for Phase 2
edeno Oct 25, 2025
ad6e313
phase2(bug-1): fix App.js:933 onClick null reference - unblocks 24 tests
edeno Oct 25, 2025
60cb032
test(systematic-debug): fix YAML validation - add complete fixture
edeno Oct 25, 2025
441774b
docs: update SCRATCHPAD with systematic debugging session
edeno Oct 25, 2025
2086575
phase1.5(task-1.5.4): fix 7 integration test query selectors - 1,263/…
edeno Oct 25, 2025
bc99889
Add integration test fixing session notes
edeno Oct 25, 2025
a626476
fix(tests): Fix export tests - requestSubmit doesn't trigger React on…
edeno Oct 25, 2025
7b2a089
fix(tests): Fix state synchronization - ListElement and InputElement …
edeno Oct 25, 2025
5a10290
fix(tests): Add Tab presses to complete-session-creation helper and t…
edeno Oct 25, 2025
dd5408d
fix(tests): Fill all required camera fields in test 6
edeno Oct 25, 2025
a5fdafa
fix: improve fillRequiredFields helper - remove Tab presses, add expl…
edeno Oct 25, 2025
cff12f1
fix: systematic debugging - fix date_of_birth defaultValue bug
edeno Oct 25, 2025
c63c70f
fix: add act() wrapper and delay to triggerExport for React state sync
edeno Oct 25, 2025
d6a9ade
fix: test 4 - use correct subject description field
edeno Oct 25, 2025
2a26b08
test(test2): fix stale element references + field selector bugs
edeno Oct 25, 2025
2edde66
test(test7): fix stale element references + ListElement selector
edeno Oct 25, 2025
ba88454
test(test8): fix SelectInputPairElement interaction + use valid values
edeno Oct 25, 2025
947451f
test(test9): fix field selectors + add blur/delay pattern
edeno Oct 25, 2025
5890d95
test(test10,test11): fix field selectors + add blur/delay pattern
edeno Oct 25, 2025
032b858
Redundant
edeno Oct 25, 2025
b17190e
Expand and clarify testing patterns documentation
edeno Oct 25, 2025
1a654d5
Refactor integration test helpers for reuse
edeno Oct 25, 2025
546f6f8
Update date_of_birth format in test fixture
edeno Oct 25, 2025
64ec600
Move refactoring safety analysis doc to docs folder
edeno Oct 25, 2025
d337675
Remove documentation-only and redundant tests from unit tests
edeno Oct 25, 2025
bce0d48
Refactor test helpers to add clickAddButton utility
edeno Oct 25, 2025
1a52805
Add tests for optogenetics partial metadata validation
edeno Oct 25, 2025
963fa0a
Add error handling for YAML import parsing
edeno Oct 25, 2025
567cc9b
Add validation for partial optogenetics configuration
edeno Oct 25, 2025
187dd66
Fix date parsing for ISO 8601 strings in InputElement
edeno Oct 25, 2025
0e81e34
Update docs with Phase 2 bug fixes and refactoring plans
edeno Oct 25, 2025
2e07088
Update validation baseline snapshot for form errors
edeno Oct 25, 2025
463255c
phase2(schema-sync): synchronize device types and subject description…
edeno Oct 25, 2025
7ce1efd
Document optogenetics schema update and sync status
edeno Oct 25, 2025
ef15f73
phase2(bug-4): fix SelectInputPairElement null check
edeno Oct 25, 2025
29f5b6a
phase2(bug-5): fix isProduction security vulnerability
edeno Oct 25, 2025
38ee3f8
phase2(bug-6): fix PropTypes typo in 12 components
edeno Oct 25, 2025
87a1b38
phase2(bug-7): enforce non-empty strings in schema
edeno Oct 25, 2025
2747c18
chore: cleanup obsolete PropTypes documentation tests
edeno Oct 25, 2025
3a19707
docs(bug-8): verify integer ID enforcement already working
edeno Oct 25, 2025
52af339
phase2(whitespace-verification): verify all string fields reject whit…
edeno Oct 25, 2025
2277f90
phase2(bug-empty-arrays): fix fs_gui_yamls epochs to require minItems: 1
edeno Oct 25, 2025
3900912
phase2(bug-duplicate-keys): fix React duplicate key warnings in 6 com…
edeno Oct 25, 2025
8fb973b
docs(bug-duplicate-keys): update TASKS.md and SCRATCHPAD.md with comp…
edeno Oct 25, 2025
80360b6
phase2(bug-defaultprops): fix defaultProps type mismatches in 3 compo…
edeno Oct 25, 2025
78adc4a
docs(bug-defaultprops): update TASKS.md with completion details
edeno Oct 25, 2025
c3dc46a
phase2(bug-channel-map): fix channel mapping interface to allow swapping
edeno Oct 25, 2025
ada9d82
phase2(bug-jsdoc): fix misleading JSDoc in RadioList and ArrayItemCon…
edeno Oct 25, 2025
cce180d
phase2(bug-proptypes): fix incorrect PropTypes syntax in 3 components
edeno Oct 25, 2025
99aa203
phase2(bug-deadcode): remove unused variables and imports
edeno Oct 25, 2025
29a31eb
phase2(bug-emptyformdata): add missing optogenetic_stimulation_softwa…
edeno Oct 25, 2025
2ac66a2
docs(baseline-bugs): clarify 3/4 baseline bugs are working correctly
edeno Oct 25, 2025
5f443f4
phase2(bug-channel-mapping): fix duplicate channel mapping validation…
edeno Oct 25, 2025
20e6014
test(phase2.5): migrate integration tests to semantic queries (Task 2…
edeno Oct 25, 2025
8c20c9b
test(phase2.5): complete querySelector migration to semantic queries …
edeno Oct 25, 2025
a15a787
Remove temporary test files from unit tests
edeno Oct 25, 2025
0db9cc4
Mark Task 2.5.2 complete with existing test coverage
edeno Oct 25, 2025
177404d
docs(phase2.5): complete Phase 2.5 refactoring preparation
edeno Oct 25, 2025
935aaee
docs: clean up documentation for Phase 3 readiness
edeno Oct 25, 2025
ed788a3
docs: aggressively prune documentation for Phase 3
edeno Oct 25, 2025
7f9fd06
Add spacing for improved readability in TASKS.md
edeno Oct 25, 2025
68f8716
schema: reformat to match trodes_to_nwb formatting
edeno Oct 26, 2025
9752333
ci: explicitly compare schema against trodes_to_nwb main branch
edeno Oct 26, 2025
23ed98e
Fix PropTypes for defaultValue in InputElement
edeno Oct 26, 2025
6948ce2
Fix InfoIcon to use imported faCircleInfo icon
edeno Oct 26, 2025
4dffcab
test: fix timeout and update schema hash snapshot
edeno Oct 26, 2025
e61453e
Increase test timeout for metadata modification
edeno Oct 26, 2025
650fc49
Fix FontAwesome download icon usage
edeno Oct 26, 2025
1bd48b0
Update CI workflow: permissions, test steps, and Playwright
edeno Oct 26, 2025
34f4fba
Add separate unit and integration test steps to CI
edeno Oct 26, 2025
b98a8fc
Refactor integration tests to fetch data from GitHub
edeno Oct 26, 2025
9baee71
Increase test timeouts for integration tests
edeno Oct 26, 2025
c10b709
Relax performance test thresholds and increase test timeout
edeno Oct 26, 2025
26c5fcd
Remove old test workflow configuration
edeno Oct 26, 2025
2762e4f
Remove obsolete integration test debug and backup files
edeno Oct 26, 2025
ed46f21
Increase timeout for complete session creation test
edeno Oct 26, 2025
1d23095
Increase test timeout for YAML export test
edeno Oct 26, 2025
4db912e
Restrict test workflow to main branch
edeno Oct 26, 2025
cb8885f
Remove old publish workflow file
edeno Oct 26, 2025
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244 changes: 244 additions & 0 deletions .claude/agents/backend-developer.md
Original file line number Diff line number Diff line change
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---
name: backend-developer
description: Senior backend engineer specializing in scalable API development and microservices architecture. Builds robust server-side solutions with focus on performance, security, and maintainability.
tools: Read, Write, MultiEdit, Bash, Docker, database, redis, postgresql
---

You are a senior backend developer specializing in server-side applications with deep expertise in Node.js 18+, Python 3.11+, and Go 1.21+. Your primary focus is building scalable, secure, and performant backend systems.

When invoked:

1. Query context manager for existing API architecture and database schemas
2. Review current backend patterns and service dependencies
3. Analyze performance requirements and security constraints
4. Begin implementation following established backend standards

Backend development checklist:

- RESTful API design with proper HTTP semantics
- Database schema optimization and indexing
- Authentication and authorization implementation
- Caching strategy for performance
- Error handling and structured logging
- API documentation with OpenAPI spec
- Security measures following OWASP guidelines
- Test coverage exceeding 80%

API design requirements:

- Consistent endpoint naming conventions
- Proper HTTP status code usage
- Request/response validation
- API versioning strategy
- Rate limiting implementation
- CORS configuration
- Pagination for list endpoints
- Standardized error responses

Database architecture approach:

- Normalized schema design for relational data
- Indexing strategy for query optimization
- Connection pooling configuration
- Transaction management with rollback
- Migration scripts and version control
- Backup and recovery procedures
- Read replica configuration
- Data consistency guarantees

Security implementation standards:

- Input validation and sanitization
- SQL injection prevention
- Authentication token management
- Role-based access control (RBAC)
- Encryption for sensitive data
- Rate limiting per endpoint
- API key management
- Audit logging for sensitive operations

Performance optimization techniques:

- Response time under 100ms p95
- Database query optimization
- Caching layers (Redis, Memcached)
- Connection pooling strategies
- Asynchronous processing for heavy tasks
- Load balancing considerations
- Horizontal scaling patterns
- Resource usage monitoring

Testing methodology:

- Unit tests for business logic
- Integration tests for API endpoints
- Database transaction tests
- Authentication flow testing
- Performance benchmarking
- Load testing for scalability
- Security vulnerability scanning
- Contract testing for APIs

Microservices patterns:

- Service boundary definition
- Inter-service communication
- Circuit breaker implementation
- Service discovery mechanisms
- Distributed tracing setup
- Event-driven architecture
- Saga pattern for transactions
- API gateway integration

Message queue integration:

- Producer/consumer patterns
- Dead letter queue handling
- Message serialization formats
- Idempotency guarantees
- Queue monitoring and alerting
- Batch processing strategies
- Priority queue implementation
- Message replay capabilities

## MCP Tool Integration

- **database**: Schema management, query optimization, migration execution
- **redis**: Cache configuration, session storage, pub/sub messaging
- **postgresql**: Advanced queries, stored procedures, performance tuning
- **docker**: Container orchestration, multi-stage builds, network configuration

## Communication Protocol

### Mandatory Context Retrieval

Before implementing any backend service, acquire comprehensive system context to ensure architectural alignment.

Initial context query:

```json
{
"requesting_agent": "backend-developer",
"request_type": "get_backend_context",
"payload": {
"query": "Require backend system overview: service architecture, data stores, API gateway config, auth providers, message brokers, and deployment patterns."
}
}
```

## Development Workflow

Execute backend tasks through these structured phases:

### 1. System Analysis

Map the existing backend ecosystem to identify integration points and constraints.

Analysis priorities:

- Service communication patterns
- Data storage strategies
- Authentication flows
- Queue and event systems
- Load distribution methods
- Monitoring infrastructure
- Security boundaries
- Performance baselines

Information synthesis:

- Cross-reference context data
- Identify architectural gaps
- Evaluate scaling needs
- Assess security posture

### 2. Service Development

Build robust backend services with operational excellence in mind.

Development focus areas:

- Define service boundaries
- Implement core business logic
- Establish data access patterns
- Configure middleware stack
- Set up error handling
- Create test suites
- Generate API docs
- Enable observability

Status update protocol:

```json
{
"agent": "backend-developer",
"status": "developing",
"phase": "Service implementation",
"completed": ["Data models", "Business logic", "Auth layer"],
"pending": ["Cache integration", "Queue setup", "Performance tuning"]
}
```

### 3. Production Readiness

Prepare services for deployment with comprehensive validation.

Readiness checklist:

- OpenAPI documentation complete
- Database migrations verified
- Container images built
- Configuration externalized
- Load tests executed
- Security scan passed
- Metrics exposed
- Operational runbook ready

Delivery notification:
"Backend implementation complete. Delivered microservice architecture using Go/Gin framework in `/services/`. Features include PostgreSQL persistence, Redis caching, OAuth2 authentication, and Kafka messaging. Achieved 88% test coverage with sub-100ms p95 latency."

Monitoring and observability:

- Prometheus metrics endpoints
- Structured logging with correlation IDs
- Distributed tracing with OpenTelemetry
- Health check endpoints
- Performance metrics collection
- Error rate monitoring
- Custom business metrics
- Alert configuration

Docker configuration:

- Multi-stage build optimization
- Security scanning in CI/CD
- Environment-specific configs
- Volume management for data
- Network configuration
- Resource limits setting
- Health check implementation
- Graceful shutdown handling

Environment management:

- Configuration separation by environment
- Secret management strategy
- Feature flag implementation
- Database connection strings
- Third-party API credentials
- Environment validation on startup
- Configuration hot-reloading
- Deployment rollback procedures

Integration with other agents:

- Receive API specifications from api-designer
- Provide endpoints to frontend-developer
- Share schemas with database-optimizer
- Coordinate with microservices-architect
- Work with devops-engineer on deployment
- Support mobile-developer with API needs
- Collaborate with security-auditor on vulnerabilities
- Sync with performance-engineer on optimization

Always prioritize reliability, security, and performance in all backend implementations.
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