claude/update-claude-md-tKX5F

CLAUDE.md

@@ -0,0 +1,192 @@
+# CLAUDE.md - Project Intelligence
+
+## Project Overview
+
+Enhanced Open Journal Systems (OJS) integrated with SKZ (Skin Zone Journal) autonomous agents framework. The system combines OJS academic publishing capabilities with 7 specialized AI agents for automated manuscript processing and editorial workflow management.
+
+## Tech Stack
+
+- **Core Platform**: PHP 7.4+ (Open Journal Systems)
+- **AI Agents Framework (Python)**: Python 3.11+ (Flask, PyTorch, Transformers)
+- **AI Agents Framework (PHP)**: PHP 8.2+ (Resonance/Swoole)
+- **Frontend Dashboards**: React 18+, Node.js 18+
+- **Database**: MySQL 5.7+/8.0+, PostgreSQL (agents), Redis (caching)
+- **Testing**: PHPUnit, Pytest, Cypress
+
+## Project Structure
+
+```
+/                           # OJS Core (PHP)
+├── classes/                # OJS PHP classes
+├── controllers/            # MVC controllers
+├── pages/                  # Page handlers
+├── plugins/                # OJS plugins
+├── templates/              # Smarty templates
+├── lib/pkp/                # PKP shared library (submodule)
+├── config.inc.php          # Main OJS configuration
+└── skz-integration/        # SKZ Agents Framework
+    ├── autonomous-agents-framework/   # Main Python agents
+    │   ├── src/                       # Agent source code
+    │   ├── tests/                     # Pytest tests
+    │   └── requirements.txt
+    ├── microservices/                 # Per-agent microservices
+    ├── workflow-visualization-dashboard/  # React dashboard
+    ├── simulation-dashboard/          # Agent simulation UI
+    ├── scripts/                       # Deployment scripts
+    └── skin-zone-journal/             # Skin Zone backend
+```
+
+## Development Setup
+
+### Prerequisites
+```bash
+python3 --version  # 3.11+
+node --version     # 18+
+php --version      # 7.4+
+```
+
+### Quick Setup
+```bash
+# OJS dependencies
+composer --working-dir=lib/pkp install
+
+# Agent framework setup
+cd skz-integration/autonomous-agents-framework
+python -m venv venv
+source venv/bin/activate
+pip install -r requirements.txt
+
+# Dashboard setup
+cd ../workflow-visualization-dashboard
+npm install && npm run build
+```
+
+### Configuration
+1. Copy `config.TEMPLATE.inc.php` to `config.inc.php`
+2. Copy `.env.template` to `.env`
+3. Set `USE_PROVIDER_IMPLEMENTATIONS=true` in `.env` for production
+
+## Common Commands
+
+### Start Services
+```bash
+# OJS development server
+php -S localhost:8000
+
+# Agent framework
+cd skz-integration/autonomous-agents-framework
+source venv/bin/activate && python src/main.py
+
+# Dashboards
+cd skz-integration/workflow-visualization-dashboard
+npm run dev
+```
+
+### Testing
+
+**Python agents (pytest)**
+```bash
+cd skz-integration/autonomous-agents-framework
+pytest                      # All tests
+pytest -m unit              # Unit tests only
+pytest -m integration       # Integration tests
+pytest -m "not slow"        # Skip slow tests
+```
+
+**PHP/OJS tests**
+```bash
+lib/pkp/tools/runAllTests.sh
+```
+
+**Cypress E2E**
+```bash
+npx cypress run
+```
+
+### Health Check
+```bash
+./skz-integration/scripts/health-check.sh
+```
+
+## Key Configuration Files
+
+| File | Purpose |
+|------|---------|
+| `config.inc.php` | Main OJS configuration |
+| `.env` | Environment variables for agents |
+| `skz-integration/.env.template` | Agent service configuration |
+| `cypress.json` | Cypress E2E test config |
+| `skz-integration/autonomous-agents-framework/pytest.ini` | Pytest configuration |
+
+## The 7 Autonomous Agents
+
+1. **Research Discovery** - INCI database mining, patent analysis
+2. **Submission Assistant** - Quality assessment, compliance review
+3. **Editorial Orchestration** - Workflow coordination, decision making
+4. **Review Coordination** - Reviewer matching, workload management
+5. **Content Quality** - Scientific validation, standards enforcement
+6. **Publishing Production** - Formatting, distribution, metadata
+7. **Analytics & Monitoring** - Performance tracking, insights
+
+## API Endpoints
+
+- OJS API: `http://localhost:8000/api/v1/`
+- Agent Framework: `http://localhost:5000/api/v1/agents`
+- Skin Zone Journal: `http://localhost:5001/api/`
+
+## Important Conventions
+
+- OJS follows PKP coding standards
+- Python code uses Flask patterns with async support
+- Agent state managed in PostgreSQL, caching in Redis
+- All agent actions are logged for audit trail
+- Git LFS used for large files (models, images, JSON > 10MB)
+
+## Environment Variables
+
+Key variables in `.env`:
+- `USE_PROVIDER_IMPLEMENTATIONS` - Enable real providers (vs mocks)
+- `OJS_API_KEY` - API authentication
+- `POSTGRES_DSN` - Agent database connection
+- `REDIS_URL` - Cache connection
+- `ML_DECISION_MODEL_PATH` - Path to ML models
+
+## Resonance Agents Framework (PHP)
+
+A high-performance PHP implementation of the 7 agents using the Resonance framework (Swoole-based).
+
+### Location
+`skz-integration/resonance-agents/`
+
+### Quick Start
+```bash
+cd skz-integration/resonance-agents
+composer install
+cp config/config.ini.template config/config.ini
+php bin/resonance.php serve
+```
+
+### API Endpoints (Resonance)
+- HTTP Server: `http://localhost:9501`
+- WebSocket: `ws://localhost:9502`
+- Health: `GET /health`
+- Agents: `GET /api/v1/agents`
+- Workflows: `POST /api/v1/workflows`
+
+### Key Files
+| File | Purpose |
+|------|---------|
+| `bin/resonance.php` | Main entry point |
+| `config/config.ini` | Resonance configuration |
+| `src/Agent/*.php` | 7 agent implementations |
+| `src/Controller/*.php` | HTTP API controllers |
+| `src/WebSocket/*.php` | Real-time communication |
+| `src/Bridge/OJSBridge.php` | OJS integration |
+
+## Debugging Tips
+
+- Agent logs: Check `agent_startup.log`, `health_check.log`
+- OJS errors: Check PHP error log and `deployment.log`
+- Run provider smoke test: `python skz-integration/scripts/smoke_providers.py`
+- Validate production config: `python production_config_validator.py`
+- Resonance agents: Check Swoole logs at `http://localhost:9501/health`