This directory contains the technical documentation for the ModelSEED-UI application.
| System Domain | Target Document | Core Topics Covered |
|---|---|---|
| High-Level Design | ARCHITECTURE.md | Tech stack, TanStack Query data flow, API clients, and the MUI v7 theming system. |
| URL Parity | ROUTING.md | Algorithms for mapping legacy AngularJS Hash-bundle routes to Next.js App Router catch-all ([...path]) URLs. |
| User Sessions | AUTHENTICATION.md | RAST/PATRIC login flow, useAuth Zustand store, and Token management for API requests. |
| External Data | WORKSPACE.md | Handling PATRIC Workspace JSON-RPC objects and the modelseed-api proxy endpoints. |
| Scientific Data | BIOCHEMISTRY.md | Solr-indexed reactions/compounds lookup and chemical formula/stoichiometry UX rendering rules. |
| Legacy Codebase | LEGACY_TRANSITION.md | Transitioning from the AngularJS source code to modern React patterns. |
| Testing Platform | TESTING.md | Vitest unit tests, Playwright E2E tests, and CI/CD pipeline. |
| Contributing | DEVELOPER_GUIDE.md | Guidelines for maintaining the documentation. |
- Scientific Accuracy: Biological identifiers, chemical formulas, and network models must be rendered according to scientific standards. See
BIOCHEMISTRY.md. - URL Parity: Legacy system links must redirect predictably in the modern application. See
ROUTING.md. - Decoupled API Architecture: Network calls are encapsulated in
lib/api/using@tanstack/react-query. Avoid directfetch()calls in components. SeeARCHITECTURE.md. - MUI-Native Styling: Utilize MUI v7 customized themes in
lib/theme.ts. Custom CSS should be avoided.