sysndd

Use when adding or changing an external HTTP provider call in SysNDD (gnomAD, Ensembl, UniProt, AlphaFold, MGI, RGD, PubMed, PubTator, MONDO, JAX/HPO) or touching external-call timeouts, retries, caching, or per-request time budgets

Use when wiring a SysNDD Vue 3 view or component to the backend API, adding a typed API client, handling API errors, or binding backend data into BootstrapVueNext tables and tooltips — especially around Plumber response shapes and BVN table/tooltip quirks

Use when adding or changing a SysNDD DB migration, editing a SQL view (especially ndd_entity_view or the core read views), touching the migration runner or manifest, restoring a database, or diagnosing a startup failure related to migrations

Use when reviewing or writing SysNDD code for security vulnerabilities or correctness bugs — authorization/role gates, SQL/expression injection, credential and secret handling, data exposure through public or MCP surfaces, resource-exhaustion/DoS from external calls, error/info leakage, and the repo's known R/Plumber footguns — especially before merging a diff or PR

Use when changing gene clustering (STRING/Leiden functional axis or phenotype MCA/HCPC), the analysis snapshot builder or validator, the memoised clustering cache, cache coherence, or LLM cluster summaries — or deploying a clustering change so public endpoints and summaries reflect it

Use when writing, running, or fixing SysNDD R/Plumber API tests (testthat) — including database-writing tests, running a single test inside the API container, mocking external providers, or diagnosing SKIP-vs-PASS, helper-loading, or path-resolution issues

Use when adding or changing durable async jobs, worker-executed code, job handlers, queue lanes or priorities in SysNDD — or diagnosing why a submitted job never runs, stays queued, or fails with "No durable async job handler registered"

Use when changing the SysNDD read-only MCP sidecar, its tools, repositories, resources, capabilities, schema version, or anything the MCP layer reads or exposes — especially when a product requirement would have MCP write, generate, fetch externally, or surface non-public data

Use when reviewing or changing SysNDD code for maintainability, modularity, file size, duplication, simplicity, typed boundaries, tests, or architecture quality before handoff

Use when changing SysNDD UI, UX, visual design, page layouts, tables, mobile rows, design tokens, authenticated admin/curation surfaces, or public data views