القائمة
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
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
استنادا إلى تصنيف SOC المهني
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
| name | sysndd-mcp-readonly |
| description | 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 this skill before changing the MCP sidecar (api/start_sysndd_mcp.R, api/services/mcp-*.R, api/functions/mcp-*.R). MCP v1 is a separate, read-only process serving approved public data only. The contract is safety-critical: violating it can leak curation-in-progress or misrepresent data to LLM clients.
require_validated = TRUE).external_reference_identifier.When a product ask conflicts with these (e.g. "include the latest review even if unapproved", "generate a summary on cache miss", "present NDDScore as the authoritative classification"), the invariant wins. Implement the compliant framing and push the extra need to the authenticated main API (Curator+) or an admin/worker job — never into MCP.
Repository queries must return only approved public data:
ndd_entity_view.is_primary = 1 AND review_approved = 1. Do not drop these gates to serve "fresher" content.The sidecar binds the same memoised wrapper names as the API and mounts api_cache read-only. It must not initialize cache versions, clear cache files, compute STRING/phenotype clusters, or write entries. Phenotype correlations are cache-hit-only — never call generate_phenotype_correlations() on a miss. A fingerprint mismatch may only make MCP miss, never serve stale (that is why the exp+db artifact is mounted read-only to MCP).
get_gene_research_context for the pattern). Register in mcp-tool-registry.R; wrap execution in mcp_tool_safe(...).data_class: curated_sysndd_evidence, curated_derived_analysis, ml_prediction, llm_generated_summary, external_reference_identifier, or operational_metadata. NDDScore is always ml_prediction, not_evidence_tier, and never alters curated classifications.schema_version, error.code, and isError = true — not a raw R error or JSON-RPC -32603.response_mode = "compact" and expose budget metadata; keep schema_version at the outer envelope only.MCP_SCHEMA_VERSION (currently 1.2) is the compatibility contract — bump additively for a new tool, and keep get_sysndd_capabilities, resources/list, and resources/read aligned. Prompts are off by default (MCP_ENABLE_PROMPTS); enable only for intentional slash-command prompts.api/scripts/mcp-healthcheck.R (initialize + tools/list). The heavier api/scripts/mcp-smoke.R exercises real tools for dev/CI.api/tests/testthat/test-mcp-*.R (repository, analysis service, publication-context-verified). A new tool needs a unit test asserting approved-only reads and correct data_class labels.| Mistake | Why it's wrong |
|---|---|
Query drops review_approved = 1 for freshness | Leaks draft/in-progress curation |
| Generate an LLM summary on cache miss | MCP has no egress/creds and must not write cache; generation is admin/worker-only |
| Present NDDScore as the evidence verdict | NDDScore is ml_prediction, not an evidence tier |
| Return raw R error on bad input | Clients expect the recoverable JSON error envelope |
Add a tool without bumping MCP_SCHEMA_VERSION / updating capabilities | Breaks the discovery + compatibility contract |