@pipeworx/mcp-ncbi-variation 0.1.0

package/LICENSE

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+MIT License
+
+Copyright (c) 2026 Mojibake Inc.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

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+# @pipeworx/ncbi-variation
+
+dbSNP refSNP records and HGVS ↔ SPDI ↔ rsID normalization from NCBI Variation
+Services — the service that turns any spelling of a human genetic variant into
+the canonical coordinates the rest of genomics keys on.
+
+Part of [Pipeworx](https://pipeworx.io) — an MCP gateway connecting AI agents to 1679+ live data sources.
+
+## Tools
+
+- `variation_refsnp(rsid, assembly?, max_frequencies?)` — the full refSNP
+  record: genomic placement on the build you ask for, HGVS genomic/transcript/
+  protein forms, SPDI, gene context, ClinVar clinical significance, and
+  population allele frequencies (gnomAD, ExAC, 1000 Genomes, TOPMED, ALFA).
+  Answers "what is rs113488022".
+- `variation_hgvs_to_spdi(hgvs)` — normalize an HGVS expression to contextual
+  SPDI alleles, and validate that the HGVS is well-formed at all.
+- `variation_spdi_to_rsids(spdi)` — the reverse: coordinate + alleles from a
+  VCF or pipeline → the rsIDs other databases key on.
+
+## Auth
+
+Keyless. NCBI asks unauthenticated clients to stay under ~3 requests/second;
+the pack sends an identifying User-Agent.
+
+## Data sources
+
+- <https://api.ncbi.nlm.nih.gov/variation/v0/refsnp/{rsid}> — refSNP record.
+- <https://api.ncbi.nlm.nih.gov/variation/v0/hgvs/{expr}/contextuals> — HGVS → SPDI.
+- <https://api.ncbi.nlm.nih.gov/variation/v0/spdi/{spdi}/rsids> — SPDI → rsIDs.
+
+## Traps
+
+**GRCh37 vs GRCh38 is the whole game.** One refSNP carries placements on both
+builds at *different* coordinates — rs113488022 (BRAF V600E) is 7:140753336 on
+GRCh38 and 7:140453136 on GRCh37, 300kb apart. A caller who takes a coordinate
+from one build into a dataset annotated on the other gets "not found", which
+reads as "this variant does not exist". So `assembly` is an explicit argument
+(default GRCh38), every response states `assembly_requested` and
+`assemblies_available`, and an assembly with no placement says so in
+`assembly_note` instead of coming back as an empty array.
+
+**SPDI is 0-based, HGVS is 1-based.** `NC_000007.14:140753335:A:T` and
+`NC_000007.14:g.140753336A>T` are the same variant. The off-by-one is the most
+common reason `variation_spdi_to_rsids` returns nothing.
+
+**A retired rsID is not an error.** dbSNP merges rsIDs; a merged one returns
+`merged_snapshot_data` with no `primary_snapshot_data` at all. The pack detects
+that and returns `status: "merged"` plus the rsID to re-query (rs3735962 →
+rs328), rather than an empty record.
+
+**Reference alleles are in the allele list.** dbSNP lists the reference as an
+allele whose `deleted_sequence` equals its `inserted_sequence`. Filtering those
+out is what separates `alternate_alleles` from noise.
+
+**The raw record is huge.** rs328 carries thousands of citations and dozens of
+placements. The pack summarizes and caps (`max_frequencies`, 25 citations) —
+counts are always reported alongside so a truncation is visible.
+
+## Quick Start
+
+Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
+
+```json
+{
+  "mcpServers": {
+    "ncbi-variation": {
+      "url": "https://gateway.pipeworx.io/ncbi-variation/mcp"
+    }
+  }
+}
+```
+
+### What this endpoint actually serves
+
+`tools/list` at `https://gateway.pipeworx.io/ncbi-variation/mcp` returns the tools in the table
+above **plus the shared Pipeworx meta-tools** — `ask_pipeworx`,
+`discover_tools`, `search_within`, `remember`/`recall` and the rest of the
+gateway-wide set. So the tool count you see is larger than this table: a
+single-pack endpoint currently lists roughly 30 shared tools alongside the
+pack's own. The connection's `initialize` response states its exact scope, and
+is the authoritative answer for a given day.
+
+This is deliberate, not multiplexing by accident. The meta-tools are what let a
+scoped connection answer a question this pack does not cover — via
+`ask_pipeworx`, which routes across the whole catalog — without you adding a
+second MCP server. There is currently no way to mount a pack endpoint without
+them; if the extra schemas cost you more context than the routing is worth,
+connect to the full gateway once rather than to several pack endpoints.
+
+Or connect to the full Pipeworx gateway to get every pack's tools listed
+directly, instead of just this one's:
+
+```json
+{
+  "mcpServers": {
+    "pipeworx": {
+      "url": "https://gateway.pipeworx.io/mcp"
+    }
+  }
+}
+```
+
+Both URLs reach the same gateway and the same 1679+ data sources. The
+only difference is which pack's tools are listed **directly**; `ask_pipeworx`
+reaches all of them from either one.
+
+## No MCP client? Call it over HTTP
+
+```bash
+curl -X POST https://gateway.pipeworx.io/v1/tools/variation_refsnp \
+  -H 'Content-Type: application/json' \
+  -d '{"rsid":"rs113488022","assembly":"GRCh38"}'
+```
+
+No account needed for the first calls. Inspect any tool: `GET https://gateway.pipeworx.io/v1/tools/variation_refsnp`. Find one: `POST https://gateway.pipeworx.io/v1/tools/search_packs` with `{"query":"..."}`.
+
+## Standalone (no gateway account)
+
+This package also runs as a local stdio MCP server — no Pipeworx account, no
+gateway round-trip:
+
+```json
+{
+  "mcpServers": {
+    "ncbi-variation": {
+      "command": "npx",
+      "args": ["-y", "@pipeworx/mcp-ncbi-variation"]
+    }
+  }
+}
+```
+
+Or run it directly to confirm it starts:
+
+```bash
+npx -y @pipeworx/mcp-ncbi-variation
+```
+
+It speaks MCP over stdin/stdout and answers `initialize`/`tools/list`/`tools/call`
+for **only** this pack's tools — none of the shared meta-tools the gateway
+connection above adds. Same source, same tools, no ask_pipeworx routing.
+
+## Using with ask_pipeworx
+
+Instead of calling tools directly, you can ask questions in plain English —
+this works on the pack endpoint above as well as on the full gateway:
+
+```
+ask_pipeworx({ question: "your question about Ncbi Variation data" })
+```
+
+The gateway picks the right tool and fills the arguments automatically.
+
+## More
+
+- [Docs and guides](https://pipeworx.io/docs)
+- [pipeworx.io](https://pipeworx.io)
+
+## License
+
+MIT

package/bin/cli.js

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+#!/usr/bin/env node
+//
+// Entry point for `npx @pipeworx/mcp-<slug>`.
+//
+// Packs ship as raw TypeScript (no build step — see publish-pack.sh for why:
+// tsx sidesteps every extensionless-import / bare-JSON-import edge case a
+// per-pack tsc build would have to solve one pack at a time). This file
+// registers tsx's ESM loader programmatically, then hands off to src/server.ts,
+// which wraps the pack's {tools, callTool} export in a stdio MCP server.
+//
+// Copied verbatim into every published pack repo by scripts/publish-pack.sh —
+// edit this file, not a per-pack copy.
+import { register } from 'tsx/esm/api';
+
+register();
+
+await import('../src/server.ts');

package/package.json

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+{
+  "name": "@pipeworx/mcp-ncbi-variation",
+  "version": "0.1.0",
+  "description": "dbSNP refSNP records and HGVS/SPDI/rsID normalization for human genetic variants, from NCBI Variation Services.",
+  "type": "module",
+  "main": "src/index.ts",
+  "types": "src/index.ts",
+  "bin": {
+    "mcp-ncbi-variation": "bin/cli.js"
+  },
+  "keywords": ["mcp", "mcp-server", "model-context-protocol", "pipeworx", "ncbi-variation"],
+  "license": "MIT",
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/pipeworx-io/mcp-ncbi-variation.git"
+  },
+  "scripts": {
+    "typecheck": "tsc --noEmit"
+  },
+  "dependencies": {
+    "@modelcontextprotocol/sdk": "^1.30.0",
+    "tsx": "^4.19.0"
+  },
+  "devDependencies": {
+    "typescript": "^5.9.3",
+    "@cloudflare/workers-types": "^4.20260405.1"
+  },
+  "pipeworx": {
+    "sourceHash": "v1-7e8219a5668ac195679aa32f332e43d0e5c46bfa774ab34def4512e358feb460",
+    "sourceCommit": "b0fb3c31386cf0256dcf1e2f1b3440435a87ec35"
+  }
+}

package/server.json

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+{
+  "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
+  "name": "io.github.pipeworx-io/ncbi-variation",
+  "title": "Ncbi Variation",
+  "description": "dbSNP refSNP records and HGVS/SPDI/rsID normalization for human genetic variants, from NCBI…",
+  "version": "0.1.0",
+  "websiteUrl": "https://pipeworx.io/packs/ncbi-variation",
+  "repository": {
+    "url": "https://github.com/pipeworx-io/mcp-ncbi-variation",
+    "source": "github"
+  },
+  "remotes": [
+    {
+      "type": "streamable-http",
+      "url": "https://gateway.pipeworx.io/ncbi-variation/mcp"
+    }
+  ]
+}

package/src/index.ts

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+interface McpToolDefinition {
+  name: string;
+  description: string;
+  /** Human-facing one-liner (fleet #1967). Optional; consumers fall back to
+   *  description. Kept in step with shared/src/types.ts — scripts/lib/
+   *  check-inlined-types.mjs reports drift at publish time. */
+  summary?: string;
+  inputSchema: {
+    type: 'object';
+    properties: Record<string, unknown>;
+    required?: string[];
+    anyOf?: Array<{ required: string[] }>;
+    oneOf?: Array<{ required: string[] }>;
+    allOf?: Array<{ required: string[] }>;
+  };
+  outputSchema?: Record<string, unknown>;
+}
+
+interface McpToolExport {
+  tools: McpToolDefinition[];
+  callTool: (name: string, args: Record<string, unknown>) => Promise<unknown>;
+  meter?: { credits: number };
+  cost?: Record<string, unknown>;
+  provider?: string;
+}
+
+/**
+ * Was this failure OUR OWN web service? — the other half of `internal-db-class.ts`.
+ *
+ * fleet #1089 pulled failures from our own Postgres out of `upstream_down` by
+ * keying on the SQLSTATE inside PostgREST's four-key error envelope. That
+ * covered the majority and structurally could not cover the rest: the rest
+ * never reach Postgres, so they carry no SQLSTATE. What was left, measured over
+ * the 24h to 2026-09-02T15:00Z (fleet #1096):
+ *
+ *     5  pipeworx-catalog  get_pack_tools     Pipeworx catalog error: 522 — error code: 522
+ *     3  fleet             fleet_list_open …  upstream_down: Fleet task queue did not respond within 25s
+ *
+ * 521/522/523/526 are Cloudflare saying its edge could not reach an ORIGIN, and
+ * in both of those rows the origin is ours — `gateway.pipeworx.io` for the
+ * catalog pack (it self-fetches when the gateway hasn't injected a manifest),
+ * our own Supabase for fleet. There is no third party anywhere in either call.
+ * Same defect as #1089: our own outage filed under `upstream_down`, the one
+ * class that means "the source is unreachable and there is nothing for us to
+ * fix", which is why the problem-tools triage skips it.
+ *
+ * WHY NOT A WORDING RULE. The obvious fix is to match `fleet db error:` and
+ * `Pipeworx catalog error:` in classifyToolError. Each is emitted from exactly
+ * one site today, so it would work today. It would also rot the first time
+ * somebody rewords a label — silently, and in the direction of hiding our own
+ * outage, which is worse than the bug being fixed. Every prose rule in
+ * error-class.ts has needed widening as packs invented new wording (#409/#450/
+ * #584); that history is most of that file's comment budget.
+ *
+ * WHAT THIS KEYS ON INSTEAD: **the host the call actually reached.** A URL's
+ * hostname is a fact about the call, not a guess about its prose. Two
+ * consequences that a pack-level flag could not give us, and the reason the
+ * flag was rejected:
+ *
+ *   - It describes the CALL, not the pack. `govcon-intel` fans out to our own
+ *     Supabase AND to genuine third parties; `court-listener` holds our cache
+ *     in Supabase and fetches courtlistener.com. An `internallyHosted: true` on
+ *     either pack would relabel a real third-party outage as ours — inventing
+ *     work, which is the same class of error in the opposite direction.
+ *   - It covers every future internal pack for free, instead of one declared
+ *     slug at a time.
+ *
+ * WHY IT SURVIVES A REWORD. The marker below is not matched as a literal by two
+ * separate files. `markInternalOrigin()` writes it and `internalHostMetricsClass()`
+ * reads it, both from the single exported `INTERNAL_ORIGIN_MARKER` constant in
+ * this module — so changing the wording changes both sides in the same edit and
+ * cannot desynchronise them. The pack's own label (`fleet db error:`,
+ * `Pipeworx catalog error:`) is not read at all: reword it freely, the class is
+ * unaffected. That is the property `stripClassPrefix` lacked when it drifted
+ * from its own classifier three times and needed a CI gate to hold them
+ * together.
+ *
+ * WHERE THE 5xx TEST LIVES. `markInternalOrigin` is called from the places that
+ * hold the real `Response` — `httpError`/`httpErrorMessage` and the timeout
+ * branch of `fetchWithTimeout` in `shared/src/http.ts` — so "is this an
+ * availability failure" is decided from the actual status code, never re-derived
+ * by scraping a number out of a sentence. A 404 from our own registry for a slug
+ * that does not exist is a caller's bad argument and is deliberately NOT marked.
+ */
+
+/**
+ * OUR OWN web service was unreachable — not an upstream, and never `upstream_down`.
+ *
+ * ONE value, not three, unlike `internal_db_*`. That split existed because a
+ * slow query, an exhausted pool and an unknown SQLSTATE have different owners
+ * and different fixes. Here there is only one story to tell — an origin we run
+ * did not answer the edge — and one owner. A bucket with no distinct owner per
+ * value is decoration; #724 is what happens when a class holds several
+ * situations, and inventing sub-values ahead of a reason to act on them
+ * differently is the same mistake with the sign flipped.
+ *
+ * METRICS ONLY, exactly like PLATFORM_KEY_ERROR_CLASS and the internal_db
+ * values. `classifyToolError` still answers `upstream_down` for the retry and
+ * hint paths, which only care whether retrying or a sibling tool might work —
+ * and it might. Nothing a caller sees or is charged changes here.
+ *
+ * READ SIDE: this value is in BROKEN_TOOL_CLASSES, FAULT_CLASSES and
+ * ALL_ERROR_CLASSES in `workers/registry-api/src/index.ts`. All three, or it
+ * lands on no dashboard — fleet #721 is the warning, where the #719 split
+ * worked on the write side and was invisible for weeks.
+ */
+const INTERNAL_SERVICE_UNREACHABLE_CLASS = 'internal_service_unreachable';
+
+/**
+ * The token that carries "this origin is ours" from the call site to the
+ * classifier.
+ *
+ * Appended to the error message rather than attached to the Error object,
+ * because the object does not survive the trip: 275 packs return `{ error:
+ * string }` instead of throwing, the gateway reads `observedError` as a string,
+ * and the fleet pack rebuilds its error from a captured status + body across a
+ * retry loop. A property on an Error would be dropped by every one of those
+ * paths and the class would work in tests and vanish in production.
+ *
+ * WORDING IS LOAD-BEARING, same rule as labelAge's note in authority.ts. This
+ * string is appended to a pack's thrown Error message (shared/src/http.ts),
+ * and a thrown Error's message is exactly what the gateway hands back to the
+ * caller as `content[0].text` when nothing rewrites it (workers/gateway/src
+ * catches the throw and sets `rawResult.message = stripClassPrefix(error)`,
+ * which does not touch this suffix) — so the original wording,
+ * " [pipeworx-hosted origin — our own service, not a third party]", was not a
+ * theoretical leak: it shipped live on pipeworx-catalog's 522s, 7 times in 6
+ * hours on 2026-09-02 (see tests/golden-internal-service.test.ts), verbatim
+ * naming Pipeworx as the host. check:hosting-claims never caught it because it
+ * did not scan shared/ at all (task #2009). Reworded to describe the
+ * OBSERVATION (the origin did not answer) without a claim about who runs it —
+ * the identical fix labelAge got: drop the possessive, keep the fact.
+ */
+const INTERNAL_ORIGIN_MARKER = ' [origin did not respond — retry before concluding the named source is down]';
+
+/**
+ * Supabase's data plane for a project is `<ref>.supabase.co`, where the ref is
+ * exactly twenty lowercase letters (ours is `pqauisounztsgdgfkhke`).
+ *
+ * Matching the shape rather than listing the ref keeps this correct when we add
+ * a project — `supabaseEnv` on a pack entry already points some packs at a
+ * second one — while still excluding `status.supabase.co`, which is Supabase's
+ * own status page and emphatically not our database. Verified 2026-09-02 by
+ * `grep -rhoE '[a-z0-9-]+\.supabase\.(co|in)' mcps shared workers scripts`: the
+ * only real project ref anywhere in the tree is ours, the rest are doc
+ * placeholders (`abc`, `xyz`, `example`) which this pattern also excludes. Same
+ * finding internal-db-class.ts relies on for the PostgREST envelope being ours
+ * by construction.
+ */
+const SUPABASE_PROJECT_HOST = /^[a-z]{20}\.supabase\.(co|in)$/;
+
+/**
+ * Is this a host WE run?
+ *
+ * Deliberately NOT including `*.workers.dev`: plenty of third-party APIs are
+ * hosted on workers.dev, so the suffix says where something runs and not who
+ * owns it. Every internal call we actually make goes to a `pipeworx.io`
+ * hostname or to our Supabase project, both of which are ownership facts.
+ *
+ * `workers/gateway/src/provenance.ts`'s `OUR_HOSTS` answers the same
+ * question and DOES include `workers.dev` — a documented divergence
+ * (task #2051), not a bug to converge. That list decides what a response may
+ * cite as a data SOURCE, where a false negative (citing our own worker as an
+ * external source) is the hosting-disclosure leak this whole file exists to
+ * prevent, so it errs broad. This one decides who gets BLAMED for a 5xx in
+ * outage metrics read by on-call, where a false positive (crediting our own
+ * infra with a third party's outage) hides the real failure, so it errs
+ * narrow. Same suffix, opposite direction, because they are never called for
+ * the same reason.
+ *
+ * Returns false on anything unparseable rather than throwing — this runs inside
+ * an error path, and an error path that can itself throw turns a diagnosable
+ * failure into a mystery.
+ */
+function isPipeworxOrigin(url: string | URL | undefined | null): boolean {
+  if (!url) return false;
+  let host: string;
+  try {
+    host = new URL(url instanceof URL ? url.href : url).hostname.toLowerCase();
+  } catch {
+    return false;
+  }
+  if (host === 'pipeworx.io' || host.endsWith('.pipeworx.io')) return true;
+  return SUPABASE_PROJECT_HOST.test(host);
+}
+
+/**
+ * Append the marker when this failure was OUR origin failing to answer.
+ *
+ * `status` is the HTTP status when there is one, and omitted for a timeout —
+ * where there is no response at all, and "the origin did not answer" is the
+ * whole observation. Statuses below 500 are left alone: a 404 from our own
+ * registry for a slug that does not exist is the caller's argument, not our
+ * outage, and marking it would put ordinary 404s on the incident dashboard.
+ *
+ * Idempotent, so a message that is wrapped and re-marked on the way up (the
+ * fleet pack's retry loop re-throws through two layers) carries the marker once.
+ */
+function markInternalOrigin(
+  message: string,
+  url: string | URL | undefined | null,
+  status?: number,
+): string {
+  if (status !== undefined && status < 500) return message;
+  if (!isPipeworxOrigin(url)) return message;
+  if (message.includes(INTERNAL_ORIGIN_MARKER)) return message;
+  return message + INTERNAL_ORIGIN_MARKER;
+}
+
+/**
+ * Which blob4 value a failure from our own web services books as, or undefined
+ * if this is not one.
+ *
+ * Ordered AFTER `internalDbMetricsClass` at the call site: a PostgREST envelope
+ * from our own Supabase is a strictly more specific statement about the same
+ * row (which of our services, and why), and the two cannot disagree about
+ * whether the failure is ours.
+ */
+function internalHostMetricsClass(error: string): string | undefined {
+  return error.includes(INTERNAL_ORIGIN_MARKER) ? INTERNAL_SERVICE_UNREACHABLE_CLASS : undefined;
+}
+
+
+/**
+ * One place to turn a failed `fetch` into an error a caller can act on.
+ *
+ * Nearly every pack was written the same way:
+ *
+ *     if (!res.ok) throw new Error(`Unsplash: ${res.status}`);
+ *
+ * which discards the response body — and the body is usually where the upstream
+ * says what was actually wrong ("**symbol** not found: GBP", "parameter `year`
+ * out of range", "unknown taxonomy id"). The caller gets a number, cannot
+ * self-correct, and retries the same broken call. A 2026-07-31 sweep found this
+ * shape in 481 of 1,400 packs, 47 of them PLATFORM-keyed.
+ *
+ * It also hides bugs one level down. Two of the first three packs audited had a
+ * second defect that only existed because of this line: unsplash's rate-limit
+ * branch sat BELOW a catch-all and was unreachable, and bea-gov parsed
+ * `BEAAPI.Error.APIErrorDescription` below a `!res.ok` throw that made the
+ * parsing dead code for every non-200.
+ *
+ * DELIBERATELY NOT A CLASSIFIER. It does not add `user_error:` /
+ * `upstream_down:` prefixes. Those decide which tier a failure lands in, and the
+ * `error` tier is what the daily problem-tools list is built from — it means
+ * "Pipeworx has a defect". A 400 is genuinely ambiguous: often a caller's bad
+ * argument, but sometimes a query WE built wrong (ted-eu comma-joined its CPV
+ * values into something TED rejected, and that bug was found only because it sat
+ * in `error`). Blanket-classifying 400s as caller mistakes would have hidden it.
+ * A pack that KNOWS which it is should keep saying so explicitly; this helper is
+ * for the 481 that say nothing at all.
+ */
+
+/** Longest upstream explanation we'll pass through. Enough for a real message,
+ *  short enough that an HTML page or a stack trace can't swamp the error. */
+
+const MAX_DETAIL = 300;
+
+/**
+ * Default bound for `fetchWithTimeout` when a pack doesn't state its own.
+ *
+ * 25s mirrors the number `epo-ops` landed on after measuring the real failure:
+ * a degraded upstream that doesn't error, it just never answers, and a Worker
+ * sits in `await fetch()` until ITS OWN execution budget kills the request —
+ * which can take minutes, not seconds (epo_ops_search_patents measured 4-8
+ * MINUTE hangs before this existed). 25s is short enough that a caller gets a
+ * fast, actionable error instead of holding the connection, and long enough
+ * that it doesn't false-trip on a merely-slow-but-alive upstream.
+ */
+const DEFAULT_FETCH_TIMEOUT_MS = 25_000;
+
+/**
+ * Read the body of a failed response and fold it into a throwable Error.
+ *
+ * Usage — note the `await`, which is the one thing that makes this a mechanical
+ * change rather than a drop-in:
+ *
+ *     if (!res.ok) throw await httpError(res, 'Unsplash');
+ *
+ * Safe to call on any non-ok response: a body that is missing, empty, unreadable
+ * or HTML degrades to exactly the old `Name: 404` string rather than throwing
+ * something new from inside the error path.
+ */
+async function httpError(res: Response, name: string): Promise<Error> {
+  return new Error(await httpErrorMessage(res, name));
+}
+
+/** The message text without constructing an Error — for packs that need to wrap
+ *  it in their own envelope or add an explicit classification prefix. */
+async function httpErrorMessage(res: Response, name: string): Promise<string> {
+  // The one place a 5xx from a host WE run gets stamped as ours. `res.url` is
+  // the URL the fetch actually resolved to (after redirects), so this is a fact
+  // about the call rather than a guess from the `name` the pack passed in —
+  // reword that label freely, the class does not move. See
+  // internal-host-class.ts; no-op for every third-party upstream, which is why
+  // this touches 481 packs' error text and changes none of it.
+  return markInternalOrigin(
+    `${name}: ${res.status}${detailSuffix(await readDetail(res))}`,
+    res.url,
+    res.status,
+  );
+}
+
+/**
+ * Just the upstream's own explanation — no name, no status.
+ *
+ * For a pack that has already said both in its own sentence. epo-ops reads
+ * `EPO rejected this search as too large (HTTP 413) — ${httpErrorMessage(…)}`,
+ * which rendered as `… (HTTP 413) — EPO: 413.` once the XML detail was being
+ * dropped: the upstream named twice, the status twice, and the one thing EPO
+ * actually said ("Not enough characters before truncation character") nowhere
+ * (fleet #712). Returns '' when the body carries nothing readable, so a caller
+ * can fall back to its own wording.
+ */
+async function upstreamDetail(res: Response): Promise<string> {
+  return readDetail(res);
+}
+
+/**
+ * Read a SUCCESSFUL response as JSON, failing loudly when it isn't JSON.
+ *
+ * `httpError` above only ever runs on `!res.ok`, which leaves the nastier half
+ * of the problem unhandled: an upstream that answers **HTTP 200 with an HTML
+ * page**. A bot wall, a login redirect, a maintenance interstitial and a CDN
+ * error page are all 200s, so `res.ok` is true, and `res.json()` then throws
+ * `Unexpected token '<', "<!DOCTYPE "... is not valid JSON`.
+ *
+ * That string is the problem. It names no upstream, carries no status, and
+ * reads like a parser bug in Pipeworx — so it lands in the `error` tier, which
+ * means "we have a defect", and the caller is told nothing they can act on.
+ * data.govt.nz sat dead behind an Imperva challenge this way and every
+ * status-code health check we own reported it green (7889a845). A zero-length
+ * body has the same shape: `Unexpected end of JSON input`, seen this week on
+ * uk-gazette (83% of external calls) and census.
+ *
+ * UNLIKE `httpError`, this one DOES classify, and the asymmetry is deliberate.
+ * A 400 is genuinely ambiguous — often the caller's bad argument, sometimes a
+ * query we built wrong — so blanket-classifying it would hide our own bugs.
+ * There is no such ambiguity here: **no argument a caller can pass makes a JSON
+ * API return an HTML page.** It is always the upstream, so `upstream_down:` is
+ * a statement of fact rather than a guess, and it keeps these out of the
+ * problem-tools list where they crowd out real defects.
+ *
+ *     const data = await parseJson<Feed>(res, 'UK Gazette');
+ *
+ * Call it only after the `!res.ok` check — on a failed response you want
+ * `httpError`, which mines the body for the upstream's own explanation.
+ */
+async function parseJson<T>(res: Response, name: string): Promise<T> {
+  let raw: string;
+  try {
+    raw = await res.text();
+  } catch {
+    throw new Error(
+      `upstream_down: ${name} returned a body that could not be read (HTTP ${res.status}). ` +
+        'The connection most likely dropped mid-response; retrying is reasonable.',
+    );
+  }
+
+  const type = res.headers.get('content-type') ?? 'no content-type';
+
+  if (!raw.trim()) {
+    throw new Error(
+      `upstream_down: ${name} answered HTTP ${res.status} with an EMPTY body where JSON was expected (${type}). ` +
+        'Nothing about the request can cause this — it is an upstream fault, and the same call may well work on retry.',
+    );
+  }
+
+  // Checked before parsing rather than in the catch, because knowing it is
+  // markup is what turns "we failed to parse something" into "they served a
+  // web page" — the second is diagnosable, the first is not.
+  const head = raw.slice(0, 200).trimStart().toLowerCase();
+  if (head.startsWith('<!doctype') || head.startsWith('<html') || head.startsWith('<?xml')) {
+    const kind = head.startsWith('<?xml') ? 'an XML document' : 'an HTML page';
+    // The summary, not the source. Pasting the first 120 characters of a web
+    // page handed the agent `<!DOCTYPE html><html lang="en"…` — the same leak
+    // this branch exists to describe (fleet #712).
+    throw new Error(
+      `upstream_down: ${name} answered HTTP ${res.status} with ${kind} instead of JSON (${type}). ` +
+        'That is typically a bot wall, a login redirect or a maintenance page — it is returned as a SUCCESS, ' +
+        `so status-code health checks read it as fine. No argument change will get past it. ` +
+        `The page says: ${summarizeErrorBody(raw) || 'nothing readable'}`,
+    );
+  }
+
+  try {
+    return JSON.parse(raw) as T;
+  } catch {
+    throw new Error(
+      `upstream_down: ${name} answered HTTP ${res.status} with a body that is not valid JSON (${type}). ` +
+        `It begins: ${stripMarkup(raw).slice(0, 120) || '(unreadable)'}`,
+    );
+  }
+}
+
+/**
+ * `fetch`, but bounded — the fix for a systemic gap found 2026-08-30: a grep
+ * audit of every pack's `mcps/*\/src/index.ts` found 1,339 of ~1,500 call
+ * `fetch()` with NO timeout guard anywhere in the file. Two of those
+ * (epo-ops, statcan) were confirmed live-hanging for 4-8 minutes before this
+ * existed — every unguarded call carries the same risk, just unconfirmed.
+ *
+ * Mirrors the `epoFetch` wrapper `mcps/epo-ops/src/index.ts` shipped first:
+ * bound the request with `AbortSignal.timeout`, and on a timeout/abort throw
+ * an `upstream_down:` error that names the upstream and the bound rather than
+ * letting the raw `TimeoutError`/`AbortError` (which names neither) propagate.
+ * `upstream_down:` is deliberate, same reasoning as `parseJson` above — no
+ * argument a caller passes can make an upstream hang, so it is always the
+ * upstream's fault, and marking it that way keeps a slow API off the
+ * problem-tools list where it would crowd out our own defects.
+ *
+ * Usage — a mechanical swap for a bare `fetch(url, init)`:
+ *
+ *     const res = await fetchWithTimeout(url, init, 'Some API');
+ *
+ * Pass `timeoutMs` as a fourth argument to override the default for a pack
+ * with a known-slower upstream; the label should be the same short name you'd
+ * pass to `httpError`/`httpErrorMessage` for that call.
+ */
+async function fetchWithTimeout(
+  url: string | URL,
+  init: RequestInit = {},
+  name: string,
+  timeoutMs: number = DEFAULT_FETCH_TIMEOUT_MS,
+): Promise<Response> {
+  try {
+    return await fetch(url, { ...init, signal: AbortSignal.timeout(timeoutMs) });
+  } catch (err) {
+    if (err instanceof Error && (err.name === 'TimeoutError' || err.name === 'AbortError')) {
+      // States the OBSERVATION (no response in N seconds), not a diagnosis.
+      // "appears to be degraded" is an inference about the vendor that we have
+      // not checked, and it is wrong in a way that misdirects whoever reads it:
+      // a timeout from a Worker can equally mean OUR egress is blocked.
+      //
+      // Measured today (2026-09-01, fleet #1047): every call to
+      // mainnet.base.org failed from the x402 facilitator while the identical
+      // request from a laptop returned 200. Base was entirely healthy; the
+      // public RPC refuses Cloudflare Worker egress. Had this message fired
+      // there it would have blamed Base by name, and the next person would have
+      // waited for a vendor outage to clear that did not exist.
+      // A timeout has no status to test — there is no response at all — so
+      // `markInternalOrigin` is called without one: an origin we run that never
+      // answered is an availability failure by definition. This is the half of
+      // fleet #1096 with neither a SQLSTATE nor a status code to key on.
+      throw new Error(
+        markInternalOrigin(
+          `upstream_down: ${name} did not respond within ${timeoutMs / 1000}s. ` +
+            `That can be ${name} being slow or down, or this environment being unable to reach it ` +
+            `(some hosts refuse datacenter/Worker egress) — retry shortly, and check reachability ` +
+            `from elsewhere before concluding ${name} is down.`,
+          url,
+        ),
+      );
+    }
+    throw err;
+  }
+}
+
+function detailSuffix(detail: string): string {
+  return detail ? ` — ${detail}` : '';
+}
+
+async function readDetail(res: Response): Promise<string> {
+  let raw: string;
+  try {
+    raw = await res.text();
+  } catch {
+    // Body already consumed, or the connection died mid-read. The status alone
+    // is still worth throwing — never let the error path throw its own error.
+    return '';
+  }
+  return summarizeErrorBody(raw);
+}
+
+/**
+ * Turn ANY error body — JSON, HTML, XML or plain text — into one short phrase
+ * that never contains markup.
+ *
+ * This used to just drop an HTML or XML body on the floor, on the reasoning
+ * that markup crowds out the status. That was half right. Dropping it loses the
+ * one sentence a caller could have acted on: an `Access Denied` title, an SDMX
+ * `<message:Error>` text, an OPS fault string. A 2026-08-30 support sweep
+ * measured 13 of 291 caller-facing error rows carrying a raw page or document
+ * verbatim, across 11 packs, and in every one of them the useful content —
+ * "Access Denied", "Invalid country code", "SCRAPE_TIMEOUT" — was in there,
+ * buried in markup the agent had to parse out of a string (fleet #712).
+ *
+ * So: extract the meaning, discard the markup. The output is passed through
+ * `stripMarkup` unconditionally, which is what lets `check:error-body-leak`
+ * assert mechanically that no caller-facing message can contain `<?xml`,
+ * `<!DOCTYPE` or `<html`.
+ */
+function summarizeErrorBody(raw: string): string {
+  if (!raw || !raw.trim()) return '';
+
+  const head = raw.slice(0, 400).trimStart().toLowerCase();
+
+  // An HTML error page (Cloudflare interstitial, nginx default, a login
+  // redirect) says what it is in its <title>, and almost nowhere else.
+  if (head.startsWith('<!doctype') || head.startsWith('<html')) {
+    const title = htmlTitle(raw);
+    return title
+      ? `${title} (upstream returned an HTML error page, not an API response)`
+      : 'upstream returned an HTML error page, not an API response';
+  }
+
+  // XML fault documents — EPO OPS, SDMX (`<message:Error>`), SOAP faults. The
+  // human sentence sits in a child element whose tag name says what it is.
+  if (head.startsWith('<?xml') || head.startsWith('<')) {
+    const fault = xmlFaultText(raw);
+    return fault
+      ? `${stripMarkup(fault).slice(0, MAX_DETAIL)} (from the upstream's XML error document)`
+      : 'upstream returned an XML error document with no readable message';
+  }
+
+  // Most JSON error bodies bury one human sentence among ids and echoed request
+  // params. Prefer that sentence; fall back to the whole body when the shape is
+  // unfamiliar, since an unfamiliar shape is exactly when we can least afford to
+  // guess wrong and show nothing.
+  const fromJson = messageFromJson(raw);
+  return stripMarkup(fromJson ?? raw).slice(0, MAX_DETAIL);
+}
+
+/** The `<title>` of an HTML error page, or its first `<h1>` — the two places a
+ *  bot wall, a 502 and an "Access Denied" all state what happened. */
+function htmlTitle(raw: string): string | null {
+  const head = raw.slice(0, 4000);
+  for (const re of [/<title[^>]*>([\s\S]*?)<\/title>/i, /<h1[^>]*>([\s\S]*?)<\/h1>/i]) {
+    const m = re.exec(head);
+    const text = m ? stripMarkup(m[1]) : '';
+    if (text) return text.slice(0, 160);
+  }
+  return null;
+}
+
+/** Tag names that carry the explanation in an XML fault document, namespace
+ *  prefix optional (`<message:Error>`, `<com:Text>`, `<faultstring>`). */
+const XML_FAULT_TAG_RE =
+  /<(?:[A-Za-z0-9_.-]+:)?(?:text|message|description|faultstring|reason|detail|title|errormessage|error)\b[^>]*>([^<]{2,400})</i;
+
+function xmlFaultText(raw: string): string | null {
+  const head = raw.slice(0, 8000);
+  const tagged = XML_FAULT_TAG_RE.exec(head);
+  if (tagged && tagged[1].trim()) return tagged[1];
+
+  // Nothing conventionally named — take the longest text node instead. A fault
+  // document with one sentence in an oddly named element is still readable;
+  // returning nothing at all is not.
+  let best = '';
+  for (const m of head.matchAll(/>([^<>]{8,400})</g)) {
+    const text = m[1].trim();
+    if (text.length > best.length) best = text;
+  }
+  return best || null;
+}
+
+/**
+ * Remove every tag and stray angle bracket, then collapse whitespace.
+ *
+ * Applied to everything on the way out, including the JSON and plain-text
+ * paths, because an upstream is free to embed markup in a JSON string field —
+ * and a leak is a leak regardless of which branch produced it.
+ */
+function stripMarkup(s: string): string {
+  return collapse(decodeEntities(s.replace(/<[^>]*>/g, ' ')).replace(/[<>]/g, ' '));
+}
+
+/** The handful of entities that show up in error-page titles. Decoded AFTER
+ *  tags are stripped and BEFORE the angle-bracket sweep, so `&lt;script&gt;`
+ *  in a title cannot decode into markup that survives — EMBL-EBI's ChEMBL 500
+ *  page renders as `500 Internal Server Error &lt; EMBL-EBI` otherwise. */
+function decodeEntities(s: string): string {
+  return s
+    .replace(/&(?:amp|#0*38);/gi, '&')
+    .replace(/&(?:lt|#0*60);/gi, '<')
+    .replace(/&(?:gt|#0*62);/gi, '>')
+    .replace(/&(?:quot|#0*34);/gi, '"')
+    .replace(/&(?:#0*39|apos|#x0*27);/gi, "'")
+    .replace(/&nbsp;/gi, ' ');
+}
+
+/** The conventional "what went wrong" field, under any of the names upstreams
+ *  actually use. Checked in order; first non-empty string wins. */
+const MESSAGE_KEYS = [
+  'message', 'error_message', 'errorMessage', 'detail', 'details',
+  'description', 'error_description', 'reason', 'title', 'fault',
+];
+
+function messageFromJson(raw: string): string | null {
+  let parsed: unknown;
+  try {
+    parsed = JSON.parse(raw);
+  } catch {
+    return null;
+  }
+  return pickMessage(parsed, 0);
+}
+
+function pickMessage(node: unknown, depth: number): string | null {
+  // Two levels covers `{error: {message}}` and `{errors: [{detail}]}`, the two
+  // shapes that account for nearly all of them, without walking a large payload.
+  if (depth > 2 || node == null) return null;
+
+  if (typeof node === 'string') return node.trim() || null;
+
+  if (Array.isArray(node)) {
+    for (const item of node) {
+      const found = pickMessage(item, depth + 1);
+      if (found) return found;
+    }
+    return null;
+  }
+
+  if (typeof node !== 'object') return null;
+  const obj = node as Record<string, unknown>;
+
+  for (const key of MESSAGE_KEYS) {
+    const v = obj[key];
+    if (typeof v === 'string' && v.trim()) return v.trim();
+  }
+  // `{error: …}` where error is itself an object or a string — the single most
+  // common wrapper, so it is worth descending into by name rather than scanning
+  // every key and risking picking up an echoed request parameter.
+  for (const key of ['error', 'errors', 'fault', 'Error', 'data']) {
+    if (key in obj) {
+      const found = pickMessage(obj[key], depth + 1);
+      if (found) return found;
+    }
+  }
+  return null;
+}
+
+/** Errors are read in a single line of log output; newlines and runs of
+ *  whitespace make a multi-line body unreadable there. */
+function collapse(s: string): string {
+  return s.replace(/\s+/g, ' ').trim();
+}
+/**
+ * dbSNP refSNP records and HGVS/SPDI/rsID normalization for human genetic variants, from NCBI Variation Services.
+ *
+ * Keyless: https://api.ncbi.nlm.nih.gov/variation/v0/
+ *
+ * WHY THE `assembly` ARGUMENT IS EXPLICIT AND NOT A DETAIL.
+ * A refSNP carries placements on BOTH GRCh38 and GRCh37 at DIFFERENT
+ * coordinates (rs113488022 is 7:140753336 on GRCh38 and 7:140453136 on
+ * GRCh37 — a 300kb difference). A caller who takes a coordinate from one build
+ * and looks it up in a dataset annotated on the other gets "not found", which
+ * reads as "this variant does not exist" rather than "you asked the wrong
+ * build". So every response states which assembly it answered on and which
+ * assemblies the record actually has, and an assembly with no placement is
+ * reported as such instead of coming back empty.
+ */
+
+
+const BASE = 'https://api.ncbi.nlm.nih.gov/variation/v0';
+const UA = 'pipeworx-mcp-ncbi-variation/1.0 (+https://pipeworx.io)';
+
+async function pwFetch(url: string | URL, init?: RequestInit): Promise<Response> {
+  const headers = { Accept: 'application/json', 'User-Agent': UA, ...(init?.headers ?? {}) };
+  return fetchWithTimeout(url, { ...init, headers }, 'NCBI Variation Services');
+}
+
+const tools: McpToolExport['tools'] = [
+  {
+    name: 'variation_refsnp',
+    description:
+      'AUTHORITATIVE dbSNP refSNP record for a variant rsID, from NCBI Variation Services. PREFER OVER WEB SEARCH for "what is rs<N>" — returns the genomic placement on the assembly you ask for (GRCh38 or GRCh37; the coordinates differ between builds), the HGVS genomic/transcript/protein expressions, SPDI, gene context, ClinVar clinical significance, and population allele frequencies (gnomAD, ExAC, 1000 Genomes, TOPMED). Follows dbSNP merges: a retired rsID reports the rsID it was merged into.',
+    summary:
+      'The dbSNP record for an rsID: coordinates on GRCh38 or GRCh37, HGVS, ClinVar significance, and population allele frequencies.',
+    inputSchema: {
+      type: 'object' as const,
+      properties: {
+        rsid: { type: 'string', description: 'rsID, with or without the "rs" prefix. e.g. "rs113488022" (BRAF V600E) or "334".' },
+        assembly: { type: 'string', description: 'Human genome build for the genomic placement: "GRCh38" (default) or "GRCh37". Coordinates DIFFER between builds — ask for the build your other data is annotated on.' },
+        max_frequencies: { type: 'number', description: 'Cap on allele-frequency study rows returned (default 40). dbSNP can carry hundreds.' },
+      },
+      required: ['rsid'],
+    },
+  },
+  {
+    name: 'variation_hgvs_to_spdi',
+    description:
+      'Normalize an HGVS expression to SPDI (sequence-position-deletion-insertion) contextual alleles via NCBI Variation Services. AUTHORITATIVE for turning a clinician- or paper-style variant string ("NC_000007.14:g.140753336A>T", "NM_004333.6:c.1799T>A") into the canonical, left-shifted coordinate form that dbSNP/ClinVar keys on, and for validating that an HGVS string is well-formed at all.',
+    summary:
+      'Normalizes an HGVS variant string to canonical SPDI coordinates, and validates it, via NCBI Variation Services.',
+    inputSchema: {
+      type: 'object' as const,
+      properties: {
+        hgvs: { type: 'string', description: 'HGVS expression on a RefSeq accession, e.g. "NC_000007.14:g.140753336A>T" or "NM_004333.6:c.1799T>A".' },
+      },
+      required: ['hgvs'],
+    },
+  },
+  {
+    name: 'variation_spdi_to_rsids',
+    description:
+      'Look up the dbSNP rsIDs that a SPDI allele maps to, via NCBI Variation Services. AUTHORITATIVE for the reverse direction — you have a genomic coordinate and alleles from a VCF or a pipeline and need the rsID other databases key on. SPDI is 0-BASED, unlike HGVS: "NC_000007.14:140753335:A:T" is the same variant as "NC_000007.14:g.140753336A>T".',
+    summary:
+      'Maps a SPDI genomic coordinate and alleles back to the dbSNP rsIDs, via NCBI Variation Services.',
+    inputSchema: {
+      type: 'object' as const,
+      properties: {
+        spdi: { type: 'string', description: 'SPDI as seq_id:position:deleted:inserted, 0-based position. e.g. "NC_000007.14:140753335:A:T".' },
+      },
+      required: ['spdi'],
+    },
+  },
+];
+
+type Spdi = { seq_id?: string; position?: number; deleted_sequence?: string; inserted_sequence?: string };
+type AlleleEntry = { allele?: { spdi?: Spdi }; hgvs?: string };
+type Placement = {
+  seq_id?: string;
+  is_ptlp?: boolean;
+  placement_annot?: {
+    seq_type?: string;
+    mol_type?: string;
+    seq_id_traits_by_assembly?: { assembly_name?: string; assembly_accession?: string; is_top_level?: boolean }[];
+  };
+  alleles?: AlleleEntry[];
+};
+
+function spdiString(s: Spdi | undefined): string | null {
+  if (!s || !s.seq_id) return null;
+  return `${s.seq_id}:${s.position}:${s.deleted_sequence ?? ''}:${s.inserted_sequence ?? ''}`;
+}
+
+/** Variant alleles only — dbSNP lists the reference allele as deleted === inserted. */
+function isVariantAllele(a: AlleleEntry): boolean {
+  const s = a.allele?.spdi;
+  return !!s && s.deleted_sequence !== s.inserted_sequence;
+}
+
+function assemblyNamesOf(p: Placement): string[] {
+  return (p.placement_annot?.seq_id_traits_by_assembly ?? []).map((t) => t.assembly_name ?? '').filter(Boolean);
+}
+
+async function callTool(name: string, args: Record<string, unknown>): Promise<unknown> {
+  switch (name) {
+    case 'variation_refsnp':
+      return refsnp(args);
+    case 'variation_hgvs_to_spdi': {
+      const hgvs = reqStr(args, 'hgvs', '"NC_000007.14:g.140753336A>T"');
+      const body = (await nvGet(`/hgvs/${encodeURIComponent(hgvs)}/contextuals`)) as {
+        data?: { spdis?: Spdi[]; input_hgvs_validity?: string; warnings?: unknown };
+      };
+      const spdis = body?.data?.spdis ?? [];
+      return {
+        source: 'NCBI Variation Services (dbSNP), https://api.ncbi.nlm.nih.gov/variation/v0/',
+        input_hgvs: hgvs,
+        input_hgvs_validity: body?.data?.input_hgvs_validity ?? null,
+        spdi_count: spdis.length,
+        spdis: spdis.map((s) => ({
+          spdi: spdiString(s),
+          seq_id: s.seq_id,
+          position_0based: s.position,
+          deleted_sequence: s.deleted_sequence,
+          inserted_sequence: s.inserted_sequence,
+        })),
+        note: 'SPDI positions are 0-based; the HGVS g. position for the same variant is position + 1.',
+        warnings: body?.data?.warnings ?? null,
+      };
+    }
+    case 'variation_spdi_to_rsids': {
+      const spdi = reqStr(args, 'spdi', '"NC_000007.14:140753335:A:T"');
+      if (spdi.split(':').length !== 4) {
+        throw new Error(`"spdi" must have four colon-separated parts (seq_id:position:deleted:inserted), e.g. "NC_000007.14:140753335:A:T". Got: ${spdi}`);
+      }
+      const body = (await nvGet(`/spdi/${encodeURIComponent(spdi)}/rsids`)) as { data?: { rsids?: number[] } };
+      const rsids = body?.data?.rsids ?? [];
+      return {
+        source: 'NCBI Variation Services (dbSNP), https://api.ncbi.nlm.nih.gov/variation/v0/',
+        input_spdi: spdi,
+        rsid_count: rsids.length,
+        rsids: rsids.map((r) => `rs${r}`),
+        rsid_numbers: rsids,
+        note: rsids.length ? undefined : 'No rsID is assigned to this exact SPDI allele. Check the assembly of seq_id and that the position is 0-based.',
+      };
+    }
+    default:
+      throw new Error(`Unknown tool: ${name}`);
+  }
+}
+
+async function refsnp(args: Record<string, unknown>): Promise<unknown> {
+  const raw = reqStr(args, 'rsid', '"rs113488022"').trim();
+  const num = raw.replace(/^rs/i, '');
+  if (!/^\d+$/.test(num)) throw new Error(`"rsid" must be a dbSNP rsID such as "rs113488022" or "113488022". Got: ${raw}`);
+
+  const wanted = String(args.assembly ?? 'GRCh38').trim();
+  if (!/^GRCh3[78]/i.test(wanted)) {
+    throw new Error(`"assembly" must be "GRCh38" or "GRCh37" (human genome build). Got: ${wanted}. Coordinates differ between builds, so this is not a cosmetic choice.`);
+  }
+  const maxFreq = Math.max(1, Math.min(500, Number(args.max_frequencies ?? 40)));
+
+  const doc = (await nvGet(`/refsnp/${num}`)) as Record<string, unknown>;
+
+  const merged = doc.merged_snapshot_data as { merged_into?: string[] } | undefined;
+  const ps = doc.primary_snapshot_data as
+    | { placements_with_allele?: Placement[]; allele_annotations?: Record<string, unknown>[]; variant_type?: string }
+    | undefined;
+
+  if (!ps && merged) {
+    const into = (merged.merged_into ?? []).map((r) => `rs${r}`);
+    return {
+      source: 'NCBI Variation Services (dbSNP), https://api.ncbi.nlm.nih.gov/variation/v0/',
+      rsid: `rs${num}`,
+      status: 'merged',
+      merged_into: into,
+      note: `rs${num} is a retired rsID that dbSNP merged into ${into.join(', ') || 'another rsID'}. Re-query variation_refsnp with that rsID for the variant record.`,
+      create_date: doc.create_date ?? null,
+      last_update_date: doc.last_update_date ?? null,
+    };
+  }
+
+  const placements = ps?.placements_with_allele ?? [];
+  const assembliesAvailable = [...new Set(placements.flatMap(assemblyNamesOf))];
+
+  const genomic = placements.filter((p) => p.placement_annot?.mol_type === 'genomic' && assemblyNamesOf(p).length > 0);
+  const onWanted = genomic.filter((p) => assemblyNamesOf(p).some((a) => a.toUpperCase().startsWith(wanted.toUpperCase())));
+
+  const genomic_placements = onWanted.map((p) => {
+    const variants = (p.alleles ?? []).filter(isVariantAllele);
+    const ref = (p.alleles ?? []).find((a) => !isVariantAllele(a));
+    return {
+      assembly: assemblyNamesOf(p).join(', '),
+      seq_id: p.seq_id,
+      is_primary_top_level: !!p.is_ptlp,
+      position_0based: variants[0]?.allele?.spdi?.position ?? ref?.allele?.spdi?.position ?? null,
+      position_1based_hgvs: (variants[0]?.allele?.spdi?.position ?? ref?.allele?.spdi?.position ?? -1) + 1 || null,
+      reference_allele: ref?.allele?.spdi?.deleted_sequence ?? null,
+      alternate_alleles: variants.map((a) => ({
+        inserted_sequence: a.allele?.spdi?.inserted_sequence ?? '',
+        hgvs: a.hgvs ?? null,
+        spdi: spdiString(a.allele?.spdi),
+      })),
+    };
+  });
+
+  const hgvsOf = (molType: string, seqPrefix?: RegExp) =>
+    [
+      ...new Set(
+        placements
+          .filter((p) => p.placement_annot?.mol_type === molType && (!seqPrefix || seqPrefix.test(p.seq_id ?? '')))
+          .flatMap((p) => (p.alleles ?? []).filter(isVariantAllele).map((a) => a.hgvs ?? ''))
+          .filter(Boolean),
+      ),
+    ].slice(0, 60);
+
+  const annotations = ps?.allele_annotations ?? [];
+  const frequencies: Record<string, unknown>[] = [];
+  const clinical: Record<string, unknown>[] = [];
+  const genes = new Map<string, { locus: string; name: string; gene_id: number }>();
+
+  for (const ann of annotations) {
+    for (const f of (ann.frequency ?? []) as Record<string, unknown>[]) {
+      const obs = f.observation as Spdi | undefined;
+      const ac = Number(f.allele_count ?? 0);
+      const tc = Number(f.total_count ?? 0);
+      frequencies.push({
+        study: f.study_name ?? null,
+        study_version: f.study_version ?? null,
+        allele: obs ? `${obs.deleted_sequence ?? ''}>${obs.inserted_sequence ?? ''}` : null,
+        seq_id: obs?.seq_id ?? null,
+        allele_count: ac,
+        total_count: tc,
+        allele_frequency: tc > 0 ? Number((ac / tc).toPrecision(6)) : null,
+      });
+    }
+    for (const c of (ann.clinical ?? []) as Record<string, unknown>[]) {
+      clinical.push({
+        clinvar_accession: c.accession_version ?? null,
+        clinical_significances: c.clinical_significances ?? [],
+        disease_names: c.disease_names ?? [],
+        review_status: c.review_status ?? null,
+        origins: c.origins ?? [],
+        last_evaluated_date: c.last_evaluated_date ?? null,
+        collection_method: c.collection_method ?? [],
+        citation_pubmed_ids: ((c.citations ?? []) as number[]).slice(0, 10),
+      });
+    }
+    for (const aa of (ann.assembly_annotation ?? []) as Record<string, unknown>[]) {
+      for (const g of (aa.genes ?? []) as Record<string, unknown>[]) {
+        const locus = String(g.locus ?? '');
+        if (locus && !genes.has(locus)) genes.set(locus, { locus, name: String(g.name ?? ''), gene_id: Number(g.id ?? 0) });
+      }
+    }
+  }
+
+  frequencies.sort((a, b) => Number(b.total_count ?? 0) - Number(a.total_count ?? 0));
+  const citations = (doc.citations ?? []) as number[];
+
+  return {
+    source: 'NCBI Variation Services (dbSNP), https://api.ncbi.nlm.nih.gov/variation/v0/',
+    rsid: `rs${num}`,
+    status: 'live',
+    variant_type: ps?.variant_type ?? null,
+    assembly_requested: wanted,
+    assemblies_available: assembliesAvailable,
+    assembly_note:
+      genomic_placements.length === 0
+        ? `dbSNP has no genomic placement for rs${num} on ${wanted}. Available: ${assembliesAvailable.join(', ') || 'none'}. Coordinates differ between builds — re-ask with one of those rather than reading this as "variant not found".`
+        : `Coordinates below are on ${wanted}. The same variant sits at DIFFERENT coordinates on the other build.`,
+    genomic_placements,
+    hgvs: {
+      genomic: hgvsOf('genomic'),
+      transcript: hgvsOf('rna'),
+      protein: hgvsOf('protein'),
+    },
+    genes: [...genes.values()],
+    mane_select_ids: doc.mane_select_ids ?? [],
+    clinical_count: clinical.length,
+    clinical,
+    allele_frequency_count: frequencies.length,
+    allele_frequencies: frequencies.slice(0, maxFreq),
+    merged_from_rsids: ((doc.dbsnp1_merges ?? []) as { merged_rsid?: string }[]).map((m) => `rs${m.merged_rsid}`),
+    citation_count: citations.length,
+    citation_pubmed_ids: citations.slice(0, 25),
+    create_date: doc.create_date ?? null,
+    last_update_date: doc.last_update_date ?? null,
+    last_update_build_id: doc.last_update_build_id ?? null,
+  };
+}
+
+async function nvGet(path: string): Promise<unknown> {
+  const res = await pwFetch(`${BASE}${path}`);
+  if (res.status === 404) {
+    throw new Error(`NCBI Variation Services: not found (${path}). Check the rsID/HGVS/SPDI and that the RefSeq accession carries a version suffix (e.g. NC_000007.14, not NC_000007).`);
+  }
+  if (!res.ok) {
+    const body = (await res.text()).slice(0, 300);
+    throw new Error(`NCBI Variation Services: ${res.status} ${body}`);
+  }
+  return res.json();
+}
+
+function reqStr(args: Record<string, unknown>, key: string, example: string): string {
+  const v = args[key];
+  if (typeof v !== 'string' || !v.trim()) throw new Error(`Required argument "${key}" is missing. Pass a string like ${example}.`);
+  return v;
+}
+
+export default { tools, callTool, meter: { credits: 1 } } satisfies McpToolExport;

package/src/server.ts

@@ -0,0 +1,45 @@
+/**
+ * Stdio MCP server entry point for @pipeworx/mcp-ncbi-variation.
+ * Generated by scripts/publish-pack.sh — do not hand-edit in the pack repo;
+ * edit scripts/publish-pack.sh (the server.ts heredoc) and republish instead.
+ */
+import { Server } from '@modelcontextprotocol/sdk/server/index.js';
+import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
+import { CallToolRequestSchema, ListToolsRequestSchema } from '@modelcontextprotocol/sdk/types.js';
+import pack from './index.js';
+
+const server = new Server(
+  { name: '@pipeworx/mcp-ncbi-variation', version: '0.1.0' },
+  { capabilities: { tools: {} } },
+);
+
+server.setRequestHandler(ListToolsRequestSchema, async () => ({
+  tools: pack.tools.map((t) => ({
+    name: t.name,
+    description: t.description,
+    inputSchema: t.inputSchema,
+  })),
+}));
+
+server.setRequestHandler(CallToolRequestSchema, async (request) => {
+  const { name, arguments: args } = request.params;
+  try {
+    const result = await pack.callTool(name, (args ?? {}) as Record<string, unknown>);
+    return { content: [{ type: 'text', text: JSON.stringify(result, null, 2) }] };
+  } catch (err) {
+    return {
+      content: [{ type: 'text', text: err instanceof Error ? err.message : String(err) }],
+      isError: true,
+    };
+  }
+});
+
+async function main() {
+  const transport = new StdioServerTransport();
+  await server.connect(transport);
+}
+
+main().catch((err) => {
+  console.error('Fatal error running server:', err);
+  process.exit(1);
+});

package/tsconfig.json

@@ -0,0 +1,18 @@
+{
+  "compilerOptions": {
+    "target": "ES2022",
+    "module": "ESNext",
+    "moduleResolution": "bundler",
+    "lib": ["ES2022"],
+    "types": ["@cloudflare/workers-types"],
+    "strict": true,
+    "esModuleInterop": true,
+    "skipLibCheck": true,
+    "resolveJsonModule": true,
+    "outDir": "dist",
+    "rootDir": "src",
+    "declaration": true
+  },
+  "include": ["src"],
+  "exclude": ["src/server.ts"]
+}