@pipeworx/mcp-bold-systems 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/bold-systems
+
+The global DNA barcode reference library from BOLD Systems (Barcode of Life Data System, Centre for
+Biodiversity Genomics, University of Guelph) — specimen vouchers with locality, institution and
+taxonomy, the COI/rbcL/matK barcode sequences themselves, and BIN species-proxy clusters.
+
+Part of [Pipeworx](https://pipeworx.io) — an MCP gateway connecting AI agents to 1679+ live data sources.
+
+## Tools
+
+- `bold_specimens(taxon?, country?, bin?, institution?, query?, limit?, offset?)` — specimen records:
+  process ID, full taxonomy, BIN, collection date, locality with coordinates, holding institution,
+  marker and GenBank accession. Filters AND together.
+- `bold_sequences(taxon?, country?, bin?, institution?, marker?, query?, limit?, offset?)` — the
+  barcode sequences, with primers, base count, INSDC accession and a ready-to-paste FASTA block.
+- `bold_taxonomy(name, rank?)` — resolve a name against BOLD's own index: lineage, record/species/BIN
+  counts at each rank above it, a plain-language description, and alternative matches with counts.
+
+## Auth
+
+Keyless.
+
+## Data sources
+
+- <https://portal.boldsystems.org/api/terms> — term index; resolves a plain name to a query triplet.
+- <https://portal.boldsystems.org/api/query> — turns a triplet query into a `query_id`.
+- <https://portal.boldsystems.org/api/documents/{query_id}> — the records, `nuc` sequence inline.
+- <https://portal.boldsystems.org/api/taxonomy/{description,hierarchy}> — lineage, counts, prose.
+- Swagger: <https://portal.boldsystems.org/api/docs> (the spec itself is at
+  <https://portal.boldsystems.org/openapi.json>, NOT under `/api/`).
+
+## Traps
+
+**The v4 API is dead.** `v4.boldsystems.org/index.php/API_Public/{specimen,sequence,combined}` — what
+every tutorial and most R packages still point at — answers with a "BOLD Public Offline" HTML page,
+not JSON, so a naive client reports a parse error rather than a retirement. Everything here is the
+v5 portal API.
+
+**The query language is `scope:field:value` triplets and the scope/field pair is not guessable from
+the value.** `Canada` is `geo:country/ocean`, `Danaus` is `tax:genus`, `BOLD:AAA9566` is `bin:uri`,
+`Smithsonian Institution` is `inst:name`. Free text gets a 400 `{"detail":"Invalid triplet token"}`.
+The pack resolves every typed argument through `/api/terms` first, which is what turns a plain name
+into a query that matches instead of a 400 or a silent zero.
+
+**`/api/counts` reports the SUM of the per-term counts, not the size of the intersection.** For
+`tax:species:Danaus plexippus;geo:country/ocean:Canada` it says **2,520,553** records; the actual
+match set is **7**. That is a clean 200 carrying a number wrong by five orders of magnitude, and it
+is the number a naive integration would quote. The pack does not use it — `matchingRecords` comes
+from `recordsTotal` on the document query, which is the real count. (Semicolon-separated triplets
+AND on `/documents` even though they sum on `/counts`.)
+
+**`/api/query/preprocessor` falls back to ID-field matching on a multi-word string.** Feeding it
+"Danaus plexippus Canada" returns `ids:processid:...;ids:sampleid:...;ids:insdcacs:...` — a query
+that matches nothing and errors nowhere. Resolve each filter separately, which is what
+`resolveTriplet` does.
+
+**BOLD holds specimen records that were never sequenced.** `bold_sequences` filters to records with a
+`nuc` field and says so in `note` when the result is empty, so "this taxon has no barcodes" is
+distinguishable from "this taxon has no records".
+
+**The marker filter is applied to the returned page, not upstream** (BOLD's term index has no entry
+for `COI-5P`). The pack over-fetches 5× when a marker is set and reports which markers were actually
+present in the page it scanned, so an empty result names the markers you could have asked for.
+
+**`identifier_email` is dropped before anything leaves the pack** — it is a contact address on a
+person, not specimen data. Collector and identifier NAMES are kept: those are the published
+attribution on a museum voucher and appear on every biodiversity record.
+
+## Quick Start
+
+Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
+
+```json
+{
+  "mcpServers": {
+    "bold-systems": {
+      "url": "https://gateway.pipeworx.io/bold-systems/mcp"
+    }
+  }
+}
+```
+
+### What this endpoint actually serves
+
+`tools/list` at `https://gateway.pipeworx.io/bold-systems/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/bold_specimens \
+  -H 'Content-Type: application/json' \
+  -d '{"taxon":"Danaus plexippus","country":"Canada","limit":3}'
+```
+
+No account needed for the first calls. Inspect any tool: `GET https://gateway.pipeworx.io/v1/tools/bold_specimens`. 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": {
+    "bold-systems": {
+      "command": "npx",
+      "args": ["-y", "@pipeworx/mcp-bold-systems"]
+    }
+  }
+}
+```
+
+Or run it directly to confirm it starts:
+
+```bash
+npx -y @pipeworx/mcp-bold-systems
+```
+
+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 Bold Systems 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-bold-systems",
+  "version": "0.1.0",
+  "description": "BOLD Systems (Barcode of Life Data System, University of Guelph) — the global DNA barcode reference library: specimen records with collection locality, institution and taxonomy, the COI/rbcL/matK barcode sequences themselves, and BIN (species-proxy cluster) assignments. Keyless.",
+  "type": "module",
+  "main": "src/index.ts",
+  "types": "src/index.ts",
+  "bin": {
+    "mcp-bold-systems": "bin/cli.js"
+  },
+  "keywords": ["mcp", "mcp-server", "model-context-protocol", "pipeworx", "bold-systems"],
+  "license": "MIT",
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/pipeworx-io/mcp-bold-systems.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-d794cb2800cc6d4646f1705662ed070740c13309d2d4ccb407a8f63c7b12c8d6",
+    "sourceCommit": "60f04b68c347e970c6be94a53439d1364061fc06"
+  }
+}

package/server.json

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+{
+  "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
+  "name": "io.github.pipeworx-io/bold-systems",
+  "title": "Bold Systems",
+  "description": "BOLD Systems (Barcode of Life Data System, University of Guelph) — the global DNA barcode…",
+  "version": "0.1.0",
+  "websiteUrl": "https://pipeworx.io/packs/bold-systems",
+  "repository": {
+    "url": "https://github.com/pipeworx-io/mcp-bold-systems",
+    "source": "github"
+  },
+  "remotes": [
+    {
+      "type": "streamable-http",
+      "url": "https://gateway.pipeworx.io/bold-systems/mcp"
+    }
+  ]
+}