@cyanheads/gbif-biodiversity-mcp-server 0.2.1 → 0.2.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/CLAUDE.md +23 -39
- package/README.md +1 -1
- package/dist/index.js +2 -0
- package/dist/index.js.map +1 -1
- package/dist/mcp-server/resources/definitions/gbif-species.resource.js +2 -2
- package/dist/mcp-server/resources/definitions/gbif-species.resource.js.map +1 -1
- package/dist/mcp-server/tools/definitions/gbif-search-occurrences.tool.d.ts +5 -0
- package/dist/mcp-server/tools/definitions/gbif-search-occurrences.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/gbif-search-occurrences.tool.js +7 -1
- package/dist/mcp-server/tools/definitions/gbif-search-occurrences.tool.js.map +1 -1
- package/package.json +3 -3
- package/server.json +3 -3
package/CLAUDE.md
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# Developer Protocol
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**Server:** @cyanheads/gbif-biodiversity-mcp-server
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**Version:** 0.2.
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.
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**Version:** 0.2.2
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.13`
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**Engines:** Bun ≥1.3.0, Node ≥24.0.0
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**MCP SDK:** `@modelcontextprotocol/sdk` ^1.29.0
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**Zod:** ^4.4.3
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- **Use `ctx.state`** for tenant-scoped storage. Never access persistence directly.
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- **Check `ctx.elicit` / `ctx.sample`** for presence before calling.
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- **Secrets in env vars only** — never hardcoded.
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- **Close the loop on issues.** When implementing work tracked by a GitHub issue, comment on the issue with what landed
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- **Close the loop on issues.** When implementing work tracked by a GitHub issue, comment on the issue with what landed and close it. Do both — a comment without a close leaves stale issues open; a close without a comment leaves no record of what shipped. The comment is for future readers — state the concrete changes, not the conversation that produced them.
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---
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});
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```
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### Server instructions
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`createApp({ instructions })` — optional server-level orientation, sent to clients on every `initialize` as session-level context. Use it for deployment guidance (connection aliases, regional notes, scope hints) instead of repeating the same context across tool descriptions. Client adoption is uneven, but there's no downside when set.
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---
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### Server config
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```ts
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**Recommended: typed error contract.** Declare `errors: [{ reason, code, when, recovery, retryable? }]` on `tool()` / `resource()` to receive `ctx.fail(reason, …)` typed against the reason union. TypeScript catches typos at compile time, `data.reason` is auto-populated for observability, linter enforces conformance against the handler body. `recovery` is required descriptive metadata for the agent's next move (≥ 5 words, lint-validated); for the wire `data.recovery.hint` (mirrored into `content[]` text), pass explicitly at the throw site when dynamic context matters: `ctx.fail('reason', msg, { recovery: { hint: '...' } })`. Baseline codes (`InternalError`, `ServiceUnavailable`, `Timeout`, `ValidationError`, `SerializationError`) bubble freely and don't need declaring.
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```ts
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import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
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errors: [
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{ reason: 'no_match', code: JsonRpcErrorCode.NotFound,
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when: 'No item matched the query',
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| `add-service` | Scaffold a new service integration |
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| `add-test` | Scaffold test file for a tool, resource, or service |
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| `field-test` | Exercise tools/resources/prompts with real inputs, verify behavior, report issues |
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| `tool-defs-analysis` | Read-only audit of MCP definition language across the surface — voice, leaks, defaults, recovery hints, output descriptions |
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| `security-pass` | Audit server for MCP-flavored security gaps: output injection, scope blast radius, input sinks, tenant isolation |
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| `code-simplifier` | Post-session cleanup against `git diff` — modernize syntax, consolidate duplication, align with the codebase |
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| `devcheck` | Lint, format, typecheck, audit |
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| `polish-docs-meta` | Finalize docs, README, metadata, and agent protocol for shipping |
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| `git-wrapup` |
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| `git-wrapup` | Land working-tree changes as a versioned commit + annotated tag — version bump, changelog, verify, tag. Local only. |
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| `release-and-publish` | Push + npm + MCP Registry + GH Release + Docker. Picks up from `git-wrapup` |
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| `maintenance` | Investigate changelogs, adopt upstream changes, sync skills to agent dirs |
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| `report-issue-framework` | File a bug or feature request against `@cyanheads/mcp-ts-core` via `gh` CLI |
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| `report-issue-local` | File a bug or feature request against this server's own repo via `gh` CLI |
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| `api-config` | AppConfig, parseConfig, env vars |
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| `api-context` | Context interface, logger, state, progress |
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| `api-errors` | McpError, JsonRpcErrorCode, error patterns |
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| `api-linter` | Definition linter rule catalog — invoked by `bun run lint:mcp` and `devcheck` |
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| `api-services` | LLM, Speech, Graph services |
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| `api-testing` | createMockContext, test patterns |
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| `api-utils` | Formatting, parsing, security, pagination, scheduling, telemetry helpers |
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| `npm run rebuild` | Clean + build |
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| `npm run clean` | Remove build artifacts |
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| `npm run devcheck` | Lint + format + typecheck + security + changelog sync |
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| `bun run audit:refresh` | Delete `bun.lock`, reinstall, re-audit
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| `bun run audit:refresh` | Delete `bun.lock`, reinstall, and re-run `bun audit`. Use when `devcheck` flags a transitive advisory — Bun's `update` is sticky on transitive resolutions, so the advisory may be a stale-lockfile false positive. If it survives the refresh, it's real. |
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| `npm run tree` | Generate directory structure doc |
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| `npm run format` | Auto-fix formatting |
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| `npm test` | Run tests |
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**Adding an env var requires both files:** `server.json` (registry discovery, `environmentVariables[]`) and `manifest.json` (bundle install UX, `mcp_config.env` + `user_config`). `lint:packaging` (run by `devcheck`) verifies the env var names match.
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**README install badges
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| Client | Mechanism |
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|:-------|:----------|
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| Claude Desktop | Browser downloads the `.mcpb` from the latest GitHub Release; OS file handler routes it to Claude Desktop, which opens the install dialog. No deep-link URL scheme yet — this is the canonical path. |
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| Cursor | Official `https://cursor.com/en/install-mcp` endpoint with base64 JSON config. |
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| VS Code / Insiders | Official `vscode:mcp/install?...` deep link, wrapped in `https://vscode.dev/redirect?url=` so GitHub-rendered markdown doesn't strip the non-HTTP scheme. |
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| Claude Code / Codex | CLI only (`claude mcp add` / `codex mcp add`); no URL scheme. |
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```markdown
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[](https://github.com/<OWNER>/<REPO>/releases/latest/download/<PACKAGE_NAME>.mcpb)
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[](https://cursor.com/en/install-mcp?name=<PACKAGE_NAME>&config=<BASE64_CONFIG>)
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[](https://vscode.dev/redirect?url=vscode:mcp/install?<URLENCODED_JSON>)
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```
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Both install links route through HTTPS endpoints (`cursor.com/en/install-mcp` and `vscode.dev/redirect`) — GitHub-rendered markdown strips non-HTTP URL schemes from anchors, so a raw `cursor://` or `vscode:` link won't click through from github.com.
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Generate the encoded configs (replace `<PACKAGE_NAME>` and add env vars for any required API keys):
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```bash
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# Cursor: base64-encoded JSON. Split command/args, add env when keys are needed.
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echo -n '{"command":"npx","args":["-y","<PACKAGE_NAME>"],"env":{"API_KEY":"your-api-key"}}' | base64
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# Without env (no required keys):
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echo -n '{"command":"npx","args":["-y","<PACKAGE_NAME>"]}' | base64
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# VS Code: URL-encoded JSON. Same shape plus a `name` field.
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node -p 'encodeURIComponent(JSON.stringify({name:"<SHORT_NAME>",command:"npx",args:["-y","<PACKAGE_NAME>"],env:{API_KEY:"your-api-key"}}))'
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# Without env:
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node -p 'encodeURIComponent(JSON.stringify({name:"<SHORT_NAME>",command:"npx",args:["-y","<PACKAGE_NAME>"]}))'
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```
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Both clients use the same `{command, args, env}` shape (matching `mcp.json` schema). VS Code adds a top-level `name` field. Omit `env` entirely when no API keys are needed — don't include empty objects or framework-only vars like `MCP_TRANSPORT_TYPE`.
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The Claude Desktop badge requires the bundle to ship with a stable filename — `bun run bundle` outputs `dist/<PACKAGE_NAME>.mcpb`, and `release-and-publish` attaches that file to the GitHub Release. `releases/latest/download/<PACKAGE_NAME>.mcpb` then redirects to the most recent release.
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**README install badges** (Claude Desktop `.mcpb`, Cursor, VS Code) and the `base64` / `encodeURIComponent` config-generation commands are ship-time concerns — run the `polish-docs-meta` skill, which carries the badge format, layout, and generation snippets in `skills/polish-docs-meta/references/readme.md`.
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---
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`breaking: true` renders a `· ⚠️ Breaking` badge — use it when consumers must update code on upgrade (signature changes, removed APIs, config renames). `security: true` renders a `· 🛡️ Security` badge and pairs with a `## Security` body section. When both are set, badges render `· ⚠️ Breaking · 🛡️ Security`.
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`agent-notes` is an optional free-form field for maintenance agents processing the release downstream. Content here won't appear in the rendered CHANGELOG — it's consumed by agents running the `maintenance` skill. Use it for adoption instructions that don't fit the human-facing sections: new files to create, fields to populate, one-time migration steps. Omit entirely when there's nothing to say.
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**Section order** (Keep a Changelog): Added, Changed, Deprecated, Removed, Fixed, Security. Include only sections with entries — don't ship empty headers.
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**Tag annotations** render as GitHub Release bodies via `--notes-from-tag`. They must be structured markdown — never a flat comma-separated string. Subject omits the version number (GitHub prepends it). See `changelog/template.md` for the full format reference.
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- [ ] If wrapping external API: tests include at least one sparse payload case with omitted upstream fields
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- [ ] Registered in `createApp()` arrays (directly or via barrel exports)
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- [ ] Tests use `createMockContext()` from `@cyanheads/mcp-ts-core/testing`
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- [ ] `.codex-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; `interface.displayName` = package name; `interface.shortDescription` from `package.json` description
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- [ ] `.codex-plugin/mcp.json` updated — server name key matches `package.json` name; env vars added for any required API keys
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- [ ] `.claude-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; inline `mcpServers` entry with server name key, env vars for any required API keys
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- [ ] `npm run devcheck` passes
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package/README.md
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<div align="center">
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[](./CHANGELOG.md) [](./LICENSE) [](https://github.com/users/cyanheads/packages/container/package/gbif-biodiversity-mcp-server) [](https://modelcontextprotocol.io/) [](https://www.npmjs.com/package/@cyanheads/gbif-biodiversity-mcp-server) [](https://www.typescriptlang.org/) [](https://bun.sh/)
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</div>
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package/dist/index.js
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// Public catalog — serve the full landing inventory regardless of auth mode.
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landing: { requireAuth: false },
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package/dist/index.js.map
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;GAGG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,YAAY;AACZ,OAAO,EAAE,mBAAmB,EAAE,MAAM,6DAA6D,CAAC;AAClG,OAAO,EAAE,mBAAmB,EAAE,MAAM,6DAA6D,CAAC;AAClG,OAAO,EAAE,oBAAoB,EAAE,MAAM,+DAA+D,CAAC;AACrG,OAAO,EAAE,cAAc,EAAE,MAAM,yDAAyD,CAAC;AACzF,OAAO,EAAE,iBAAiB,EAAE,MAAM,4DAA4D,CAAC;AAC/F,OAAO,EAAE,cAAc,EAAE,MAAM,yDAAyD,CAAC;AACzF,OAAO,EAAE,sBAAsB,EAAE,MAAM,kEAAkE,CAAC;AAC1G,OAAO,EAAE,4BAA4B,EAAE,MAAM,wEAAwE,CAAC;AACtH,iBAAiB;AACjB,OAAO,EAAE,gBAAgB,EAAE,MAAM,2DAA2D,CAAC;AAC7F,OAAO,EAAE,oBAAoB,EAAE,MAAM,+DAA+D,CAAC;AACrG,8BAA8B;AAC9B,OAAO,EAAE,kBAAkB,EAAE,MAAM,6DAA6D,CAAC;AACjG,mBAAmB;AACnB,OAAO,EAAE,qBAAqB,EAAE,MAAM,gEAAgE,CAAC;AACvG,OAAO,EAAE,oBAAoB,EAAE,MAAM,+DAA+D,CAAC;AACrG,OAAO,EAAE,iBAAiB,EAAE,MAAM,4DAA4D,CAAC;AAC/F,OAAO,EAAE,eAAe,EAAE,MAAM,iCAAiC,CAAC;AAElE,MAAM,SAAS,CAAC;IACd,KAAK,EAAE;QACL,gBAAgB;QAChB,cAAc;QACd,iBAAiB;QACjB,4BAA4B;QAC5B,sBAAsB;QACtB,qBAAqB;QACrB,oBAAoB;QACpB,iBAAiB;QACjB,oBAAoB;QACpB,kBAAkB;QAClB,cAAc;QACd,oBAAoB;KACrB;IACD,SAAS,EAAE,CAAC,mBAAmB,EAAE,mBAAmB,CAAC;IACrD,OAAO,EAAE,EAAE;IACX,6EAA6E;IAC7E,OAAO,EAAE,EAAE,WAAW,EAAE,KAAK,EAAE;IAC/B,KAAK,CAAC,IAAI;QACR,MAAM,GAAG,GAAG,eAAe,EAAE,CAAC;QAC9B,eAAe,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE;YACzC,OAAO,EAAE,GAAG,CAAC,OAAO;YACpB,SAAS,EAAE,GAAG,CAAC,gBAAgB;YAC/B,GAAG,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;SAC9C,CAAC,CAAC;IACL,CAAC;CACF,CAAC,CAAC"}
|
|
@@ -3,7 +3,7 @@
|
|
|
3
3
|
* @module mcp-server/resources/definitions/gbif-species
|
|
4
4
|
*/
|
|
5
5
|
import { resource, z } from '@cyanheads/mcp-ts-core';
|
|
6
|
-
import { notFound } from '@cyanheads/mcp-ts-core/errors';
|
|
6
|
+
import { notFound, validationError } from '@cyanheads/mcp-ts-core/errors';
|
|
7
7
|
import { getGbifService } from '../../../services/gbif/gbif-service.js';
|
|
8
8
|
export const gbifSpeciesResource = resource('gbif://species/{taxonKey}', {
|
|
9
9
|
name: 'gbif-species',
|
|
@@ -36,7 +36,7 @@ export const gbifSpeciesResource = resource('gbif://species/{taxonKey}', {
|
|
|
36
36
|
async handler(params, ctx) {
|
|
37
37
|
const taxonKey = parseInt(params.taxonKey, 10);
|
|
38
38
|
if (Number.isNaN(taxonKey)) {
|
|
39
|
-
throw
|
|
39
|
+
throw validationError(`Invalid taxon key: "${params.taxonKey}". Must be a numeric backbone key.`);
|
|
40
40
|
}
|
|
41
41
|
ctx.log.debug('Fetching species resource', { taxonKey });
|
|
42
42
|
const raw = await getGbifService().getSpecies(taxonKey, ctx);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"gbif-species.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/gbif-species.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;
|
|
1
|
+
{"version":3,"file":"gbif-species.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/gbif-species.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,QAAQ,EAAE,eAAe,EAAE,MAAM,+BAA+B,CAAC;AAC1E,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAEjE,MAAM,CAAC,MAAM,mBAAmB,GAAG,QAAQ,CAAC,2BAA2B,EAAE;IACvE,IAAI,EAAE,cAAc;IACpB,KAAK,EAAE,qBAAqB;IAC5B,WAAW,EACT,qFAAqF;QACrF,mEAAmE;IACrE,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;KACtE,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,0BAA0B,CAAC;QAC/D,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;QACvF,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;QACpF,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;QACnE,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;QACrF,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iBAAiB,CAAC;QACvD,eAAe,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mCAAmC,CAAC;QACpF,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;QAClE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;QAChE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;QAC9D,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;QAC9D,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;QAChE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;QAC9D,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;QAClF,OAAO,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,0CAA0C,CAAC;QACpF,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;QAC/E,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,6BAA6B,CAAC;KACxE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG;QACvB,MAAM,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC;QAC/C,IAAI,MAAM,CAAC,KAAK,CAAC,QAAQ,CAAC,EAAE,CAAC;YAC3B,MAAM,eAAe,CAAC,uBAAuB,MAAM,CAAC,QAAQ,oCAAoC,CAAC,CAAC;QACpG,CAAC;QACD,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,2BAA2B,EAAE,EAAE,QAAQ,EAAE,CAAC,CAAC;QACzD,MAAM,GAAG,GAAG,MAAM,cAAc,EAAE,CAAC,UAAU,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAC;QAE7D,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC;YACb,MAAM,QAAQ,CAAC,aAAa,QAAQ,kCAAkC,CAAC,CAAC;QAC1E,CAAC;QAED,OAAO;YACL,GAAG,EAAE,GAAG,CAAC,GAAG;YACZ,cAAc,EAAE,GAAG,CAAC,cAAc;YAClC,aAAa,EAAE,GAAG,CAAC,aAAa;YAChC,UAAU,EAAE,GAAG,CAAC,UAAU;YAC1B,cAAc,EAAE,GAAG,CAAC,cAAc;YAClC,IAAI,EAAE,GAAG,CAAC,IAAI;YACd,eAAe,EAAE,GAAG,CAAC,eAAe;YACpC,OAAO,EAAE,GAAG,CAAC,OAAO;YACpB,MAAM,EAAE,GAAG,CAAC,MAAM;YAClB,KAAK,EAAE,GAAG,CAAC,KAAK;YAChB,KAAK,EAAE,GAAG,CAAC,KAAK;YAChB,MAAM,EAAE,GAAG,CAAC,MAAM;YAClB,KAAK,EAAE,GAAG,CAAC,KAAK;YAChB,cAAc,EAAE,GAAG,CAAC,cAAc;YAClC,WAAW,EAAE,GAAG,CAAC,WAAW;YAC5B,QAAQ,EAAE,GAAG,CAAC,QAAQ;YACtB,GAAG,CAAC,OAAO,GAAG,CAAC,OAAO,KAAK,SAAS,IAAI,EAAE,OAAO,EAAE,GAAG,CAAC,OAAO,EAAE,CAAC;SAClE,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}
|
|
@@ -59,6 +59,11 @@ export declare const gbifSearchOccurrences: import("@cyanheads/mcp-ts-core").Too
|
|
|
59
59
|
limit: z.ZodNumber;
|
|
60
60
|
endOfRecords: z.ZodBoolean;
|
|
61
61
|
}, z.core.$strip>, readonly [{
|
|
62
|
+
readonly reason: "pagination_cap_exceeded";
|
|
63
|
+
readonly code: JsonRpcErrorCode.ValidationError;
|
|
64
|
+
readonly when: "offset + limit exceeds the GBIF API pagination cap of ~100,000.";
|
|
65
|
+
readonly recovery: "Reduce offset or limit so their sum stays under 100,000. Use gbif_occurrence_facets for aggregate analysis across large result sets.";
|
|
66
|
+
}, {
|
|
62
67
|
readonly reason: "upstream_error";
|
|
63
68
|
readonly code: JsonRpcErrorCode.InternalError;
|
|
64
69
|
readonly when: "The GBIF occurrence search API returned an unexpected error.";
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"gbif-search-occurrences.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/gbif-search-occurrences.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAKjE,eAAO,MAAM,qBAAqB
|
|
1
|
+
{"version":3,"file":"gbif-search-occurrences.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/gbif-search-occurrences.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAKjE,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA2ThC,CAAC"}
|
|
@@ -157,6 +157,12 @@ export const gbifSearchOccurrences = tool('gbif_search_occurrences', {
|
|
|
157
157
|
endOfRecords: z.boolean().describe('True when there are no more results after this page.'),
|
|
158
158
|
}),
|
|
159
159
|
errors: [
|
|
160
|
+
{
|
|
161
|
+
reason: 'pagination_cap_exceeded',
|
|
162
|
+
code: JsonRpcErrorCode.ValidationError,
|
|
163
|
+
when: 'offset + limit exceeds the GBIF API pagination cap of ~100,000.',
|
|
164
|
+
recovery: 'Reduce offset or limit so their sum stays under 100,000. Use gbif_occurrence_facets for aggregate analysis across large result sets.',
|
|
165
|
+
},
|
|
160
166
|
{
|
|
161
167
|
reason: 'upstream_error',
|
|
162
168
|
code: JsonRpcErrorCode.InternalError,
|
|
@@ -172,7 +178,7 @@ export const gbifSearchOccurrences = tool('gbif_search_occurrences', {
|
|
|
172
178
|
offset: input.offset,
|
|
173
179
|
});
|
|
174
180
|
if (input.offset + input.limit > PAGINATION_CAP) {
|
|
175
|
-
throw ctx.fail('
|
|
181
|
+
throw ctx.fail('pagination_cap_exceeded', `offset + limit (${input.offset + input.limit}) exceeds the GBIF pagination cap of ~100,000. Use gbif_occurrence_facets for aggregate analysis, or reduce offset/limit.`, { ...ctx.recoveryFor('pagination_cap_exceeded') });
|
|
176
182
|
}
|
|
177
183
|
const raw = await getGbifService().searchOccurrences({
|
|
178
184
|
...(input.taxonKey !== undefined && { taxonKey: input.taxonKey }),
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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AM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAC7E,CAAC;QACD,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,CAAC;YACzB,KAAK,CAAC,IAAI,CAAC,gCAAgC,MAAM,CAAC,MAAM,GAAG,MAAM,CAAC,KAAK,gBAAgB,CAAC,CAAC;QAC3F,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/gbif-biodiversity-mcp-server",
|
|
3
|
-
"version": "0.2.
|
|
3
|
+
"version": "0.2.2",
|
|
4
4
|
"mcpName": "io.github.cyanheads/gbif-biodiversity-mcp-server",
|
|
5
5
|
"description": "Search GBIF species taxonomy, occurrence records, datasets, and publishers via MCP. STDIO or Streamable HTTP.",
|
|
6
6
|
"type": "module",
|
|
@@ -75,12 +75,12 @@
|
|
|
75
75
|
"access": "public"
|
|
76
76
|
},
|
|
77
77
|
"dependencies": {
|
|
78
|
-
"@cyanheads/mcp-ts-core": "^0.9.
|
|
78
|
+
"@cyanheads/mcp-ts-core": "^0.9.13",
|
|
79
79
|
"pino-pretty": "^13.1.3",
|
|
80
80
|
"zod": "^4.4.3"
|
|
81
81
|
},
|
|
82
82
|
"devDependencies": {
|
|
83
|
-
"@biomejs/biome": "^2.4.
|
|
83
|
+
"@biomejs/biome": "^2.4.16",
|
|
84
84
|
"@types/node": "^25.9.1",
|
|
85
85
|
"depcheck": "^1.4.7",
|
|
86
86
|
"ignore": "^7.0.5",
|
package/server.json
CHANGED
|
@@ -12,14 +12,14 @@
|
|
|
12
12
|
"url": "https://gbif-biodiversity.caseyjhand.com/mcp"
|
|
13
13
|
}
|
|
14
14
|
],
|
|
15
|
-
"version": "0.2.
|
|
15
|
+
"version": "0.2.2",
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"packages": [
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{
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"registryType": "npm",
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"registryBaseUrl": "https://registry.npmjs.org",
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"identifier": "@cyanheads/gbif-biodiversity-mcp-server",
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"runtimeHint": "bun",
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22
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-
"version": "0.2.
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+
"version": "0.2.2",
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"packageArguments": [
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{
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"type": "positional",
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@@ -54,7 +54,7 @@
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"registryBaseUrl": "https://registry.npmjs.org",
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"identifier": "@cyanheads/gbif-biodiversity-mcp-server",
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"runtimeHint": "bun",
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-
"version": "0.2.
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+
"version": "0.2.2",
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"packageArguments": [
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{
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"type": "positional",
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